Python for Scientific Computing

Introduction
UMR MISTEA Montpellier France

2016

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Plan

Introduction.......................... p 3
Python for sciences............... p 11
Structure and types............... p 16
Data manipulations............... p 40
Matrix Operations................. p 50
Exercises.............................. p 78
Practices and performance.... p 59

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Introduction
Python:
- Powerful programming language
- Available on different platforms
- Effective approach to object-oriented programming
- Dynamic typing and interpreted
- Easy to learn, (help function) and Web resources
Some Spanish references:
http://es.wikipedia.org/wiki/Python
http://docs.python.org.ar/tutorial/contenido.html
Current versions: 3.3 or 2.7 ( 3.3 vs 2.7?)

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Introduction
Invoking python
- Script mode
pn@pn-laptop:~/PYTHON$ cat prog1.py
print 2+3
pn@pn-laptop:~/PYTHON$ python prog1.py
5
- Interactive mode
pn@pn-laptop:~/PYTHON$ python
Python 2.6.5 (r265:79063, Oct 1 2012, 22:04:36)
[GCC 4.4.3] on linux2
Type "help", "copyright", "credits" or "license" ...
>>> 1+2
3
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Introduction: list

>>>
>>>
[1,
>>>
1
>>>
3

numbers=[1,2,3]
numbers
2, 3]
numbers[0]
numbers[2]

>>> numbers=array(numbers) # numpy module

>>> help(array)
.......

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Introduction: if statement
>>> x=2
>>> if x>1 : x=x+1
...
>>> x
3
>>> if x < 0:
...
x = 0
...
print Negative changed to zero
... elif x == 0:
...
print Zero
... else:
...
print More
...
More
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Introduction: for statement

>>> words= [cat,dog,horse]

>>> for w in words:
...
print it is a ,w
...
it is a cat
it is a dog
it is a horse

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Introduction: for statement (cont.)

>>> range(3)
[0, 1, 2]
>>> for i in range(3):
...
print i,is a ,words[i]
...
0 is a cat
1 is a dog
2 is a horse

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Introduction: while statement

>>> while a>0:

...
print a=,a
...
a=a-1
...
a= 3
a= 2
a= 1

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Introduction: function definition

>>> def addFive(n):

...
return(n+5)
...
>>> addFive(3)
8
import or from instructions allow to use modules or packages
A module is a file containing Python definitions and statements
A package is a collection of modules.

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Scientific computing with Python

Python + Packages: Numpy / Scipy / Matplotlib

Characteristics:
Free software for scientific computing
Available on Linux, Windows, MacOs,...
A large Community of researchers and engineers
Universal programming language (a lot of functionalities)

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Numpy / Scipy / Matplotlib

Pylab: Numpy / Scipy / matplotlib
Web site www.scipy.org
Numpy: vector, matrix and vectorised instructions
Scipy: scientific libraries
Matplotlib: graphic library
SciKits: Scipy extensions (Toolboxes)
Fipy: Partial Differential Equation
IPython: meta-package
Mpmath: high precision

Similar software: Matlab (Commercial), Scilab, Octave, SAGE

http://www.scipy.org/NumPy_for_Matlab_Users
http://mathesaurus.sourceforge.net/matlab-python-xref.pdf
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Starting: first way

Explicitly import: needs to use name-spaces
>>> import numpy as np
>>> import scipy as sc
>>> a=3
>>> b=8
>>> max(a,b)
8
>>> np.max(a,b)
3
>>> np.max([a,b])
8

# better to use amax

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Starting: second way

>>> from numpy import *

>>> from scipy import *
>>> x=3
>>> y=2
>>> log(x) + 2
3.09861228866811
>>> max(log(x), y)
2
You can inadvertently overriding other functions or objects
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Starting: third way

ipython -pylab
In [1]: a=4 ; b=3
In [2]: max(a,b)
Out[2]: 4
In [3]: history -n
a=4 ; b=3
max(a,b)
In [4]: whos
Variable
Type
Data/Info
---------------------------a
int
4
b
int
3
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Main data types

bool
int
int8
uint8
float
float16
float32
complex
string

Boolean (True or False)

Platform integer (int32 or int64)
Byte (-128 to 127)
Unsigned integer (0 to 255)
float64 8 bytes.
Half precision 2 bytes
Single precision 4 bytes
complex128 32 bytes
string

http://docs.scipy.org/doc/numpy/user/basics.types.html

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Predefined constants

True
False
e
1j
inf
nan
pi

boolean true representation

boolean false representation
e constant
imaginary part of complex number
infinite value representation
not a number (sometime missing value)
constant

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Main structures

Scipy provides following structures:

vector: array
matrix: array and matrix
hypermatrix: array
list: list

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Matrix and Array

Which one is better?
Array:
array is the standard structure
A*B : element by element product
multidimensional

Matrix:
Matlab behavior
A*B : matrix product
dimension 2 (only)

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Vector creating
Unidimensional array (ordering values)
>>> a=array([1,2,3,4])
>>> a
array([1, 2, 3, 4])
>>> size(a)
4
# index from 0
>>> a[2]
3
# select elements 4 and 2
>>> a[[3,1]]
array([4, 2])

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Vector creating (cont.)

Column vector
>>> a.reshape(4,1)
array([[1],
[2],
[3],
[4]])
Vectors of character strings
>>> A = array([texte, chaine])
>>> A
array([texte, chaine],
dtype=|S6)
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Vector generating
>>> v=r_[1:11]
array([ 1, 2,

3,

4,

5,

6,

7,

8,

9, 10])

>>> v=linspace(0,pi,5)
array([ 0. , 0.7853981, 1.5707963, 2.3561944, 3.1415926])
>>> v=arange(5)
array([0, 1, 2, 3, 4])
>>> v=arange(1,11,3)
array([ 1, 4, 7, 10])
>>> v=arange(1,11,2.5)
array([ 1. , 3.5, 6. ,

8.5])
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Vector generating (cont.)

Attention: range and arange functions are differents
>>> a=range(5)
[0, 1, 2, 3, 4]
>>> arange(5)
array([0, 1, 2, 3, 4])
>>> range(5)*2
[0, 1, 2, 3, 4, 0, 1, 2, 3, 4]
>>> arange(5)*2
array([0, 2, 4, 6, 8])

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Matrix creating with array

>>> A=array([[1.,2,3],[4,5,6]])
array([[ 1., 2., 3.],
[ 4., 5., 6.]])
>>> B=array(([1,2,3],[4,5,6]))
array([[1, 2, 3],
[4, 5, 6]])
>>> C=array(([1,2,3],[4,5,6]),int32)
>>> D=array([[1,2,3],[4,5,6]],int16)
>>> whos
Variable
Type
Data/Info
----------------------------A
ndarray
2x3: 6 elems, type
B
ndarray
2x3: 6 elems, type
C
ndarray
2x3: 6 elems, type
D
ndarray
2x3: 6 elems, type

float64, 48 bytes
int64, 48 bytes
int32, 24 bytes
int16, 12 bytes
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Matrix creating with mat

>>> A=mat("1 2 3; 4 5 6")
>>> A
matrix([[1, 2, 3],
[4, 5, 6]])
row vector (dimension: 2)
>>> mat("1 2 3")
matrix([[1, 2, 3]])
column vector (dimension: 2)
>>> mat("1;2;3")
matrix([[1],
[2],
[3]])
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Matrix creating with mat

>>> A
matrix([[1, 2, 3],
[4, 5, 6]])
>>> A[1,2]
6
>>> A[1]
matrix([[4, 5, 6]])
>>> A[1,:]
matrix([[4, 5, 6]])
>>> A[:,2]
matrix([[3],
[6]])
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Matrix generating

Identity matrix: eye(3)

Matrix with 1 elements: ones((2,6))
Matrix with 0 elements: zeros((2,6))
Diagonal matrix: diag((4,5,6))

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Matrix generating: vector binding

>>> a=arange(2,11,2)
array([ 2, 4, 6, 8, 10])
>>> b=arange(1,10,2)
array([1, 3, 5, 7, 9])
>>> vstack((a,b))
array([[ 2, 4, 6,
[ 1, 3, 5,
>>> hstack((a,b))
array([ 2, 4, 6,

8, 10],
7, 9]])

8, 10,

1,

3,

5,

7,

9])

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Matrix generating: matrix and vector binding

>>> A
array([[1, 2, 3],
[4, 5, 6]])
>>> vstack([A,arange(3)])
array([[1, 2, 3],
[4, 5, 6],
[0, 1, 2]])
>>> hstack((A,A))
array([[ 1., 2.,
[ 4., 5.,

3.,
6.,

1.,
4.,

2.,
5.,

3.],
6.]])

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Matrix and vector copy

>>> a=arange(5)
>>> b=a
>>> b[2]=100
# a is also modified
>>> a
array([ 0,
1, 100,

3,

4])

>>> A=mat("1 2 3; 4 5 6")

matrix([[1, 2, 3],
[4, 5, 6]])
>>> B=A
>>> A[0,1]=12

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Matrix and vector copy (cont.)

>>> A
matrix([[
[
>>> B
matrix([[
[

1, 12,
4, 5,

3],
6]])

1, 12,
4, 5,

3],
6]])

>>> B=A.copy()
>>> A[0,1] = 3
>>> B
matrix([[ 1, 12,
[ 4, 5,

3],
6]])

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Logical operators

==
!=
>
>=
<
<=
~
not
and
or
xor

equal
not equal
greater
greater and equal
lower
lower and equal
not
not
logical and
logical or
exclusive OR

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Logical operators (cont.)

Logical arrays: True or False elements

In arithmetic context:
True becomes 1
False becomes 0

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Logical array

>>> A
array([[1, 2, 3],
[4, 5, 6]])
>>> A > 2
array([[False, False,
[ True, True,

True],
True]], dtype=bool)

>>> sum(A>2)
4

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File writing
In [18]: A=arange(5)
In [19]: savetxt(fichier.txt,A)
# os: operating system interface module
In [20]: import os
In [21]: os.system(cat fichier.txt)
0.000000000000000000e+00
1.000000000000000000e+00
2.000000000000000000e+00
3.000000000000000000e+00
4.000000000000000000e+00
Out[21]: 0
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File reading

In [22]: B=loadtxt(fichier.txt)
In [23]: B
Out[23]: array([ 0.,

1.,

2.,

3.,

4.])

In [24]: B=B.astype(int)

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Explicit reference
Attention
>>> import numpy as np
>>> A = np.array([[1,2,3],[4,5,6]])
>>> sum(A)
array([5, 7, 9])
>>> np.sum(A)
21

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Constant manipulation
>>> sqrt(-1)
1j
>>> A = array([1,nan,2])
>>> A
array([ 1., NaN,
2.])
>>> max(A)
nan
>>> sum(A)
nan
>>> 1/inf
0.0

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Constant manipulation (cont.)

Attention:
>>> nan == nan
False
>>> isnan(nan)
True

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Manipulations
Data manipulation, two ways:
with index
with logical

Vector manipulations with index

>>> v
array([ 1,

2,

3,

4,

5,

6,

7,

8,

9, 10])

>>> v[:]
array([ 1,

2,

3,

4,

5,

6,

7,

8,

9, 10])

>>> v[2:]
array([ 3,

4,

5,

6,

7,

8,

9, 10])

>>> v[2:-1]
array([3, 4, 5, 6, 7, 8, 9])

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Manipulations (cont.)

>>> v[2:-3]
array([3, 4, 5, 6, 7])
>>> v[::2]
array([1, 3, 5, 7, 9])
>>> v[1::2]
array([ 2, 4,

6,

8, 10])

>>> v[[3,1]]
array([4, 2])

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Manipulations (cont.)
Array manipulations with logical
>>> v
array([ 1,

2,

3,

4,

5,

6,

7,

8,

9, 10])

>>> v>2
array([False, False, True, True, True, True, True,
True, True, True], dtype=bool)
>>> v[v>2]
array([ 3,

4,

5,

6,

7,

8,

9, 10])

>>> v[(v>2)*(v<5)]
array([3, 4])
>>> v[((v>2)&(v<5))]
array([3, 4])

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Matrix manipulation with index

>>> A
array([[ 1,
[ 4,

2,
5,

3],
6]])

>>> A[1,2]
6
>>> A[(0,1),1]
array([2, 5])
>>> A[1,(1,2)]
array([5, 6])
>>> A[:,1]
array([2, 5])
>>> A[[1,0],[1,2]]
array([5, 3])
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Matrix manipulation with logical

>>> A<3
array([[ True, True, False],
[False, False, False]], dtype=bool)
>>> A[A<3]
array([1, 2])
>>> A[A<3]=10
>>> A
array([[10, 10,
[ 4, 5,

3],
6]])

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Structure manipulation
>>> a=arange(8)
>>> a
array([0, 1, 2, 3, 4, 5, 6, 7])
>>> a.reshape(2,-1)
array([[0, 1, 2, 3],
[4, 5, 6, 7]])
>>> a.reshape(-1,2)
array([[0, 1],
[2, 3],
[4, 5],
[6, 7]])
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Structure manipulation (cont.)

>>> a
array([0, 1, 2, 3, 4, 5, 6, 7])
>>> a.reshape(-1,2).transpose()
>>> a.reshape(-1,2).T
array([[0, 2, 4, 6],
[1, 3, 5, 7]])

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Matrix operations

>>> A=mat("1; 2; 3; 4; 5; 6")

>>> A
matrix([[1],
[2],
[3],
[4],
[5],
[6]])
>>> A.T
matrix([[1, 2, 3, 4, 5, 6]])

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Matrix operations (cont.)

>>> A=mat("1 2 3 ; 4 5 6")
>>> B=A.T
matrix([[1, 4],
[2, 5],
[3, 6]])
>>> A*B
matrix([[14, 32],
[32, 77]])
>>> dot(A,B)
matrix([[14, 32],
[32, 77]])
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Matrix operations (cont.)

>>> A=mat("1 2 3 ; 4 5 6")
>>> A=asarray(A)
>>> dot(A,B)
array([[14, 32],
[32, 77]])
>>> A*B
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ValueError: shape mismatch: objects cannot be broadcast

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Matrix operations (cont.)

linear equation system: A X = b
In [10]: A
Out[10]:
matrix([[1, 2],
[2, 3]])
In [11]: b
Out[11]: array([0, 1])
In [12]: solve(A,b)
Out[12]: array([ 2., -1.])

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Matrix operation: dimension computing

>>> x=array([pi*2 , pi*3])
>>> x
array([ 6.28318531, 9.42477796])
>>> x.round(3)
array([ 6.283, 9.425])
>>> A
array([[ 1., 2., 3.],
[ 4., 5., 6.]])
>>> A.sum(axis=0)
array([ 5., 7., 9.])
>>> A.sum(axis=1)
array([ 6., 15.])

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Matrix operation: dimension computing (cont.)

>>> A
array([[
[
[
[

0.52,
0.99,
0.5 ,
0.13,

>>> A[A>0.7]
array([ 0.99,

0.59,
0.88,
0.58,
0.03,

0.88,

0.3 ,
0.26,
0.29,
0.19,

0.44,
0.77,
0.41,
0.63,

0.05],
0.41],
0.26],
0.38]])

0.77])

>>> where(A>.6)
(array([1, 1, 1, 3]), array([0, 1, 3, 3]))

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Matrix operation: dimension computing (cont.)

>>> A
array([[
[
[
[

0.52,
0.99,
0.5 ,
0.13,

0.59,
0.88,
0.58,
0.03,

0.3 ,
0.26,
0.29,
0.19,

0.44,
0.77,
0.41,
0.63,

0.05],
0.41],
0.26],
0.38]])

>>> sort(A.flatten())
array([ 0.03, 0.05, 0.13, 0.19, 0.26, 0.26, 0.29,...
0.3 , 0.38, 0.41, 0.41, 0.44, 0.5 , 0.52, 0.58,...
0.59, 0.63, 0.77, 0.88, 0.99])
>>> sort(A)
array([[ 0.05,
[ 0.26,
[ 0.26,
[ 0.03,

0.3 ,
0.41,
0.29,
0.13,

0.44,
0.77,
0.41,
0.19,

0.52,
0.88,
0.5 ,
0.38,

0.59],
0.99],
0.58],
0.63]])
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Matrix operation: dimension computing (cont.)

>>> sort(A,axis=0)
array([[ 0.13, 0.03,
[ 0.5 , 0.58,
[ 0.52, 0.59,
[ 0.99, 0.88,

0.19,
0.26,
0.29,
0.3 ,

0.41,
0.44,
0.63,
0.77,

0.05],
0.26],
0.38],
0.41]])

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Least squares for parameter optimization and graphics

>>> x
array([ 0, 1, 2, 3,... , 26, 27, 28, 29])
>>> y
array([ 1.696963, 7.498109, ... , 545.60116814, 577.57219145])
>>> figure(0)
>>> plot(x,y,ks)

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Least squares for parameter optimization and graphics

(cont.)
>>> def f(p,x):
... return p[2]*x**2+p[1]*x+p[0]
...
>>> def err(p,x,y):
...
return f(p,x)-y
...
>>> p
array([0, 1, 2])
>>> pp = leastsq(err,p,args=(x,y))
>>> pp
(array([-1.39042612, 6.99088574, 0.45505577]), 1)
>>> ys=f(pp,x)
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Least squares for parameter optimization and graphics

(cont.)
>>> figure(1) # open a window
>>> plot(x,y,ks, x, ys, r-, lw=2)
>>> ginput(1) # locating points on a graphic

See examples and gallery (code sources are available)

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http://matplotlib.sourceforge.net/

A program
import sys
from numpy import *
from scipy import *
import matplotlib.pyplot as plt
from scipy.integrate import odeint
# modele de "peche"
# x(t)=rx(t)*(1-x(t)/K)-qEx(t)
# 2 arguments r and E
# r : reproduction
# E : effort
# syntax checking
if ( size(sys.argv) != 3 ):
print Syntax error \n usage : +sys.argv[0]+ r E
exit(0)
r=float( sys.argv[1] ) # r
E=float( sys.argv[2] ) # E
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A program (cont.)
# cond initials
x0=([8.0])
# temps
t=arange(0.0,80,0.003)
# capturability
q=0.25
# max
K=20.0
# axis labels
xl = plt.xlabel(temps)
yl = plt.ylabel(Biomass)
# graphic title visualize parameter value
titre=parameters : r=+sys.argv[1]+
... et E=+sys.argv[2]
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A program (cont.)
ttl = plt.title(titre)
# diff eq of the modele
def funci(x,t):
return r*x*(1-x/K)-q*E*x
# integration init cond
y=odeint(funci,x0,t)

x0 and time

# visualisation
plt.plot(t,y)
plt.show()

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Exercices
- Install python 2.7
- Install numpy, scipy, matplotlib and ipython modules
- Create v1 as numerical vector with values from 1 to 12
- Calculate the sum of v1 elements
- Calculate the number of v1 elements that are strictly greater than 5
- Calculate the sum of v1 elements that are strictly greater than 5
- Create a vector V of length 100 that contains random values in [0,1]
Use rand from numpy.random library.
- Give a simple instruction to get 12! value (factorial)
- Create the matrix A
array([[ 0,
[ 4,
[ 8,

1, 2, 3],
5, 6, 7],
9, 10, 11]])

- calculate A*A (matrix product)

- Create a matrix A of 20 rows and 6 columns with
random uniform elements
- round A to 3 decimals

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Exercices (cont.)
- Calculate row means of A
Sergio has 3 daughters, we know:
The sum of 3 daughter ages is 66 years.
The double of the age of one of them is equal to the sum
of the 2 others.
The older has 12 years less than the sum of ages of
the 2 youngest daughters.
Give ages of the 3 daughters.
- x and y row vectors. We need to remove
values of vector x that are already in vector y.
For example, if x=[2, 1, 4, 5, 7, 6] and if
y = [1, 4, 7]. We want x= [2, 5, 6]
x=random(20)*3 and y=x**2+random(20)
make the plot of y vs x.
locate on the graphics the curve maximum

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Practice and performance: any and all

>>> x=random(200)
>>> x
array([ 0.89977878,
....,
>>> all(x>.2)
False

0.13654671,
0.15800227,

0.33486046,
0.46035374,

...
0.90776494])

>>> all(x>.002)
True
>>> any(x>.9)
True
>>> any(x>.999)
False
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Practice and performance

Try to not use loop
>>> import time
>>> a=random(2000000)

>>> t1=time.clock()
>>> n=0
>>> for i in range(2000000):
...
if a[i]>.5 : n=n+1
...
>>> n
1001192
>>> t2=time.clock()
>>> t2-t1
1.47

>>> t1=time.clock()
>>> n=sum(a>.5)
>>> n
1001192
>>> t2=time.clock()
>>> t2-t1
0.030000000000000027

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Practice and performance (cont.)

>>> size(a)
2000000

>>> t1=time.clock()
>>> for i in range(2000000):
...
if a[i]>.5 : a[i]=1
...
>>> t2=time.clock()
>>> t2-t1
1.5600000000000001

>>> a[(a>.5)]=1
>>>
>>> t3=time.clock()
>>> t3-t2
0.020000000000000018

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Practice and performance (cont.)

>>> size(a)
2000000

>>> t1=time.clock()
>>> for i in range(2000000):
...
if a[i]>.5 : a[i]=log(a[i])
...
>>> t2=time.clock()
>>> t2-t1
3.9399999999999995

>>> a[(a>.5)]=log(a[(a>.5)])
>>>
>>> t3=time.clock()
>>> t3-t2
0.010000000000000675

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Practice and performance (cont.)

all vs sum
>>> t1=time.clock()
>>> n=sum(a>0)
>>>
>>> t2=time.clock()
>>> t2-t1
0.020000000000000018

>>> all(a>0)
True
>>> t3=time.clock()
>>> t3-t2
0.0099999999999997868

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Practice and performance

>>> t1=time.clock()
>>> n=0
>>> for i in range(1000):
...
for j in range(1000):
...
if ((A[i,j]> .01) and (A[i,j]<0.3)): n=n+1
...
...
>>> t1-time.clock()
1.54
___________________________________________________
>>> t1=time.clock()
>>> n=0
>>> for i in range(1000):
...
for j in range(1000):
...
if ((A[i,j]< .03) and (A[i,j]>0.01)): n=n+1
...
...
>>> t1-time.clock()
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0.81000000000000005

Practice and performance

>>> x=arange(1000000)
>>> y=zeros(1000000-2)
>>>
>>>
...
...
>>>
>>>
1.0

t1=time.clock()
for i in range(1000000-2):
y[i]=x[i]+x[i+1]+x[i+2]
t2=time.clock()
t2-t1

>>> t1=time.clock()
>>> y=x[:-2]+x[1:-1]+x[2:]
>>> t2=time.clock()
>>> t2-t1
0.020000000000000018
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Practice and performance (cont.)

Some numerical aspects
>>> 2.4703e-324>0
False
>>> 2.4704e-324>0
True
>>> (1+10e-16)>1
True
>>> (1+10e-17)>1
False

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Practice and performance (cont.)

>>> a
1e-08
>>> b
1e-08
>>> c
10000
>>> (((a*b) *c) - (a* (b*c)))==0
False
>>> (((a*b) *c) - (a* (b*c)))
2.0194839173657902e-28

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Practice and performance (cont.)

>>> from mpmath import *
>>> mp.dps=20
>>> x=mpf(2.01234567890123456789012345678)
>>> y=sqrt(x)
>>> z=exp(y)
>>> w=ln(z)**2
>>> w
mpf(2.0123456789012345678888)
>>> mp.dps=35
>>> x=mpf(2.01234567890123456789012345678)
>>> y=sqrt(x)
>>> z=exp(y)
>>> w=ln(z)**2
>>> w
mpf(2.012345678901234567890123456780000004)
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