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<?xml version="1.0" encoding="utf-8" ?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="Docutils 0.12: http://docutils.sourceforge.net/" />
<title>Numpy tutorial</title>
<link rel="stylesheet" href="dana.css" type="text/css" />
<link rel="stylesheet" href="/usr/locaL/lib/python2.7/site-packages/docutils/writers/html4css1/math.css" type="text/css" />
</head>
<body>
<div class="document" id="numpy-tutorial">
<h1 class="title">Numpy tutorial</h1>
<h2 class="subtitle" id="nicolas-p-rougier">Nicolas P. Rougier</h2>
<a class="reference external image-reference" href="http://dx.doi.org/10.5281/zenodo.28817"><img alt="https://zenodo.org/badge/doi/10.5281/zenodo.28817.png" src="https://zenodo.org/badge/doi/10.5281/zenodo.28817.png" /></a>
<div class="contents local topic" id="table-of-contents">
<p class="topic-title first">Table of Contents</p>
<ul class="simple">
<li><a class="reference internal" href="#introduction" id="id2">Introduction</a></li>
<li><a class="reference internal" href="#the-game-of-life" id="id3">The Game of Life</a></li>
<li><a class="reference internal" href="#exercises" id="id4">Exercises</a></li>
<li><a class="reference internal" href="#beyond-this-tutorial" id="id5">Beyond this tutorial</a></li>
<li><a class="reference internal" href="#quick-references" id="id6">Quick references</a></li>
</ul>
</div>
<p>Sources are available from <a class="reference external" href="https://github.com/rougier/numpy-tutorial">github</a>.</p>
<p>All code and material is licensed under a <a class="reference external" href="http://creativecommons.org/licenses/by-sa/4.0">Creative Commons
Attribution-ShareAlike 4.0</a>.</p>
<p>Tutorial can be read at <a class="reference external" href="http://www.labri.fr/perso/nrougier/teaching/numpy/numpy.html">http://www.labri.fr/perso/nrougier/teaching/numpy/numpy.html</a></p>
<dl class="docutils">
<dt>See also:</dt>
<dd><ul class="first last simple">
<li><a class="reference external" href="http://www.labri.fr/perso/nrougier/teaching/matplotlib/matplotlib.html">Matplotlib tutorial</a></li>
<li><a class="reference external" href="http://www.labri.fr/perso/nrougier/teaching/numpy.100/index.html">100 Numpy exercices</a></li>
</ul>
</dd>
</dl>
<div class="section" id="introduction">
<h1><a class="toc-backref" href="#id2">Introduction</a></h1>
<p>NumPy is the fundamental package for scientific computing with Python. It
contains among other things:</p>
<ul class="simple">
<li>→ a powerful N-dimensional array object</li>
<li>→ sophisticated (broadcasting) functions</li>
<li>→ tools for integrating C/C++ and Fortran code</li>
<li>→ useful linear algebra, Fourier transform, and random number capabilities</li>
</ul>
<div class="line-block">
<div class="line"><br /></div>
</div>
<p>Besides its obvious scientific uses, NumPy can also be used as an efficient
multi-dimensional container of generic data. Arbitrary data-types can be
defined and this allows NumPy to seamlessly and speedily integrate with a wide
variety of projects. We are going to explore numpy through a simple example,
implementing the Game of Life.</p>
</div>
<div class="section" id="the-game-of-life">
<h1><a class="toc-backref" href="#id3">The Game of Life</a></h1>
<p>Numpy is slanted toward scientific computing and we'll consider in this section
the <a class="reference external" href="http://en.wikipedia.org/wiki/Conway's_Game_of_Life">game of life</a> by
John Conway which is one of the earliest example of cellular automata (see
figure below). Those cellular automaton can be conveniently considered as array
of cells that are connected together through the notion of neighbours. We'll
show in the following sections implementation of this game using pure python
and numpy in order to illustrate main differences with python and numpy.</p>
<div class="figure">
<img alt="figures/game-of-life.png" src="figures/game-of-life.png" />
<p class="caption"><strong>Figure 1</strong> Simulation of the game of life.</p>
</div>
<div class="note">
<p class="first admonition-title">Note</p>
<p class="last">This is an excerpt from <a class="reference external" href="http://en.wikipedia.org/wiki/Cellular_automaton">wikipedia</a> entry on Cellular
Automaton.</p>
</div>
<p>The Game of Life, also known simply as Life, is a cellular automaton devised
by the British mathematician John Horton Conway in 1970. It is the
best-known example of a cellular automaton. The "game" is actually a
zero-player game, meaning that its evolution is determined by its initial
state, needing no input from human players. One interacts with the Game of
Life by creating an initial configuration and observing how it evolves.</p>
<p>The universe of the Game of Life is an infinite two-dimensional orthogonal grid
of square cells, each of which is in one of two possible states, live or
dead. Every cell interacts with its eight neighbours, which are the cells that
are directly horizontally, vertically, or diagonally adjacent. At each step in
time, the following transitions occur:</p>
<ol class="arabic simple">
<li>Any live cell with fewer than two live neighbours dies, as if by needs caused
by underpopulation.</li>
<li>Any live cell with more than three live neighbours dies, as if by
overcrowding.</li>
<li>Any live cell with two or three live neighbours lives, unchanged, to the next
generation.</li>
<li>Any dead cell with exactly three live neighbours becomes a live cell.</li>
</ol>
<div class="line-block">
<div class="line"><br /></div>
</div>
<p>The initial pattern constitutes the 'seed' of the system. The first generation
is created by applying the above rules simultaneously to every cell in the seed
– births and deaths happen simultaneously, and the discrete moment at which
this happens is sometimes called a tick. (In other words, each generation is a
pure function of the one before.) The rules continue to be applied repeatedly
to create further generations.</p>
<p>We'll first use a very simple setup and more precisely, we'll use the <a class="reference external" href="http://en.wikipedia.org/wiki/Glider_(Conway's_Life)">glider</a> pattern that is known to
move one step diagonally in 4 iterations as illustrated below:</p>
<table border="1" class="docutils">
<colgroup>
<col width="17%" />
<col width="3%" />
<col width="17%" />
<col width="3%" />
<col width="17%" />
<col width="3%" />
<col width="17%" />
<col width="3%" />
<col width="17%" />
</colgroup>
<tbody valign="top">
<tr><td><img alt="figures/glider-00.png" class="first" src="figures/glider-00.png" />
<p class="last"><em>t = 0</em></p>
</td>
<td> </td>
<td><img alt="figures/glider-01.png" class="first" src="figures/glider-01.png" />
<p class="last"><em>t = 1</em></p>
</td>
<td> </td>
<td><img alt="figures/glider-02.png" class="first" src="figures/glider-02.png" />
<p class="last"><em>t = 2</em></p>
</td>
<td> </td>
<td><img alt="figures/glider-03.png" class="first" src="figures/glider-03.png" />
<p class="last"><em>t = 3</em></p>
</td>
<td> </td>
<td><img alt="figures/glider-04.png" class="first" src="figures/glider-04.png" />
<p class="last"><em>t = 4</em></p>
</td>
</tr>
</tbody>
</table>
<p>This property will help us debug our scripts.</p>
<div class="section" id="the-way-of-python">
<h2>The way of python</h2>
<div class="note">
<p class="first admonition-title">Note</p>
<p class="last">We could have used the more efficient <a class="reference external" href="https://docs.python.org/3/library/array.html">python array interface</a> but people may be more
familiar with the list object.</p>
</div>
<p>In pure python, we can code the Game of Life using a list of lists representing
the board where cells are supposed to evolve:</p>
<pre class="literal-block">
>>> Z = [[0,0,0,0,0,0],
[0,0,0,1,0,0],
[0,1,0,1,0,0],
[0,0,1,1,0,0],
[0,0,0,0,0,0],
[0,0,0,0,0,0]]
</pre>
<p>This board possesses a <tt class="docutils literal">0</tt> border that allows to accelerate things a bit by
avoiding to have specific tests for borders when counting the number of
neighbours. First step is to count neighbours:</p>
<pre class="literal-block">
def compute_neigbours(Z):
shape = len(Z), len(Z[0])
N = [[0,]*(shape[0]) for i in range(shape[1])]
for x in range(1,shape[0]-1):
for y in range(1,shape[1]-1):
N[x][y] = Z[x-1][y-1]+Z[x][y-1]+Z[x+1][y-1] \
+ Z[x-1][y] +Z[x+1][y] \
+ Z[x-1][y+1]+Z[x][y+1]+Z[x+1][y+1]
return N
</pre>
<p>To iterate one step in time, we then simply count the number of neighbours for
each internal cell and we update the whole board according to the 4 rules:</p>
<pre class="literal-block">
def iterate(Z):
N = compute_neighbours(Z)
for x in range(1,shape[0]-1):
for y in range(1,shape[1]-1):
if Z[x][y] == 1 and (N[x][y] < 2 or N[x][y] > 3):
Z[x][y] = 0
elif Z[x][y] == 0 and N[x][y] == 3:
Z[x][y] = 1
return Z
</pre>
<div class="note">
<p class="first admonition-title">Note</p>
<p class="last">The <tt class="docutils literal">show</tt> command is supplied witht he script.</p>
</div>
<p>Using a dedicated display function, we can check the program's correct:</p>
<pre class="literal-block">
>>> show(Z)
[0, 0, 1, 0]
[1, 0, 1, 0]
[0, 1, 1, 0]
[0, 0, 0, 0]
>>> for i in range(4): iterate(Z)
>>> show(Z)
[0, 0, 0, 0]
[0, 0, 0, 1]
[0, 1, 0, 1]
[0, 0, 1, 1]
</pre>
<p>You can download the full script here: <a class="reference external" href="scripts/game-of-life-python.py">game-of-life-python.py</a></p>
</div>
<div class="section" id="the-way-of-numpy">
<h2>The way of numpy</h2>
<div class="note">
<p class="first admonition-title">Note</p>
<p class="last">There exists <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/routines.array-creation.html">many more different ways</a>
to create a numpy array.</p>
</div>
<p>The first thing to do is to create the proper numpy array to hold the
cells. This can be done very easily with:</p>
<pre class="literal-block">
>>> import numpy as np
>>> Z = np.array([[0,0,0,0,0,0],
[0,0,0,1,0,0],
[0,1,0,1,0,0],
[0,0,1,1,0,0],
[0,0,0,0,0,0],
[0,0,0,0,0,0]])
</pre>
<div class="note">
<p class="first admonition-title">Note</p>
<p class="last">For a complete review on numpy data types, check the <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/arrays.dtypes.html">documentation</a>.</p>
</div>
<p>Note that we did not specify the <a class="reference internal" href="#data-type">data type</a> of the array and thus, numpy will
choose one for us. Since all elements are integers, numpy will then choose an
integer data type. This can be easily checked using:</p>
<pre class="literal-block">
>>> print(Z.dtype)
int64
</pre>
<p>We can also check the shape of the array to make sure it is 6x6:</p>
<pre class="literal-block">
>>> print(Z.shape)
(6, 6)
</pre>
<p>Each element of <tt class="docutils literal">Z</tt> can be accessed using a <tt class="docutils literal">row</tt> and a <tt class="docutils literal">column</tt>
index (in that order):</p>
<pre class="literal-block">
>>> print(Z[0,5])
0
</pre>
<div class="note">
<p class="first admonition-title">Note</p>
<p class="last">This element access is actually called <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/arrays.indexing.html">indexing</a> and this
is very powerful tool for vectorized computation.</p>
</div>
<p>But even better, we can also access a subpart of the array using the slice
notation:</p>
<pre class="literal-block">
>>> print(Z[1:5,1:5])
[[0 0 1 0]
[1 0 1 0]
[0 1 1 0]
[0 0 0 0]]
</pre>
<p>In the example above, we actually extract a subpart of <tt class="docutils literal">Z</tt> ranging from rows 1 to
5 and columns 1 to 5. It is important to understand at this point that this is
really a subpart of <tt class="docutils literal">Z</tt> in the sense that any change to this subpart will
have immediate impact on <tt class="docutils literal">Z</tt>:</p>
<blockquote>
<pre class="doctest-block">
>>> A = Z[1:5,1:5]
>>> A[0,0] = 9
>>> print(A)
[[9 0 1 0]
[1 0 1 0]
[0 1 1 0]
[0 0 0 0]]
</pre>
<pre class="doctest-block">
>>> print(Z)
[[0 0 0 0 0 0]
[0 9 0 1 0 0]
[0 1 0 1 0 0]
[0 0 1 1 0 0]
[0 0 0 0 0 0]
[0 0 0 0 0 0]]
</pre>
</blockquote>
<p>We set the value of <tt class="docutils literal">A[0,0]</tt> to 9 and we see immediate change in <tt class="docutils literal">Z[1,1]</tt>
because <tt class="docutils literal">A[0,0]</tt> actually corresponds to <tt class="docutils literal">Z[1,1]</tt>. This may seem trivial
with such simple arrays, but things can become much more complex (we'll see
that later). If in doubt, you can check easily if an array is part of another
one:</p>
<pre class="literal-block">
>>> print(Z.base is None)
True
>>> print(A.base is Z)
True
</pre>
<div class="section" id="counting-neighbours">
<h3>Counting neighbours</h3>
<div class="note">
<p class="first admonition-title">Note</p>
<p class="last">It is not always possible to vectorize computations and it requires
generally some experience. You'll acquire this experience by using numpy (of
course) but also by asking questions on the <a class="reference external" href="http://mail.scipy.org/mailman/listinfo/numpy-discussion">mailing list</a></p>
</div>
<p>We now need a function to count the neighbours. We could do it the same way as
for the python version, but this would make things very slow because of the
nested loops. We would prefer to act on the whole array whenever possible, this
is called <em>vectorization</em>.</p>
<p>Ok, let's start then...</p>
<p>First, you need to know that you can manipulate <tt class="docutils literal">Z</tt> <em>as if</em> (and only <em>as
if</em>) it was a regular scalar:</p>
<pre class="literal-block">
>>> print(1+(2*Z+3))
[[4 4 4 4 4 4]
[4 4 4 6 4 4]
[4 6 4 6 4 4]
[4 4 6 6 4 4]
[4 4 4 4 4 4]
[4 4 4 4 4 4]]
</pre>
<p>If you look carefully at the output, you may realize that the ouptut
corresponds to the formula above applied individually to each element. Said
differently, we have <tt class="docutils literal"><span class="pre">(1+(2*Z+3))[i,j]</span> == <span class="pre">(1+(2*Z[i,j]+3))</span></tt> for any i,j.</p>
<p>Ok, so far, so good. Now what happens if we add Z with one of its subpart,
let's say <tt class="docutils literal"><span class="pre">Z[-1:1,-1:1]</span></tt> ?</p>
<blockquote>
<pre class="doctest-block">
>>> Z + Z[-1:1,-1:1]
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ValueError: operands could not be broadcast together with shapes (6,6) (4,4)
</pre>
</blockquote>
<p>This raises a <tt class="docutils literal">Value Error</tt>, but more interestingly, numpy complains about
the impossibility of <em>broadcasting</em> the two arrays together. <a class="reference internal" href="#broadcasting">Broadcasting</a> is
a very powerful feature of numpy and most of the time, it saves you a lot of
hassle. Let's consider for example the following code:</p>
<pre class="literal-block">
>>> print(Z+1)
[[1 1 1 1 1 1]
[1 1 1 2 1 1]
[1 2 1 2 1 1]
[1 1 2 2 1 1]
[1 1 1 1 1 1]
[1 1 1 1 1 1]]
</pre>
<div class="note">
<p class="first admonition-title">Note</p>
<p class="last">See also <a class="reference external" href="http://docs.scipy.org/doc/numpy/user/basics.broadcasting.html">the broadcasting section</a> in the
numpy documentation.</p>
</div>
<p>How can a matrix and a scalar be added together ? Well, they can't. But numpy
is smart enough to guess that you actually want to add 1 to each of the element
of <tt class="docutils literal">Z</tt>. This concept of broadcasting is quite powerful and it will take you
some time before masterizing it fully (if even possible).</p>
<p>However, in the present case (counting neighbours if you remember), we won't
use broadcasting (uh ?). But we'll use vectorize computation using the
following code:</p>
<pre class="literal-block">
>>> N = np.zeros(Z.shape, dtype=int)
>>> N[1:-1,1:-1] += (Z[ :-2, :-2] + Z[ :-2,1:-1] + Z[ :-2,2:] +
Z[1:-1, :-2] + Z[1:-1,2:] +
Z[2: , :-2] + Z[2: ,1:-1] + Z[2: ,2:])
</pre>
<p>To understand this code, have a look at the figure below:</p>
<table border="1" class="docutils">
<colgroup>
<col width="33%" />
<col width="33%" />
<col width="33%" />
</colgroup>
<tbody valign="top">
<tr><td><img alt="figures/neighbours-1.png" class="first last" src="figures/neighbours-1.png" />
</td>
<td><img alt="figures/neighbours-2.png" class="first last" src="figures/neighbours-2.png" />
</td>
<td><img alt="figures/neighbours-3.png" class="first last" src="figures/neighbours-3.png" />
</td>
</tr>
<tr><td><img alt="figures/neighbours-4.png" class="first last" src="figures/neighbours-4.png" />
</td>
<td><img alt="figures/neighbours-5.png" class="first last" src="figures/neighbours-5.png" />
</td>
<td><img alt="figures/neighbours-6.png" class="first last" src="figures/neighbours-6.png" />
</td>
</tr>
<tr><td><img alt="figures/neighbours-7.png" class="first last" src="figures/neighbours-7.png" />
</td>
<td><img alt="figures/neighbours-8.png" class="first last" src="figures/neighbours-8.png" />
</td>
<td><img alt="figures/neighbours-9.png" class="first last" src="figures/neighbours-9.png" />
</td>
</tr>
</tbody>
</table>
<p>What we actually did with the above code is to add all the darker blue squares
together. Since they have been chosen carefully, the result will be exactly
what we expected. If you want to convince yourself, consider a cell in the
lighter blue area of the central sub-figure and check what will the result for
a given cell.</p>
</div>
<div class="section" id="iterate">
<h3>Iterate</h3>
<div class="note">
<p class="first admonition-title">Note</p>
<p class="last">Note the use of the <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ravel.html?highlight=ravel#numpy.ravel">ravel</a> function that flatten an array. This is necessary since the argwhere function returns flattened indices.</p>
</div>
<p>In a first approach, we can write the iterate function using the <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.argwhere.html">argwhere</a>
method that will give us the indices where a given condition is True.</p>
<pre class="literal-block">
def iterate(Z):
# Iterate the game of life : naive version
# Count neighbours
N = np.zeros(Z.shape, int)
N[1:-1,1:-1] += (Z[0:-2,0:-2] + Z[0:-2,1:-1] + Z[0:-2,2:] +
Z[1:-1,0:-2] + Z[1:-1,2:] +
Z[2: ,0:-2] + Z[2: ,1:-1] + Z[2: ,2:])
N_ = N.ravel()
Z_ = Z.ravel()
# Apply rules
R1 = np.argwhere( (Z_==1) & (N_ < 2) )
R2 = np.argwhere( (Z_==1) & (N_ > 3) )
R3 = np.argwhere( (Z_==1) & ((N_==2) | (N_==3)) )
R4 = np.argwhere( (Z_==0) & (N_==3) )
# Set new values
Z_[R1] = 0
Z_[R2] = 0
Z_[R3] = Z_[R3]
Z_[R4] = 1
# Make sure borders stay null
Z[0,:] = Z[-1,:] = Z[:,0] = Z[:,-1] = 0
</pre>
<p>Even if this first version does not use nested loops, it is far from optimal
because of the use of the 4 argwhere calls that may be quite slow. We can
instead take advantages of numpy features the following way.</p>
<pre class="literal-block">
def iterate_2(Z):
# Count neighbours
N = (Z[0:-2,0:-2] + Z[0:-2,1:-1] + Z[0:-2,2:] +
Z[1:-1,0:-2] + Z[1:-1,2:] +
Z[2: ,0:-2] + Z[2: ,1:-1] + Z[2: ,2:])
# Apply rules
birth = (N==3) & (Z[1:-1,1:-1]==0)
survive = ((N==2) | (N==3)) & (Z[1:-1,1:-1]==1)
Z[...] = 0
Z[1:-1,1:-1][birth | survive] = 1
return Z
</pre>
<p>If you look at the <tt class="docutils literal">birth</tt> and <tt class="docutils literal">survive</tt> lines, you'll see that these two
variables are indeed arrays. The right-hand side of these two expressions are
in fact logical expressions that will result in boolean arrays (just print them
to check). We then set all <tt class="docutils literal">Z</tt> values to 0 (all cells become dead) and we use
the <tt class="docutils literal">birth</tt> and <tt class="docutils literal">survive</tt> arrays to conditionally set <tt class="docutils literal">Z</tt> values
to 1. And we're done ! Let's test this:</p>
<pre class="literal-block">
>>> print(Z)
[[0 0 0 0 0 0]
[0 0 0 1 0 0]
[0 1 0 1 0 0]
[0 0 1 1 0 0]
[0 0 0 0 0 0]
[0 0 0 0 0 0]]
>>> for i in range(4): iterate_2(Z)
>>> print(Z)
[[0 0 0 0 0 0]
[0 0 0 0 0 0]
[0 0 0 0 1 0]
[0 0 1 0 1 0]
[0 0 0 1 1 0]
[0 0 0 0 0 0]]
</pre>
<p>You can download the full script here: <a class="reference external" href="scripts/game-of-life-numpy.py">game-of-life-numpy.py</a></p>
</div>
<div class="section" id="getting-bigger">
<h3>Getting bigger</h3>
<p>While numpy works perfectly with very small arrays, you'll really benefit from
numpy power with big to very big arrays. So let us reconsider the game of life
with a bigger array. First, we won't initalize the array by hand but initalize
it randomly:</p>
<pre class="literal-block">
>>> Z = np.random.randint(0,2,(256,512))
</pre>
<p>and we simply iterate as previously:</p>
<pre class="literal-block">
>>> for i in range(100): iterate(Z)
</pre>
<p>and display result:</p>
<pre class="literal-block">
>>> size = np.array(Z.shape)
>>> dpi = 72.0
>>> figsize= size[1]/float(dpi),size[0]/float(dpi)
>>> fig = plt.figure(figsize=figsize, dpi=dpi, facecolor="white")
>>> fig.add_axes([0.0, 0.0, 1.0, 1.0], frameon=False)
>>> plt.imshow(Z,interpolation='nearest', cmap=plt.cm.gray_r)
>>> plt.xticks([]), plt.yticks([])
>>> plt.show()
</pre>
<img alt="figures/game-of-life-big.png" src="figures/game-of-life-big.png" />
<div class="line-block">
<div class="line"><br /></div>
</div>
<p>Easy enough, no ?</p>
</div>
</div>
<div class="section" id="a-step-further">
<h2>A step further</h2>
<p>We have reviewed the very basics of numpy so let's move on to more complex (and
more fun) things.</p>
<div class="note">
<p class="first admonition-title">Note</p>
<p class="last">Description taken from the <a class="reference external" href="http://groups.csail.mit.edu/mac/projects/amorphous/GrayScott/">Gray-Scott homepage</a></p>
</div>
<p>Reaction and diffusion of chemical species can produce a variety of patterns,
reminiscent of those often seen in nature. The Gray Scott equations model such
a reaction. For more information on this chemical system see the article
<strong>Complex Patterns in a Simple System</strong>, John E. Pearson, Science, Volume 261,
9 July 1993.</p>
<p>Let's consider two chemical species <span class="formula"><i>U</i></span> and <span class="formula"><i>V</i></span> with respective
concentrations <span class="formula"><i>u</i></span> and <span class="formula"><i>v</i></span> and diffusion rates <span class="formula"><i>r</i><sub><i>u</i></sub></span> and
<span class="formula"><i>r</i><sub><i>v</i></sub></span>. <span class="formula"><i>V</i></span> is converted into <span class="formula"><i>P</i></span> with a rate of conversion
<span class="formula"><i>k</i></span>. <span class="formula"><i>f</i></span> represents the rate of the process that feeds <span class="formula"><i>U</i></span>
and drains <span class="formula"><i>U</i></span>, <span class="formula"><i>V</i></span> and <span class="formula"><i>P</i></span>. We can now write:</p>
<table border="1" class="docutils">
<colgroup>
<col width="50%" />
<col width="50%" />
</colgroup>
<thead valign="bottom">
<tr><th class="head">Chemical reaction</th>
<th class="head">Equations</th>
</tr>
</thead>
<tbody valign="top">
<tr><td><ul class="first last simple">
<li><span class="formula"><i>U</i> + 2<i>V</i>⟶3<i>V</i></span></li>
<li><span class="formula"><i>V</i>⟶<i>P</i></span></li>
</ul>
</td>
<td><ul class="first last simple">
<li><span class="formula"><span class="fraction"><span class="ignored">(</span><span class="numerator">∂<i>u</i></span><span class="ignored">)/(</span><span class="denominator">∂<i>t</i></span><span class="ignored">)</span></span> = <i>r</i><sub><i>u</i></sub>∇<sup>2</sup><i>u</i> − <i>uv</i><sup>2</sup> + <i>f</i>(1 − <i>u</i>)</span></li>
<li><span class="formula"><span class="fraction"><span class="ignored">(</span><span class="numerator">∂<i>v</i></span><span class="ignored">)/(</span><span class="denominator">∂<i>t</i></span><span class="ignored">)</span></span> = <i>r</i><sub><i>v</i></sub>∇<sup>2</sup><i>v</i> + <i>uv</i><sup>2</sup> − (<i>f</i> + <i>k</i>)<i>v</i></span></li>
</ul>
</td>
</tr>
</tbody>
</table>
<div class="line-block">
<div class="line"><strong>Examples</strong></div>
<div class="line">(click figure to see movie)</div>
</div>
<a class="reference external image-reference" href="movies/bacteria.mp4"><img alt="figures/bacteria.png" src="figures/bacteria.png" /></a>
<a class="reference external image-reference" href="movies/fingerprint.mp4"><img alt="figures/fingerprint.png" src="figures/fingerprint.png" /></a>
<a class="reference external image-reference" href="movies/zebra.mp4"><img alt="figures/zebra.png" src="figures/zebra.png" /></a>
<p>Obviously, you may think we need two arrays, one for <tt class="docutils literal">U</tt> and for <tt class="docutils literal">V</tt>. But
since <tt class="docutils literal">U</tt> and <tt class="docutils literal">V</tt> are tighly linked, it may be indeed better to use a
single array. Numpy allows to do that with the notion of <a class="reference external" href="http://docs.scipy.org/doc/numpy/user/basics.rec.html">structured array</a>:</p>
<pre class="literal-block">
>>> n = 200
>>> Z = np.zeros((n+2,n+2), [('U', np.double),
('V', np.double)])
>>> print(Z.dtype)
[('U', '<f8'), ('V', '<f8')]
</pre>
<p>The size of the array is (n+2,n+2) since we need the borders when computing the
neighbours. However, we'll compute differential equation only in the center
part, so we can already creates some useful views of this array:</p>
<pre class="literal-block">
>>> U,V = Z['U'], Z['V']
>>> u,v = U[1:-1,1:-1], V[1:-1,1:-1]
</pre>
<p>Next, we need to compute the Laplacian and we'll use a discrete approximation
obtained via the <a class="reference external" href="http://en.wikipedia.org/wiki/Discrete_Laplace_operator#Finite_Differences">finite difference method</a> using the same vectorization as for the Game of Life:</p>
<pre class="literal-block">
def laplacian(Z):
return ( Z[0:-2,1:-1] +
Z[1:-1,0:-2] - 4*Z[1:-1,1:-1] + Z[1:-1,2:] +
Z[2: ,1:-1] )
</pre>
<p>Finally, we can iterate the computation after havong choosed some interesting parameters:</p>
<pre class="literal-block">
for i in range(25000):
Lu = laplacian(U)
Lv = laplacian(V)
uvv = u*v*v
u += (Du*Lu - uvv + F *(1-u))
v += (Dv*Lv + uvv - (F+k)*v )
</pre>
<p>And we're done !</p>
<p>You can download the full script here: <a class="reference external" href="scripts/gray-scott.py">gray-scott.py</a></p>
</div>
</div>
<div class="section" id="exercises">
<h1><a class="toc-backref" href="#id4">Exercises</a></h1>
<p>Here are some exercises, try to do them without looking at the solution (just
highligh the blank part to see it).</p>
<div class="section" id="neophyte">
<h2>Neophyte</h2>
<ol class="arabic">
<li><p class="first">Import the numpy package under the name <tt class="docutils literal">np</tt></p>
<pre class="code python solution literal-block">
<span class="keyword namespace">import</span> <span class="name namespace">numpy</span> <span class="keyword namespace">as</span> <span class="name namespace">np</span>
</pre>
</li>
<li><p class="first">Print the numpy version and the configuration.</p>
<pre class="code python solution literal-block">
<span class="keyword">print</span> <span class="name">np</span><span class="operator">.</span><span class="name">__version__</span>
<span class="name">np</span><span class="operator">.</span><span class="name">__config__</span><span class="operator">.</span><span class="name">show</span><span class="punctuation">()</span>
</pre>
</li>
</ol>
<div class="admonition-hint admonition">
<p class="first admonition-title">Hint</p>
<p class="last">See <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.zeros.html">np.zeros</a></p>
</div>
<ol class="arabic" start="3">
<li><p class="first">Create a null vector of size 10</p>
<pre class="code python solution literal-block">
<span class="name">Z</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">zeros</span><span class="punctuation">(</span><span class="literal number integer">10</span><span class="punctuation">)</span>
</pre>
</li>
<li><p class="first">Create a null vector of size 10 but the fifth value which is 1</p>
<pre class="code python solution literal-block">
<span class="name">Z</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">zeros</span><span class="punctuation">(</span><span class="literal number integer">10</span><span class="punctuation">)</span>
<span class="name">Z</span><span class="punctuation">[</span><span class="literal number integer">4</span><span class="punctuation">]</span> <span class="operator">=</span> <span class="literal number integer">1</span>
</pre>
</li>
</ol>
<div class="admonition-hint admonition">
<p class="first admonition-title">Hint</p>
<p class="last">See <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.arange.html">np.arange</a></p>
</div>
<ol class="arabic" start="5">
<li><p class="first">Create a vector with values ranging from 10 to 99</p>
<pre class="code python solution literal-block">
<span class="name">Z</span> <span class="operator">=</span> <span class="literal number integer">10</span> <span class="operator">+</span> <span class="name">np</span><span class="operator">.</span><span class="name">arange</span><span class="punctuation">(</span><span class="literal number integer">90</span><span class="punctuation">)</span>
</pre>
</li>
<li><p class="first">Create a 3x3 matrix with values ranging from 0 to 8</p>
<pre class="code python solution literal-block">
<span class="name">Z</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">arange</span><span class="punctuation">(</span><span class="literal number integer">9</span><span class="punctuation">)</span><span class="operator">.</span><span class="name">reshape</span><span class="punctuation">(</span><span class="literal number integer">3</span><span class="punctuation">,</span><span class="literal number integer">3</span><span class="punctuation">)</span>
</pre>
</li>
</ol>
<div class="admonition-hint admonition">
<p class="first admonition-title">Hint</p>
<p class="last">See <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.nonzero.html">np.nonzero</a></p>
</div>
<ol class="arabic" start="7">
<li><p class="first">Find indices of non-zero elements from [1,2,0,0,4,0]</p>
<pre class="code python solution literal-block">
<span class="keyword">print</span> <span class="name">np</span><span class="operator">.</span><span class="name">nonzero</span><span class="punctuation">([</span><span class="literal number integer">1</span><span class="punctuation">,</span><span class="literal number integer">2</span><span class="punctuation">,</span><span class="literal number integer">0</span><span class="punctuation">,</span><span class="literal number integer">0</span><span class="punctuation">,</span><span class="literal number integer">4</span><span class="punctuation">,</span><span class="literal number integer">0</span><span class="punctuation">])</span>
</pre>
</li>
<li><p class="first">Declare a 3x3 identity matrix</p>
<pre class="code python solution literal-block">
<span class="name">Z</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">eye</span><span class="punctuation">(</span><span class="literal number integer">3</span><span class="punctuation">)</span>
</pre>
</li>
<li><p class="first">Declare a 5x5 matrix with values 1,2,3,4 just below the diagonal</p>
<pre class="code python solution literal-block">
<span class="name">Z</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">diag</span><span class="punctuation">(</span><span class="literal number integer">1</span><span class="operator">+</span><span class="name">np</span><span class="operator">.</span><span class="name">arange</span><span class="punctuation">(</span><span class="literal number integer">4</span><span class="punctuation">),</span><span class="name">k</span><span class="operator">=-</span><span class="literal number integer">1</span><span class="punctuation">)</span>
</pre>
</li>
</ol>
<div class="admonition-hint admonition">
<p class="first admonition-title">Hint</p>
<p class="last">See <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/routines.random.html">Random sampling</a></p>
</div>
<ol class="arabic" start="10">
<li><p class="first">Declare a 10x10x10 array with random values</p>
<pre class="code python solution literal-block">
<span class="name">Z</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">random</span><span class="operator">.</span><span class="name">random</span><span class="punctuation">((</span><span class="literal number integer">10</span><span class="punctuation">,</span><span class="literal number integer">10</span><span class="punctuation">,</span><span class="literal number integer">10</span><span class="punctuation">))</span>
</pre>
</li>
</ol>
</div>
<div class="section" id="novice">
<h2>Novice</h2>
<ol class="arabic">
<li><p class="first">Declare a 8x8 matrix and fill it with a checkerboard pattern</p>
<pre class="code python solution literal-block">
<span class="name">Z</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">zeros</span><span class="punctuation">((</span><span class="literal number integer">8</span><span class="punctuation">,</span><span class="literal number integer">8</span><span class="punctuation">))</span>
<span class="name">Z</span><span class="punctuation">[</span><span class="literal number integer">1</span><span class="punctuation">::</span><span class="literal number integer">2</span><span class="punctuation">,::</span><span class="literal number integer">2</span><span class="punctuation">]</span> <span class="operator">=</span> <span class="literal number integer">1</span>
<span class="name">Z</span><span class="punctuation">[::</span><span class="literal number integer">2</span><span class="punctuation">,</span><span class="literal number integer">1</span><span class="punctuation">::</span><span class="literal number integer">2</span><span class="punctuation">]</span> <span class="operator">=</span> <span class="literal number integer">1</span>
</pre>
</li>
<li><p class="first">Declare a 10x10 array with random values and find the minimum and maximum values</p>
<pre class="code python solution literal-block">
<span class="name">Z</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">random</span><span class="operator">.</span><span class="name">random</span><span class="punctuation">((</span><span class="literal number integer">10</span><span class="punctuation">,</span><span class="literal number integer">10</span><span class="punctuation">,</span><span class="literal number integer">10</span><span class="punctuation">))</span>
<span class="name">Zmin</span><span class="punctuation">,</span> <span class="name">Zmax</span> <span class="operator">=</span> <span class="name">Z</span><span class="operator">.</span><span class="name">min</span><span class="punctuation">(),</span> <span class="name">Z</span><span class="operator">.</span><span class="name">max</span><span class="punctuation">()</span>
</pre>
</li>
<li><p class="first">Create a checkerboard 8x8 matrix using the tile function</p>
<pre class="code python solution literal-block">
<span class="name">Z</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">tile</span><span class="punctuation">(</span> <span class="name">np</span><span class="operator">.</span><span class="name">array</span><span class="punctuation">([[</span><span class="literal number integer">0</span><span class="punctuation">,</span><span class="literal number integer">1</span><span class="punctuation">],[</span><span class="literal number integer">1</span><span class="punctuation">,</span><span class="literal number integer">0</span><span class="punctuation">]]),</span> <span class="punctuation">(</span><span class="literal number integer">4</span><span class="punctuation">,</span><span class="literal number integer">4</span><span class="punctuation">))</span>
</pre>
</li>
<li><p class="first">Normalize a 5x5 random matrix (between 0 and 1)</p>
<pre class="code python solution literal-block">
<span class="name">Z</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">random</span><span class="operator">.</span><span class="name">random</span><span class="punctuation">((</span><span class="literal number integer">5</span><span class="punctuation">,</span><span class="literal number integer">5</span><span class="punctuation">))</span>
<span class="name">Zmax</span><span class="punctuation">,</span><span class="name">Zmin</span> <span class="operator">=</span> <span class="name">Z</span><span class="operator">.</span><span class="name">max</span><span class="punctuation">(),</span> <span class="name">Z</span><span class="operator">.</span><span class="name">min</span><span class="punctuation">()</span>
<span class="name">Z</span> <span class="operator">=</span> <span class="punctuation">(</span><span class="name">Z</span> <span class="operator">-</span> <span class="name">Zmin</span><span class="punctuation">)</span><span class="operator">/</span><span class="punctuation">(</span><span class="name">Zmax</span> <span class="operator">-</span> <span class="name">Zmin</span><span class="punctuation">)</span>
</pre>
</li>
</ol>
<div class="admonition-hint admonition">
<p class="first admonition-title">Hint</p>
<p class="last">See the <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/routines.linalg.html">linear algebra documentation</a></p>
</div>
<ol class="arabic" start="5">
<li><p class="first">Multiply a 5x3 matrix by a 3x2 matrix (real matrix product)</p>
<pre class="code python solution literal-block">
<span class="name">Z</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">dot</span><span class="punctuation">(</span><span class="name">np</span><span class="operator">.</span><span class="name">ones</span><span class="punctuation">((</span><span class="literal number integer">5</span><span class="punctuation">,</span><span class="literal number integer">3</span><span class="punctuation">)),</span> <span class="name">np</span><span class="operator">.</span><span class="name">ones</span><span class="punctuation">((</span><span class="literal number integer">3</span><span class="punctuation">,</span><span class="literal number integer">2</span><span class="punctuation">)))</span>
</pre>
</li>
<li><p class="first">Create a 10x10 matrix with row values ranging from 0 to 9</p>
<pre class="code python solution literal-block">
<span class="name">Z</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">zeros</span><span class="punctuation">((</span><span class="literal number integer">10</span><span class="punctuation">,</span><span class="literal number integer">10</span><span class="punctuation">))</span>
<span class="name">Z</span> <span class="operator">+=</span> <span class="name">np</span><span class="operator">.</span><span class="name">arange</span><span class="punctuation">(</span><span class="literal number integer">10</span><span class="punctuation">)</span>
</pre>
</li>
<li><p class="first">Create a vector of size 1000 with values ranging from 0 to 1, both excluded</p>
<pre class="code python solution literal-block">
<span class="name">Z</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">random</span><span class="operator">.</span><span class="name">linspace</span><span class="punctuation">(</span><span class="literal number integer">0</span><span class="punctuation">,</span><span class="literal number integer">1</span><span class="punctuation">,</span><span class="literal number integer">1002</span><span class="punctuation">,</span><span class="name">endpoint</span><span class="operator">=</span><span class="name builtin pseudo">True</span><span class="punctuation">)[</span><span class="literal number integer">1</span><span class="punctuation">:</span><span class="operator">-</span><span class="literal number integer">1</span><span class="punctuation">]</span>
</pre>
</li>
<li><p class="first">Create a random vector of size 100 and sort it</p>
<pre class="code python solution literal-block">
<span class="name">Z</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">random</span><span class="operator">.</span><span class="name">random</span><span class="punctuation">(</span><span class="literal number integer">100</span><span class="punctuation">)</span>
<span class="name">Z</span><span class="operator">.</span><span class="name">sort</span><span class="punctuation">()</span>
</pre>
</li>
<li><p class="first">Consider two random matrices A anb B, check if they are equal.</p>
<pre class="code python solution literal-block">
<span class="name">A</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">random</span><span class="operator">.</span><span class="name">randint</span><span class="punctuation">(</span><span class="literal number integer">0</span><span class="punctuation">,</span><span class="literal number integer">2</span><span class="punctuation">,(</span><span class="literal number integer">2</span><span class="punctuation">,</span><span class="literal number integer">2</span><span class="punctuation">))</span>
<span class="name">B</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">random</span><span class="operator">.</span><span class="name">randint</span><span class="punctuation">(</span><span class="literal number integer">0</span><span class="punctuation">,</span><span class="literal number integer">2</span><span class="punctuation">,(</span><span class="literal number integer">2</span><span class="punctuation">,</span><span class="literal number integer">2</span><span class="punctuation">))</span>
<span class="name">equal</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">allclose</span><span class="punctuation">(</span><span class="name">A</span><span class="punctuation">,</span><span class="name">B</span><span class="punctuation">)</span>
</pre>
</li>
<li><p class="first">Create a random vector of size 1000 and find the mean value</p>
<pre class="code python solution literal-block">
<span class="name">Z</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">random</span><span class="operator">.</span><span class="name">random</span><span class="punctuation">(</span><span class="literal number integer">1000</span><span class="punctuation">)</span>
<span class="name">m</span> <span class="operator">=</span> <span class="name">Z</span><span class="operator">.</span><span class="name">mean</span><span class="punctuation">()</span>
</pre>
</li>
</ol>
</div>
<div class="section" id="apprentice">
<h2>Apprentice</h2>
<ol class="arabic">
<li><p class="first">Consider a random 100x2 matrix representing cartesian coordinates, convert
them to polar coordinates</p>
<pre class="code python solution literal-block">
<span class="name">Z</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">random</span><span class="operator">.</span><span class="name">random</span><span class="punctuation">((</span><span class="literal number integer">100</span><span class="punctuation">,</span><span class="literal number integer">2</span><span class="punctuation">))</span>
<span class="name">X</span><span class="punctuation">,</span><span class="name">Y</span> <span class="operator">=</span> <span class="name">Z</span><span class="punctuation">[:,</span><span class="literal number integer">0</span><span class="punctuation">],</span> <span class="name">Z</span><span class="punctuation">[:,</span><span class="literal number integer">1</span><span class="punctuation">]</span>
<span class="name">R</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">sqrt</span><span class="punctuation">(</span><span class="name">X</span><span class="operator">**</span><span class="literal number integer">2</span><span class="operator">+</span><span class="name">Y</span><span class="operator">**</span><span class="literal number integer">2</span><span class="punctuation">)</span>
<span class="name">T</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">arctan2</span><span class="punctuation">(</span><span class="name">Y</span><span class="punctuation">,</span><span class="name">X</span><span class="punctuation">)</span>
</pre>
</li>
<li><p class="first">Create random vector of size 100 and replace the maximum value by 0</p>
<pre class="code python solution literal-block">
<span class="name">Z</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">random</span><span class="operator">.</span><span class="name">random</span><span class="punctuation">(</span><span class="literal number integer">100</span><span class="punctuation">)</span>
<span class="name">Z</span><span class="punctuation">[</span><span class="name">Z</span><span class="operator">.</span><span class="name">argmax</span><span class="punctuation">()]</span> <span class="operator">=</span> <span class="literal number integer">0</span>
</pre>
</li>
</ol>
<div class="admonition-hint admonition">
<p class="first admonition-title">Hint</p>
<p class="last">See the documentation on <a class="reference external" href="http://docs.scipy.org/doc/numpy/user/basics.rec.html">Structured arrays</a></p>
</div>
<ol class="arabic" start="3">
<li><p class="first">Declare a structured array with <tt class="docutils literal">x</tt> and <tt class="docutils literal">y</tt> coordinates covering the
[0,1]x[0,1] area.</p>
<pre class="code python solution literal-block">
<span class="name">Z</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">zeros</span><span class="punctuation">((</span><span class="literal number integer">10</span><span class="punctuation">,</span><span class="literal number integer">10</span><span class="punctuation">),</span> <span class="punctuation">[(</span><span class="literal string">'x'</span><span class="punctuation">,</span><span class="name builtin">float</span><span class="punctuation">),(</span><span class="literal string">'y'</span><span class="punctuation">,</span><span class="name builtin">float</span><span class="punctuation">)])</span>
<span class="name">Z</span><span class="punctuation">[</span><span class="literal string">'x'</span><span class="punctuation">],</span> <span class="name">Z</span><span class="punctuation">[</span><span class="literal string">'y'</span><span class="punctuation">]</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">meshgrid</span><span class="punctuation">(</span><span class="name">np</span><span class="operator">.</span><span class="name">linspace</span><span class="punctuation">(</span><span class="literal number integer">0</span><span class="punctuation">,</span><span class="literal number integer">1</span><span class="punctuation">,</span><span class="literal number integer">10</span><span class="punctuation">),</span>
<span class="name">np</span><span class="operator">.</span><span class="name">linspace</span><span class="punctuation">(</span><span class="literal number integer">0</span><span class="punctuation">,</span><span class="literal number integer">1</span><span class="punctuation">,</span><span class="literal number integer">10</span><span class="punctuation">))</span>
</pre>
</li>
</ol>
<div class="admonition-hint admonition">
<p class="first admonition-title">Hint</p>
<p class="last">Have a look at <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/routines.dtype.html">Data type routines</a></p>
</div>
<ol class="arabic" start="4">
<li><p class="first">Print the minimum and maximum representable value for each numpy scalar type</p>
<pre class="code python solution literal-block">
<span class="keyword">for</span> <span class="name">dtype</span> <span class="operator word">in</span> <span class="punctuation">[</span><span class="name">np</span><span class="operator">.</span><span class="name">int8</span><span class="punctuation">,</span> <span class="name">np</span><span class="operator">.</span><span class="name">int32</span><span class="punctuation">,</span> <span class="name">np</span><span class="operator">.</span><span class="name">int64</span><span class="punctuation">]:</span>
<span class="keyword">print</span> <span class="name">np</span><span class="operator">.</span><span class="name">iinfo</span><span class="punctuation">(</span><span class="name">dtype</span><span class="punctuation">)</span><span class="operator">.</span><span class="name">min</span>
<span class="keyword">print</span> <span class="name">np</span><span class="operator">.</span><span class="name">iinfo</span><span class="punctuation">(</span><span class="name">dtype</span><span class="punctuation">)</span><span class="operator">.</span><span class="name">max</span>
<span class="keyword">for</span> <span class="name">dtype</span> <span class="operator word">in</span> <span class="punctuation">[</span><span class="name">np</span><span class="operator">.</span><span class="name">float32</span><span class="punctuation">,</span> <span class="name">np</span><span class="operator">.</span><span class="name">float64</span><span class="punctuation">]:</span>
<span class="keyword">print</span> <span class="name">np</span><span class="operator">.</span><span class="name">finfo</span><span class="punctuation">(</span><span class="name">dtype</span><span class="punctuation">)</span><span class="operator">.</span><span class="name">min</span>
<span class="keyword">print</span> <span class="name">np</span><span class="operator">.</span><span class="name">finfo</span><span class="punctuation">(</span><span class="name">dtype</span><span class="punctuation">)</span><span class="operator">.</span><span class="name">max</span>
<span class="keyword">print</span> <span class="name">np</span><span class="operator">.</span><span class="name">finfo</span><span class="punctuation">(</span><span class="name">dtype</span><span class="punctuation">)</span><span class="operator">.</span><span class="name">eps</span>
</pre>
</li>
<li><p class="first">Create a structured array representing a position (x,y) and a color (r,g,b)</p>
<pre class="code python solution literal-block">
<span class="name">Z</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">zeros</span><span class="punctuation">(</span><span class="literal number integer">10</span><span class="punctuation">,</span> <span class="punctuation">[</span> <span class="punctuation">(</span><span class="literal string">'position'</span><span class="punctuation">,</span> <span class="punctuation">[</span> <span class="punctuation">(</span><span class="literal string">'x'</span><span class="punctuation">,</span> <span class="name builtin">float</span><span class="punctuation">,</span> <span class="literal number integer">1</span><span class="punctuation">),</span>
<span class="punctuation">(</span><span class="literal string">'y'</span><span class="punctuation">,</span> <span class="name builtin">float</span><span class="punctuation">,</span> <span class="literal number integer">1</span><span class="punctuation">)]),</span>
<span class="punctuation">(</span><span class="literal string">'color'</span><span class="punctuation">,</span> <span class="punctuation">[</span> <span class="punctuation">(</span><span class="literal string">'r'</span><span class="punctuation">,</span> <span class="name builtin">float</span><span class="punctuation">,</span> <span class="literal number integer">1</span><span class="punctuation">),</span>
<span class="punctuation">(</span><span class="literal string">'g'</span><span class="punctuation">,</span> <span class="name builtin">float</span><span class="punctuation">,</span> <span class="literal number integer">1</span><span class="punctuation">),</span>
<span class="punctuation">(</span><span class="literal string">'b'</span><span class="punctuation">,</span> <span class="name builtin">float</span><span class="punctuation">,</span> <span class="literal number integer">1</span><span class="punctuation">)])])</span>
</pre>
</li>
<li><p class="first">Consider a random vector with shape (100,2) representing coordinates, find
point by point distances</p>
<pre class="code python solution literal-block">
<span class="name">Z</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">random</span><span class="operator">.</span><span class="name">random</span><span class="punctuation">((</span><span class="literal number integer">10</span><span class="punctuation">,</span><span class="literal number integer">2</span><span class="punctuation">))</span>
<span class="name">X</span><span class="punctuation">,</span><span class="name">Y</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">atleast_2d</span><span class="punctuation">(</span><span class="name">Z</span><span class="punctuation">[:,</span><span class="literal number integer">0</span><span class="punctuation">]),</span> <span class="name">np</span><span class="operator">.</span><span class="name">atleast_2d</span><span class="punctuation">(</span><span class="name">Z</span><span class="punctuation">[:,</span><span class="literal number integer">1</span><span class="punctuation">])</span>
<span class="name">D</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">sqrt</span><span class="punctuation">(</span> <span class="punctuation">(</span><span class="name">X</span><span class="operator">-</span><span class="name">X</span><span class="operator">.</span><span class="name">T</span><span class="punctuation">)</span><span class="operator">**</span><span class="literal number integer">2</span> <span class="operator">+</span> <span class="punctuation">(</span><span class="name">Y</span><span class="operator">-</span><span class="name">Y</span><span class="operator">.</span><span class="name">T</span><span class="punctuation">)</span><span class="operator">**</span><span class="literal number integer">2</span><span class="punctuation">)</span>
</pre>
</li>
<li><p class="first">Generate a generic 2D Gaussian-like array</p>
<pre class="code python solution literal-block">
<span class="name">X</span><span class="punctuation">,</span> <span class="name">Y</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">meshgrid</span><span class="punctuation">(</span><span class="name">np</span><span class="operator">.</span><span class="name">linspace</span><span class="punctuation">(</span><span class="operator">-</span><span class="literal number integer">1</span><span class="punctuation">,</span><span class="literal number integer">1</span><span class="punctuation">,</span><span class="literal number integer">100</span><span class="punctuation">),</span> <span class="name">np</span><span class="operator">.</span><span class="name">linspace</span><span class="punctuation">(</span><span class="operator">-</span><span class="literal number integer">1</span><span class="punctuation">,</span><span class="literal number integer">1</span><span class="punctuation">,</span><span class="literal number integer">100</span><span class="punctuation">))</span>
<span class="name">D</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">sqrt</span><span class="punctuation">(</span><span class="name">X</span><span class="operator">*</span><span class="name">X</span><span class="operator">+</span><span class="name">Y</span><span class="operator">*</span><span class="name">Y</span><span class="punctuation">)</span>
<span class="name">sigma</span><span class="punctuation">,</span> <span class="name">mu</span> <span class="operator">=</span> <span class="literal number float">1.0</span><span class="punctuation">,</span> <span class="literal number float">0.0</span>
<span class="name">G</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">exp</span><span class="punctuation">(</span><span class="operator">-</span><span class="punctuation">(</span> <span class="punctuation">(</span><span class="name">D</span><span class="operator">-</span><span class="name">mu</span><span class="punctuation">)</span><span class="operator">**</span><span class="literal number integer">2</span> <span class="operator">/</span> <span class="punctuation">(</span> <span class="literal number float">2.0</span> <span class="operator">*</span> <span class="name">sigma</span><span class="operator">**</span><span class="literal number integer">2</span> <span class="punctuation">)</span> <span class="punctuation">)</span> <span class="punctuation">)</span>
</pre>
</li>
<li><p class="first">Consider the vector [1, 2, 3, 4, 5], how to build a new vector with 3
consecutive zeros interleaved between each value ?</p>
<pre class="code python solution literal-block">
<span class="name">Z</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">array</span><span class="punctuation">([</span><span class="literal number integer">1</span><span class="punctuation">,</span><span class="literal number integer">2</span><span class="punctuation">,</span><span class="literal number integer">3</span><span class="punctuation">,</span><span class="literal number integer">4</span><span class="punctuation">,</span><span class="literal number integer">5</span><span class="punctuation">])</span>
<span class="name">nz</span> <span class="operator">=</span> <span class="literal number integer">3</span>
<span class="name">Z0</span> <span class="operator">=</span> <span class="name">np</span><span class="operator">.</span><span class="name">zeros</span><span class="punctuation">(</span><span class="name builtin">len</span><span class="punctuation">(</span><span class="name">Z</span><span class="punctuation">)</span> <span class="operator">+</span> <span class="punctuation">(</span><span class="name builtin">len</span><span class="punctuation">(</span><span class="name">Z</span><span class="punctuation">)</span><span class="operator">-</span><span class="literal number integer">1</span><span class="punctuation">)</span><span class="operator">*</span><span class="punctuation">(</span><span class="name">nz</span><span class="punctuation">))</span>
<span class="name">Z0</span><span class="punctuation">[::</span><span class="name">nz</span><span class="operator">+</span><span class="literal number integer">1</span><span class="punctuation">]</span> <span class="operator">=</span> <span class="name">Z</span>
</pre>
</li>
</ol>
</div>
</div>
<div class="section" id="beyond-this-tutorial">
<h1><a class="toc-backref" href="#id5">Beyond this tutorial</a></h1>
<p>Numpy benefits from extensive documentation as well as a large community of
users and developpers. Here are some links of interest:</p>
<div class="section" id="other-tutorials">
<h2>Other Tutorials</h2>
<ul>
<li><p class="first"><a class="reference external" href="http://scipy-lectures.github.io">The SciPy Lecture Notes</a></p>
<p>The SciPy Lecture notes offers a teaching material on the scientific Python
ecosystem as well as quick introduction to central tools and techniques. The
different chapters each correspond to a 1 to 2 hours course with increasing
level of expertise, from beginner to expert.</p>
</li>
<li><p class="first"><a class="reference external" href="http://www.scipy.org/Tentative_NumPy_Tutorial">A Tentative numpy tutorial</a></p>
<ul class="simple">
<li>Prerequisites</li>
<li>The Basics</li>
<li>Shape Manipulation</li>
<li>Copies and Views</li>
<li>Less Basic</li>
<li>Fancy indexing and index tricks</li>
<li>Linear Algebra</li>
<li>Tricks and Tips</li>
</ul>
</li>
</ul>
<div class="line-block">
<div class="line"><br /></div>
</div>
<ul>
<li><p class="first"><a class="reference external" href="http://mentat.za.net/numpy/numpy_advanced_slides/">Numpy MedKit</a></p>
<blockquote>
<p>A first-aid kit for the numerically adventurous by Stéfan van der Walt.</p>
</blockquote>
</li>
<li><p class="first"><a class="reference external" href="http://www.engr.ucsb.edu/~shell/che210d/numpy.pdf">An introduction to Numpy and Scipy</a></p>
<p>A short introduction to Numpy and Scipy by M. Scott Shell.</p>
</li>
</ul>
</div>
<div class="section" id="numpy-documentation">
<h2>Numpy documentation</h2>
<ul>
<li><p class="first"><a class="reference external" href="http://docs.scipy.org/doc/numpy/user/">User guide</a></p>
<blockquote>
<p>This guide is intended as an introductory overview of NumPy and explains how
to install and make use of the most important features of NumPy.</p>
</blockquote>
</li>
<li><p class="first"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/index.html#reference">Numpy reference</a></p>
<p>This reference manual details functions, modules, and objects included in
Numpy, describing what they are and what they do.</p>
</li>
<li><p class="first"><a class="reference external" href="http://www.scipy.org/FAQ">FAQ</a></p>
<blockquote>
<ul class="simple">
<li>General questions about numpy</li>
<li>General questions about SciPy</li>
<li>Basic SciPy/numpy usage</li>
<li>Advanced NumPy/SciPy usage</li>
<li>NumPy/SciPy installation</li>
<li>Miscellaneous Issues</li>
</ul>
</blockquote>
</li>
</ul>
</div>
<div class="section" id="code-documentation">
<h2>Code documentation</h2>
<p>The code is fairly well documented and you can quickly access a specific
command from within a python session:</p>
<pre class="literal-block">
>>> import numpy as np
>>> help(np.ones)
Help on function ones in module numpy.core.numeric:
ones(shape, dtype=None, order='C')
Return a new array of given shape and type, filled with ones.
Please refer to the documentation for `zeros` for further details.
See Also
--------
zeros, ones_like
Examples
--------
>>> np.ones(5)
array([ 1., 1., 1., 1., 1.])
>>> np.ones((5,), dtype=np.int)
array([1, 1, 1, 1, 1])
>>> np.ones((2, 1))
array([[ 1.],
[ 1.]])
>>> s = (2,2)
>>> np.ones(s)
array([[ 1., 1.],
[ 1., 1.]])
</pre>
</div>
<div class="section" id="mailing-lists">
<h2>Mailing lists</h2>
<p>Finally, there is a <a class="reference external" href="https://lists.sourceforge.net/lists/listinfo/numpy-discussion">mailing list</a> where you can
ask for help.</p>
</div>
</div>
<div class="section" id="quick-references">
<h1><a class="toc-backref" href="#id6">Quick references</a></h1>
<div class="section" id="data-type">
<h2>Data type</h2>
<table border="1" class="compact-table docutils">
<colgroup>
<col width="13%" />
<col width="87%" />
</colgroup>
<thead valign="bottom">
<tr><th class="head">Data type</th>
<th class="head">Description</th>
</tr>
</thead>
<tbody valign="top">
<tr><td>bool</td>
<td>Boolean (True or False) stored as a byte</td>
</tr>
<tr><td>int</td>
<td>Platform integer (normally either int32 or int64)</td>
</tr>
<tr><td>int8</td>
<td>Byte (-128 to 127)</td>
</tr>
<tr><td>int16</td>
<td>Integer (-32768 to 32767)</td>
</tr>
<tr><td>int32</td>
<td>Integer (-2147483648 to 2147483647)</td>
</tr>
<tr><td>int64</td>
<td>Integer (9223372036854775808 to 9223372036854775807)</td>
</tr>
<tr><td>uint8</td>
<td>Unsigned integer (0 to 255)</td>
</tr>
<tr><td>uint16</td>
<td>Unsigned integer (0 to 65535)</td>
</tr>
<tr><td>uint32</td>
<td>Unsigned integer (0 to 4294967295)</td>
</tr>
<tr><td>uint64</td>
<td>Unsigned integer (0 to 18446744073709551615)</td>
</tr>
<tr><td>float</td>
<td>Shorthand for float64.</td>
</tr>
<tr><td>float16</td>
<td>Half precision float: sign bit, 5 bits exponent, 10 bits mantissa</td>
</tr>
<tr><td>float32</td>
<td>Single precision float: sign bit, 8 bits exponent, 23 bits mantissa</td>
</tr>