Python Scientific lecture notes

Release 2011

EuroScipy tutorial team

Editors: Valentin Haenel, Emmanuelle Gouillart, Gal Varoquaux
http://scipy-lectures.github.com

August 25, 2011

Contents

Getting started with Python for science

Scientific computing with tools and workflow

1.1 Why Python? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.2 Scientific Python building blocks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.3 The interactive workflow: IPython and a text editor . . . . . . . . . . . . . . . . . . . . . . . . .

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5
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The Python language

2.1 First steps . . . . . . . . . . . . . . .
2.2 Basic types . . . . . . . . . . . . . .
2.3 Assignment operator . . . . . . . . .
2.4 Control Flow . . . . . . . . . . . . .
2.5 Defining functions . . . . . . . . . .
2.6 Reusing code: scripts and modules .
2.7 Input and Output . . . . . . . . . . .
2.8 Standard Library . . . . . . . . . . .
2.9 Exceptions handling in Python . . . .
2.10 Object-oriented programming (OOP)

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8
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32
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39

NumPy: creating and manipulating numerical data

3.1 Intro . . . . . . . . . . . . . . . . . . . . . . .
3.2 1. Basics I . . . . . . . . . . . . . . . . . . . .
3.3 2. Basics II . . . . . . . . . . . . . . . . . . . .
3.4 3. Moving on . . . . . . . . . . . . . . . . . . .
3.5 4. Under the hood . . . . . . . . . . . . . . . .

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40
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56
76
87

Getting help and finding documentation

Matplotlib
5.1 Introduction . . . . . . . .
5.2 IPython . . . . . . . . . . .
5.3 pylab . . . . . . . . . . . .
5.4 Simple Plots . . . . . . . .
5.5 Properties . . . . . . . . . .
5.6 Text . . . . . . . . . . . . .
5.7 Ticks . . . . . . . . . . . .
5.8 Figures, Subplots, and Axes
5.9 Other Types of Plots . . . .
5.10 The Class Library . . . . .

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110

II

Scipy : high-level scientific computing

6.1 Scipy builds upon Numpy . . . . . . . . . . . .
6.2 File input/output: scipy.io . . . . . . . . . .
6.3 Signal processing: scipy.signal . . . . . .
6.4 Special functions: scipy.special . . . . . .
6.5 Statistics and random numbers: scipy.stats
6.6 Linear algebra operations: scipy.linalg . .
6.7 Numerical integration: scipy.integrate . .
6.8 Fast Fourier transforms: scipy.fftpack . .
6.9 Interpolation: scipy.interpolate . . . . .
6.10 Optimization and fit: scipy.optimize . . .
6.11 Image processing: scipy.ndimage . . . . .
6.12 Summary exercises on scientific computing . . .

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Advanced topics

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133

147

Advanced Python Constructs

7.1 Iterators, generator expressions and generators . . . . . . . . . . . . . . . . . . . . . . . . . . .
7.2 Decorators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7.3 Context managers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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161

Advanced Numpy
8.1 Life of ndarray . . . . . . . . . . . . . . . . . . .
8.2 Universal functions . . . . . . . . . . . . . . . . .
8.3 Interoperability features . . . . . . . . . . . . . .
8.4 Siblings: chararray, maskedarray, matrix
8.5 Summary . . . . . . . . . . . . . . . . . . . . . .
8.6 Contributing to Numpy/Scipy . . . . . . . . . . .

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Debugging code
9.1 Avoiding bugs . . . . . . . . . . . . . .
9.2 Debugging workflow . . . . . . . . . . .
9.3 Using the Python debugger . . . . . . . .
9.4 Debugging segmentation faults using gdb

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10 Optimizing code
10.1 Optimization workflow . . . .
10.2 Profiling Python code . . . .
10.3 Making code go faster . . . .
10.4 Writing faster numerical code

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212

11 Sparse Matrices in SciPy

11.1 Introduction . . . . . . .
11.2 Storage Schemes . . . . .
11.3 Linear System Solvers . .
11.4 Other Interesting Packages

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12 Image manipulation and processing using Numpy and Scipy

12.1 Opening and writing to image files . . . . . . . . . . . .
12.2 Displaying images . . . . . . . . . . . . . . . . . . . . .
12.3 Basic manipulations . . . . . . . . . . . . . . . . . . . .
12.4 Image filtering . . . . . . . . . . . . . . . . . . . . . . .
12.5 Feature extraction . . . . . . . . . . . . . . . . . . . . .
12.6 Measuring objects properties . . . . . . . . . . . . . . . .

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13 3D plotting with Mayavi

264
13.1 A simple example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 264
13.2 3D plotting functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265

ii

13.3 Figures and decorations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 268

13.4 Interaction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271
14 Sympy : Symbolic Mathematics in Python
14.1 First Steps with SymPy . . . . . . . .
14.2 Algebraic manipulations . . . . . . . .
14.3 Calculus . . . . . . . . . . . . . . . .
14.4 Equation solving . . . . . . . . . . . .
14.5 Linear Algebra . . . . . . . . . . . . .

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15 scikit-learn: machine learning in Python

15.1 Loading an example dataset . . . . . . . . . . . . . . . . . . . . . . .
15.2 Supervised learning . . . . . . . . . . . . . . . . . . . . . . . . . . .
15.3 Clustering: grouping observations together . . . . . . . . . . . . . . .
15.4 Putting it all together : face recognition with Support Vector Machines

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Bibliography

287

Index

288

iii

Python Scientific lecture notes, Release 2011

Contents

Part I

Getting started with Python for science

CHAPTER 1

Scientific computing with tools and

workflow

authors Fernando Perez, Emmanuelle Gouillart, Gal Varoquaux

1.1 Why Python?

1.1.1 The scientists needs
Get data (simulation, experiment control)
Manipulate and process data.
Visualize results... to understand what we are doing!
Communicate on results: produce figures for reports or publications, write presentations.

1.1.2 Specifications
Rich collection of already existing bricks corresponding to classical numerical methods or basic actions: we
dont want to re-program the plotting of a curve, a Fourier transform or a fitting algorithm. Dont reinvent
the wheel!
Easy to learn: computer science neither is our job nor our education. We want to be able to draw a curve,
smooth a signal, do a Fourier transform in a few minutes.
Easy communication with collaborators, students, customers, to make the code live within a labo or a
company: the code should be as readable as a book. Thus, the language should contain as few syntax
symbols or unneeded routines that would divert the reader from the mathematical or scientific understanding
of the code.
Efficient code that executes quickly... But needless to say that a very fast code becomes useless if we spend
too much time writing it. So, we need both a quick development time and a quick execution time.
A single environment/language for everything, if possible, to avoid learning a new software for each new
problem.

1.1.3 Existing solutions

Which solutions do the scientists use to work?

Python Scientific lecture notes, Release 2011

Compiled languages: C, C++, Fortran, etc.

Advantages:
Very fast. Very optimized compilers. For heavy computations, its difficult to outperform these languages.
Some very optimized scientific libraries have been written for these languages. Ex: blas (vector/matrix
operations)
Drawbacks:
Painful usage: no interactivity during development, mandatory compilation steps, verbose syntax (&,
::, }}, ; etc.), manual memory management (tricky in C). These are difficult languages for non computer scientists.
Scripting languages: Matlab
Advantages:
Very rich collection of libraries with numerous algorithms, for many different domains. Fast execution
because these libraries are often written in a compiled language.
Pleasant development environment: comprehensive and well organized help, integrated editor, etc.
Commercial support is available.
Drawbacks:
Base language is quite poor and can become restrictive for advanced users.
Not free.
Other script languages: Scilab, Octave, Igor, R, IDL, etc.
Advantages:
Open-source, free, or at least cheaper than Matlab.
Some features can be very advanced (statistics in R, figures in Igor, etc.)
Drawbacks:
fewer available algorithms than in Matlab, and the language is not more advanced.
Some software are dedicated to one domain. Ex: Gnuplot or xmgrace to draw curves. These programs
are very powerful, but they are restricted to a single type of usage, such as plotting.
What about Python?
Advantages:
Very rich scientific computing libraries (a bit less than Matlab, though)
Well-thought language, allowing to write very readable and well structured code: we code what we
think.
Many libraries for other tasks than scientific computing (web server management, serial port access,
etc.)
Free and open-source software, widely spread, with a vibrant community.
Drawbacks:
less pleasant development environment than, for example, Matlab. (More geek-oriented).
Not all the algorithms that can be found in more specialized software or toolboxes.

1.1. Why Python?

Python Scientific lecture notes, Release 2011

1.2 Scientific Python building blocks

Python, a generic and modern computing language
Python language: data types (string, int), flow control, data collections (lists, dictionaries), patterns, etc.
Modules of the standard library.
A large number of specialized modules or applications written in Python: web protocols, web framework, etc. ... and scientific computing.
Development tools (automatic tests, documentation generation)

IPython, an advanced Python shell

http://ipython.scipy.org/moin/
Numpy : provides powerful numerical arrays objects, and routines to manipulate them.
http://www.scipy.org/
Scipy : high-level data processing routines. Optimization, regression, interpolation, etc
http://www.scipy.org/
Matplotlib : 2-D visualization, publication-ready plots

http://matplotlib.sourceforge.net/
Mayavi : 3-D visualization

1.2. Scientific Python building blocks

Python Scientific lecture notes, Release 2011

http://code.enthought.com/projects/mayavi/

1.3 The interactive workflow: IPython and a text editor

Interactive work to test and understand algorithm
Python is a general-purpose language. As such, there is not one blessed environement to work into, and not only
one way of using it. Although this makes it harder for beginners to find their way, it makes it possible for Python
to be used to write programs, in web servers, or embedded devices. Here, we describe an interactive workflow
with IPython that is handy to explore and understand algorithms.
Note: Reference document for this section:
IPython user manual: http://ipython.scipy.org/doc/manual/html/

1.3.1 Command line interaction

Start ipython:
In [1]: print(Hello world)
Hello world

Getting help:
In [2]: print ?
Type:
builtin_function_or_method
Base Class:
<type builtin_function_or_method>
String Form:
<built-in function print>
Namespace:
Python builtin
Docstring:
print(value, ..., sep= , end=\n, file=sys.stdout)
Prints the values to a stream, or to sys.stdout by default.
Optional keyword arguments:
file: a file-like object (stream); defaults to the current sys.stdout.
sep: string inserted between values, default a space.
end: string appended after the last value, default a newline.

1.3. The interactive workflow: IPython and a text editor

Python Scientific lecture notes, Release 2011

1.3.2 Elaboration of the algorithm in an editor

Create a file my_file.py in a text editor. Under EPD, you can use Scite, available from the start menu. Under
Python(x,y), you can use Spyder. Under Ubuntu, if you dont already have your favorite editor, I would advise
installing Stanis Python editor. In the file, add the following lines:
s = Hello world
print(s)

Now, you can run it in ipython and explore the resulting variables:
In [3]: %run my_file.py
Hello word
In [4]: s
Out[4]: Hello word
In [5]: %whos
Variable
Type
Data/Info
---------------------------s
str
Hello word

From a script to functions

A script is not reusable, functions are.
Thinking in terms of functions helps breaking the problem in small blocks.

1.3. The interactive workflow: IPython and a text editor

CHAPTER 2

The Python language

authors Chris Burns, Christophe Combelles, Emmanuelle Gouillart, Gal Varoquaux

Python for scientific computing
We introduce here the Python language. Only the bare minimum necessary for getting started with Numpy
and Scipy is addressed here. To learn more about the language, consider going through the excellent tutorial
http://docs.python.org/tutorial. Dedicated books are also available, such as http://diveintopython.org/.

Python is a programming language, as are C, Fortran, BASIC, PHP, etc. Some specific features of Python are as
follows:
an interpreted (as opposed to compiled) language. Contrary to e.g. C or Fortran, one does not compile
Python code before executing it. In addition, Python can be used interactively: many Python interpreters
are available, from which commands and scripts can be executed.
a free software released under an open-source license: Python can be used and distributed free of charge,
even for building commercial software.
multi-platform: Python is available for all major operating systems, Windows, Linux/Unix, MacOS X,
most likely your mobile phone OS, etc.
a very readable language with clear non-verbose syntax
a language for which a large variety of high-quality packages are available for various applications, from
web frameworks to scientific computing.
a language very easy to interface with other languages, in particular C and C++.
Some other features of the language are illustrated just below. For example, Python is an object-oriented
language, with dynamic typing (the same variable can contain objects of different types during the course
of a program).
See http://www.python.org/about/ for more information about distinguishing features of Python.

Python Scientific lecture notes, Release 2011

2.1 First steps

Start the Ipython shell (an enhanced interactive Python shell):
by typing ipython from a Linux/Mac terminal, or from the Windows cmd shell,
or by starting the program from a menu, e.g. in the Python(x,y) or EPD menu if you have installed one of
these scientific-Python suites.
If you dont have Ipython installed on your computer, other Python shells are available, such as the plain Python
shell started by typing python in a terminal, or the Idle interpreter. However, we advise to use the Ipython shell
because of its enhanced features, especially for interactive scientific computing.
Once you have started the interpreter, type
>>> print "Hello, world!"
Hello, world!

The message Hello, world! is then displayed. You just executed your first Python instruction, congratulations!
To get yourself started, type the following stack of instructions
>>> a = 3
>>> b = 2*a
>>> type(b)
<type int>
>>> print b
6
>>> a*b
18
>>> b = hello
>>> type(b)
<type str>
>>> b + b
hellohello
>>> 2*b
hellohello

Two variables a and b have been defined above. Note that one does not declare the type of an variable before
assigning its value. In C, conversely, one should write:
int a = 3;

In addition, the type of a variable may change, in the sense that at one point in time it can be equal to a value of
a certain type, and a second point in time, it can be equal to a value of a different type. b was first equal to an
integer, but it became equal to a string when it was assigned the value hello. Operations on integers (b=2*a)
are coded natively in Python, and so are some operations on strings such as additions and multiplications, which
amount respectively to concatenation and repetition.

2.2 Basic types

2.2.1 Numerical types
Integer variables:
>>> 1 + 1
2
>>> a = 4

floats

2.1. First steps

Python Scientific lecture notes, Release 2011

>>> c = 2.1

complex (a native type in Python!)

>>> a = 1.5 + 0.5j
>>> a.real
1.5
>>> a.imag
0.5

and booleans:
>>> 3 > 4
False
>>> test = (3 > 4)
>>> test
False
>>> type(test)
<type bool>

A Python shell can therefore replace your pocket calculator, with the basic arithmetic operations +, -, *, /, %
(modulo) natively implemented:
>>> 7 * 3.
21.0
>>> 2**10
1024
>>> 8 % 3
2

Warning: Integer division

>>> 3 / 2
1

Trick: use floats:

>>> 3 / 2.
1.5
>>>
>>>
>>>
1
>>>
1.5

a = 3
b = 2
a / b
a / float(b)

Scalar types: int, float, complex, bool:

>>> type(1)
<type int>
>>> type(1.)
<type float>
>>> type(1. + 0j )
<type complex>
>>> a = 3
>>> type(a)
<type int>

Type conversion:

2.2. Basic types

10

Python Scientific lecture notes, Release 2011

>>> float(1)
1.0

2.2.2 Containers
Python provides many efficient types of containers, in which collections of objects can be stored.
Lists
A list is an ordered collection of objects, that may have different types. For example
>>> l = [1, 2, 3, 4, 5]
>>> type(l)
<type list>

Indexing: accessing individual objects contained in the list:

>>> l[2]
3

Counting from the end with negative indices:

>>> l[-1]
5
>>> l[-2]
4

Warning: Indexing starts at 0 (as in C), not at 1 (as in Fortran or Matlab)!

Slicing: obtaining sublists of regularly-spaced elements
>>>
[1,
>>>
[3,

l
2, 3, 4, 5]
l[2:4]
4]

Warning: Note that l[start:stop] contains the elements with indices i such as start<= i < stop
(i ranging from start to stop-1). Therefore, l[start:stop] has (stop-start) elements.
Slicing syntax: l[start:stop:stride]
All slicing parameters are optional:
>>>
[4,
>>>
[1,
>>>
[1,

l[3:]
5]
l[:3]
2, 3]
l[::2]
3, 5]

Lists are mutable objects and can be modified:

>>> l[0] =
>>> l
[28, 2, 3,
>>> l[2:4]
>>> l
[28, 2, 3,

28
4, 5]
= [3, 8]
8, 5]

Note: The elements of a list may have different types:

2.2. Basic types

11

Python Scientific lecture notes, Release 2011

>>>
>>>
[3,
>>>
(2,

l = [3, 2, hello]
l
2, hello]
l[1], l[2]
hello)

For collections of numerical data that all have the same type, it is often more efficient to use the array type
provided by the numpy module. A NumPy array is a chunk of memory containing fixed-sized items. With
NumPy arrays, operations on elements can be faster because elements are regularly spaced in memory and more
operations are perfomed through specialized C functions instead of Python loops.
Python offers a large panel of functions to modify lists, or query them. Here are a few examples; for more details,
see http://docs.python.org/tutorial/datastructures.html#more-on-lists
Add and remove elements:
>>>
>>>
>>>
[1,
>>>
6
>>>
[1,
>>>
>>>
[1,
>>>
>>>
[1,

l = [1, 2, 3, 4, 5]
l.append(6)
l
2, 3, 4, 5, 6]
l.pop()
l
2, 3, 4, 5]
l.extend([6, 7]) # extend l, in-place
l
2, 3, 4, 5, 6, 7]
l = l[:-2]
l
2, 3, 4, 5]

Reverse l:
>>> r = l[::-1]
>>> r
[5, 4, 3, 2, 1]

Concatenate and repeat lists:

>>>
[5,
>>>
[5,

r + l
4, 3, 2, 1, 1, 2, 3, 4, 5]
2 * r
4, 3, 2, 1, 5, 4, 3, 2, 1]

Sort r (in-place):
>>> r.sort()
>>> r
[1, 2, 3, 4, 5]

Note: Methods and Object-Oriented Programming

The notation r.method() (r.sort(), r.append(3), l.pop()) is our first example of object-oriented
programming (OOP). Being a list, the object r owns the method function that is called using the notation ..
No further knowledge of OOP than understanding the notation . is necessary for going through this tutorial.
Note: Discovering methods:
In IPython: tab-completion (press tab)
In [28]: r.
r.__add__
r.__class__
r.__contains__
r.__delattr__
r.__delitem__

2.2. Basic types

r.__iadd__
r.__imul__
r.__init__
r.__iter__
r.__le__

r.__setattr__
r.__setitem__
r.__setslice__
r.__sizeof__
r.__str__

12

Python Scientific lecture notes, Release 2011

r.__delslice__
r.__doc__
r.__eq__
r.__format__
r.__ge__
r.__getattribute__
r.__getitem__
r.__getslice__
r.__gt__
r.__hash__

r.__len__
r.__lt__
r.__mul__
r.__ne__
r.__new__
r.__reduce__
r.__reduce_ex__
r.__repr__
r.__reversed__
r.__rmul__

r.__subclasshook__
r.append
r.count
r.extend
r.index
r.insert
r.pop
r.remove
r.reverse
r.sort

Strings
Different string syntaxes (simple, double or triple quotes):
s = Hello, how are you?
s = "Hi, whats up"
s = Hello,
how are you
s = """Hi,
whats up?"""

# tripling the quotes allows the

# the string to span more than one line

In [1]: Hi, whats up ?

-----------------------------------------------------------File "<ipython console>", line 1
Hi, whats up?
^
SyntaxError: invalid syntax

The newline character is \n, and the tab character is \t.

Strings are collections like lists. Hence they can be indexed and sliced, using the same syntax and rules.
Indexing:
>>>
>>>
h
>>>
e
>>>
o

a = "hello"
a[0]
a[1]
a[-1]

(Remember that negative indices correspond to counting from the right end.)
Slicing:
>>> a = "hello, world!"
>>> a[3:6] # 3rd to 6th (excluded) elements: elements 3, 4, 5
lo,
>>> a[2:10:2] # Syntax: a[start:stop:step]
lo o
>>> a[::3] # every three characters, from beginning to end
hl r!

Accents
and
special
characters
can
also
be
handled
http://docs.python.org/tutorial/introduction.html#unicode-strings).

in

Unicode

strings

(see

A string is an immutable object and it is not possible to modify its contents. One may however create new strings
from the original one.
In [53]: a = "hello, world!"
In [54]: a[2] = z
---------------------------------------------------------------------------

2.2. Basic types

13

Python Scientific lecture notes, Release 2011

TypeError
last)

Traceback (most recent call

/home/gouillar/travail/sgr/2009/talks/dakar_python/cours/gael/essai/source/<ipython
console> in <module>()
TypeError: str object does not support item assignment
In [55]: a.replace(l, z, 1)
Out[55]: hezlo, world!
In [56]: a.replace(l, z)
Out[56]: hezzo, worzd!

Strings have many useful methods, such as a.replace as seen above. Remember the a. object-oriented
notation and use tab completion or help(str) to search for new methods.
Note:
Python offers advanced possibilities for manipulating strings, looking for patterns or formatting. Due to lack of time this topic is not addressed here, but the interested reader is referred to
http://docs.python.org/library/stdtypes.html#string-methods and http://docs.python.org/library/string.html#newstring-formatting
String substitution:
>>> An integer: %i; a float: %f; another string: %s % (1, 0.1, string)
An integer: 1; a float: 0.100000; another string: string
>>> i = 102
>>> filename = processing_of_dataset_%03d.txt%i
>>> filename
processing_of_dataset_102.txt

Dictionaries
A dictionary is basically an efficient table that maps keys to values. It is an unordered container:
>>> tel = {emmanuelle: 5752, sebastian: 5578}
>>> tel[francis] = 5915
>>> tel
{sebastian: 5578, francis: 5915, emmanuelle: 5752}
>>> tel[sebastian]
5578
>>> tel.keys()
[sebastian, francis, emmanuelle]
>>> tel.values()
[5578, 5915, 5752]
>>> francis in tel
True

It can be used to conveniently store and retrieve values associated with a name (a string for a date, a name, etc.).
See http://docs.python.org/tutorial/datastructures.html#dictionaries for more information.
A dictionary can have keys (resp. values) with different types:
>>> d = {a:1, b:2, 3:hello}
>>> d
{a: 1, 3: hello, b: 2}

More container types

Tuples
Tuples are basically immutable lists. The elements of a tuple are written between parentheses, or just separated
by commas:

2.2. Basic types

14

Python Scientific lecture notes, Release 2011

>>> t = 12345, 54321, hello!

>>> t[0]
12345
>>> t
(12345, 54321, hello!)
>>> u = (0, 2)

Sets: unordered, unique items:

>>> s = set((a, b, c, a))
>>> s
set([a, c, b])
>>> s.difference((a, b))
set([c])

A bag of Ipython tricks

Several Linux shell commands work in Ipython, such as ls,

pwd, cd, etc.
To get help about objects, functions, etc., type help object. Just type help() to get started.
Use tab-completion as much as possible: while typing the beginning of an objects name (variable,
function, module), press the Tab key and Ipython will complete the expression to match available
names. If many names are possible, a list of names is displayed.
History: press the up (resp. down) arrow to go through all previous (resp. next) instructions starting
with the expression on the left of the cursor (put the cursor at the beginning of the line to go through
all previous commands)
You may log your session by using the Ipython magic command %logstart. Your instructions will
be saved in a file, that you can execute as a script in a different session.

In [1]: %logstart commands.log

Activating auto-logging. Current session state plus future input
saved.
Filename
: commands.log
Mode
: backup
Output logging : False
Raw input log : False
Timestamping
: False
State
: active

2.3 Assignment operator

Python library reference says:
Assignment statements are used to (re)bind names to values and to modify attributes or items of
mutable objects.
In short, it works as follows (simple assignment):
1. an expression on the right hand side is evaluated, the corresponding object is created/obtained
2. a name on the left hand side is assigned, or bound, to the r.h.s. object
Things to note:
a single object can have several names bound to it:
In [1]:
In [2]:
In [3]:
Out[3]:
In [4]:

2.3. Assignment operator

a = [1, 2, 3]
b = a
a
[1, 2, 3]
b

15

Python Scientific lecture notes, Release 2011

Out[4]:
In [5]:
Out[5]:
In [6]:
In [7]:
Out[7]:

[1, 2, 3]
a is b
True
b[1] = hi!
a
[1, hi!, 3]

to change a list in place, use indexing/slices:

In [1]:
In [3]:
Out[3]:
In [4]:
In [5]:
Out[5]:
In [6]:
Out[6]:
In [7]:
In [8]:
Out[8]:
In [9]:
Out[9]:

a = [1, 2, 3]
a
[1, 2, 3]
a = [a, b, c] # Creates another object.
a
[a, b, c]
id(a)
138641676
a[:] = [1, 2, 3] # Modifies object in place.
a
[1, 2, 3]
id(a)
138641676 # Same as in Out[6], yours will differ...

the key concept here is mutable vs. immutable

mutable objects can be changed in place
immutable objects cannot be modified once created
A very good and detailed explanation of the above issues can be found in David M. Beazleys article Types and
Objects in Python.

2.4 Control Flow

Controls the order in which the code is executed.

2.4.1 if/elif/else
In [1]: if 2**2 == 4:
...:
print Obvious!
...:
Obvious!

Blocks are delimited by indentation

Type the following lines in your Python interpreter, and be careful to respect the indentation depth. The Ipython
shell automatically increases the indentation depth after a column : sign; to decrease the indentation depth, go
four spaces to the left with the Backspace key. Press the Enter key twice to leave the logical block.
In [2]: a = 10
In [3]: if a == 1:
...:
print(1)
...: elif a == 2:
...:
print(2)
...: else:
...:
print(A lot)
...:
A lot

Indentation is compulsory in scripts as well. As an exercise, re-type the previous lines with the same indentation
in a script condition.py, and execute the script with run condition.py in Ipython.
2.4. Control Flow

16

Python Scientific lecture notes, Release 2011

2.4.2 for/range
Iterating with an index:
In [4]: for i in range(4):
...:
print(i)
...:
0
1
2
3

But most often, it is more readable to iterate over values:

In [5]: for word in (cool, powerful, readable):
...:
print(Python is %s % word)
...:
Python is cool
Python is powerful
Python is readable

2.4.3 while/break/continue
Typical C-style while loop (Mandelbrot problem):
In [6]: z = 1 + 1j
In [7]: while abs(z) < 100:
...:
z = z**2 + 1
...:
In [8]: z
Out[8]: (-134+352j)

More advanced features

break out of enclosing for/while loop:
In [9]: z = 1 + 1j
In [10]: while abs(z) < 100:
....:
if z.imag == 0:
....:
break
....:
z = z**2 + 1
....:
....:

continue the next iteration of a loop.:

>>> a =
>>> for
...
...
...
...
1.0
0.5
0.25

[1, 0, 2, 4]
element in a:
if element == 0:
continue
print 1. / element

2.4.4 Conditional Expressions

if object
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Evaluates to False:
any number equal to zero (0, 0.0, 0+0j)
an empty container (list, tuple, set, dictionary, ...)
False, None
Evaluates to True:
everything else 1
a == b
Tests equality, with logics:
In [19]: 1 == 1.
Out[19]: True

a is b
Tests identity: both sides are the same object
In [20]: 1 is 1.
Out[20]: False
In [21]: a = 1
In [22]: b = 1
In [23]: a is b
Out[23]: True

a in b
For any collection b: b contains a
>>> b = [1, 2, 3]
>>> 2 in b
True
>>> 5 in b
False

If b is a dictionary, this tests that a is a key of b.

2.4.5 Advanced iteration

Iterate over any sequence
You can iterate over any sequence (string, list, keys in a dictionary, lines in a file, ...)
In [11]: vowels = aeiouy
In [12]: for i in powerful:
....:
if i in vowels:
....:
print(i),
....:
....:
o e u
>>> message = "Hello how are you?"
>>> message.split() # returns a list
[Hello, how, are, you?]
>>> for word in message.split():
1

User-defined classes can customize those rules by overriding the special __nonzero__ method.

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Python Scientific lecture notes, Release 2011

...
...
Hello
how
are
you?

print word

Few languages (in particular, languages for scientific computing) allow to loop over anything but integers/indices.
With Python it is possible to loop exactly over the objects of interest without bothering with indices you often
dont care about.
Warning: Not safe to modify the sequence you are iterating over.

Keeping track of enumeration number

Common task is to iterate over a sequence while keeping track of the item number.
Could use while loop with a counter as above. Or a for loop:
In [13]: for i in range(0, len(words)):
....:
print(i, words[i])
....:
....:
0 cool
1 powerful
2 readable

But Python provides enumerate for this:

>>> words = (cool, powerful, readable)
>>> for index, item in enumerate(words):
...
print index, item
...
0 cool
1 powerful
2 readable

Looping over a dictionary

Use iteritems:
In [15]: d = {a: 1, b:1.2, c:1j}
In [15]: for key, val in d.iteritems():
....:
print(Key: %s has value: %s % (key, val))
....:
....:
Key: a has value: 1
Key: c has value: 1j
Key: b has value: 1.2

2.4.6 List Comprehensions

In [16]: [i**2 for i in range(4)]
Out[16]: [0, 1, 4, 9]

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Python Scientific lecture notes, Release 2011

Exercise
Compute the decimals of Pi using the Wallis formula:
=2

Y
i=1

4i2
1

4i2

2.5 Defining functions

2.5.1 Function definition
In [56]: def test():
....:
print(in test function)
....:
....:
In [57]: test()
in test function

Warning: Function blocks must be indented as other control-flow blocks.

2.5.2 Return statement

Functions can optionally return values.
In [6]: def disk_area(radius):
...:
return 3.14 * radius * radius
...:
In [8]: disk_area(1.5)
Out[8]: 7.0649999999999995

Note: By default, functions return None.

Note: Note the syntax to define a function:
the def keyword;
is followed by the functions name, then
the arguments of the function are given between brackets followed by a colon.
the function body ;
and return object for optionally returning values.

2.5.3 Parameters
Mandatory parameters (positional arguments)
In [81]: def double_it(x):
....:
return x * 2
....:
In [82]: double_it(3)

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Python Scientific lecture notes, Release 2011

Out[82]: 6
In [83]: double_it()
--------------------------------------------------------------------------TypeError
Traceback (most recent call last)
/Users/cburns/src/scipy2009/scipy_2009_tutorial/source/<ipython console> in <module>()
TypeError: double_it() takes exactly 1 argument (0 given)

Optional parameters (keyword or named arguments)

In [84]: def double_it(x=2):
....:
return x * 2
....:
In [85]: double_it()
Out[85]: 4
In [86]: double_it(3)
Out[86]: 6

Keyword arguments allow you to specify default values.

Warning: Default values are evaluated when the function is defined, not when it is called.
In [124]: bigx = 10
In [125]: def double_it(x=bigx):
.....:
return x * 2
.....:
In [126]: bigx = 1e9

# Now really big

In [128]: double_it()
Out[128]: 20

More involved example implementing pythons slicing:

In [98]: def slicer(seq, start=None, stop=None, step=None):
....:
"""Implement basic python slicing."""
....:
return seq[start:stop:step]
....:
In [101]: rhyme = one fish, two fish, red fish, blue fish.split()
In [102]: rhyme
Out[102]: [one, fish,, two, fish,, red, fish,, blue, fish]
In [103]: slicer(rhyme)
Out[103]: [one, fish,, two, fish,, red, fish,, blue, fish]
In [104]: slicer(rhyme, step=2)
Out[104]: [one, two, red, blue]
In [105]: slicer(rhyme, 1, step=2)
Out[105]: [fish,, fish,, fish,, fish]
In [106]: slicer(rhyme, start=1, stop=4, step=2)
Out[106]: [fish,, fish,]

The order of the keyword arguments does not matter:

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In [107]: slicer(rhyme, step=2, start=1, stop=4)

Out[107]: [fish,, fish,]

but it is good practice to use the same ordering as the functions definition.
Keyword arguments are a very convenient feature for defining functions with a variable number of arguments,
especially when default values are to be used in most calls to the function.

2.5.4 Passed by value

Can you modify the value of a variable inside a function? Most languages (C, Java, ...) distinguish passing
by value and passing by reference. In Python, such a distinction is somewhat artificial, and it is a bit subtle
whether your variables are going to be modified or not. Fortunately, there exist clear rules.
Parameters to functions are references to objects, which are passed by value. When you pass a variable to a
function, python passes the reference to the object to which the variable refers (the value). Not the variable itself.
If the value is immutable, the function does not modify the callers variable. If the value is mutable, the function
may modify the callers variable in-place:
>>> def try_to_modify(x, y, z):
...
x = 23
...
y.append(42)
...
z = [99] # new reference
...
print(x)
...
print(y)
...
print(z)
...
>>> a = 77
# immutable variable
>>> b = [99] # mutable variable
>>> c = [28]
>>> try_to_modify(a, b, c)
23
[99, 42]
[99]
>>> print(a)
77
>>> print(b)
[99, 42]
>>> print(c)
[28]

Functions have a local variable table. Called a local namespace.

The variable x only exists within the function foo.

2.5.5 Global variables

Variables declared outside the function can be referenced within the function:
In [114]: x = 5
In [115]: def addx(y):
.....:
return x + y
.....:
In [116]: addx(10)
Out[116]: 15

But these global variables cannot be modified within the function, unless declared global in the function.
This doesnt work:

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In [117]: def setx(y):

.....:
x = y
.....:
print(x is %d % x)
.....:
.....:
In [118]: setx(10)
x is 10
In [120]: x
Out[120]: 5

This works:
In [121]: def setx(y):
.....:
global x
.....:
x = y
.....:
print(x is %d % x)
.....:
.....:
In [122]: setx(10)
x is 10
In [123]: x
Out[123]: 10

2.5.6 Variable number of parameters

Special forms of parameters:
*args: any number of positional arguments packed into a tuple
**kwargs: any number of keyword arguments packed into a dictionary
In [35]: def variable_args(*args, **kwargs):
....:
print args is, args
....:
print kwargs is, kwargs
....:
In [36]: variable_args(one, two, x=1, y=2, z=3)
args is (one, two)
kwargs is {y: 2, x: 1, z: 3}

2.5.7 Docstrings
Documentation about what the function does and its parameters. General convention:
In [67]: def funcname(params):
....:
"""Concise one-line sentence describing the function.
....:
....:
Extended summary which can contain multiple paragraphs.
....:
"""
....:
# function body
....:
pass
....:
In [68]: funcname ?
Type:
function
Base Class: <type function>
String Form:
<function funcname at 0xeaa0f0>

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Namespace: Interactive
File:
/Users/cburns/src/scipy2009/.../<ipython console>
Definition: funcname(params)
Docstring:
Concise one-line sentence describing the function.
Extended summary which can contain multiple paragraphs.

Note: Docstring guidelines

For the sake of standardization, the Docstring Conventions webpage documents the semantics and conventions
associated with Python docstrings.
Also, the Numpy and Scipy modules have defined a precised standard for documenting scientific
functions, that you may want to follow for your own functions, with a Parameters section, an
Examples section, etc. See http://projects.scipy.org/numpy/wiki/CodingStyleGuidelines#docstring-standard
and http://projects.scipy.org/numpy/browser/trunk/doc/example.py#L37

2.5.8 Functions are objects

Functions are first-class objects, which means they can be:
assigned to a variable
an item in a list (or any collection)
passed as an argument to another function.
In [38]: va = variable_args
In [39]: va(three, x=1, y=2)
args is (three,)
kwargs is {y: 2, x: 1}

2.5.9 Methods
Methods are functions attached to objects. Youve seen these in our examples on lists, dictionaries, strings, etc...

2.5.10 Exercises
Exercise: Quicksort
Implement the quicksort algorithm, as defined by wikipedia:
function quicksort(array)
var list less, greater
if length(array) < 2
return array
select and remove a pivot value pivot from array
for each x in array
if x < pivot + 1 then append x to less
else append x to greater
return concatenate(quicksort(less), pivot, quicksort(greater))

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Exercise: Fibonacci sequence

Write a function that displays the n first terms of the Fibonacci sequence, defined by:
u_0 = 1; u_1 = 1
u_(n+2) = u_(n+1) + u_n

2.6 Reusing code: scripts and modules

For now, we have typed all instructions in the interpreter. For longer sets of instructions we need to change tack
and write the code in text files (using a text editor), that we will call either scripts or modules. Use your favorite
text editor (provided it offers syntax highlighting for Python), or the editor that comes with the Scientific Python
Suite you may be using (e.g., Scite with Python(x,y)).

2.6.1 Scripts
Let us first write a script, that is a file with a sequence of instructions that are executed each time the script is
called.
Instructions may be e.g. copied-and-pasted from the interpreter (but take care to respect indentation rules!). The
extension for Python files is .py. Write or copy-and-paste the following lines in a file called test.py
message = "Hello how are you?"
for word in message.split():
print word

Let us now execute the script interactively, that is inside the Ipython interpreter. This is maybe the most common
use of scripts in scientific computing.
in Ipython, the syntax to execute a script is %run script.py. For example,
In [1]: %run test.py
Hello
how
are
you?
In [2]: message
Out[2]: Hello how are you?

The script has been executed. Moreover the variables defined in the script (such as message) are now available
inside the interpeters namespace.
Other interpreters also offer the possibility to execute scripts (e.g., execfile in the plain Python interpreter,
etc.).
It is also possible In order to execute this script as a standalone program, by executing the script inside a shell
terminal (Linux/Mac console or cmd Windows console). For example, if we are in the same directory as the test.py
file, we can execute this in a console:
epsilon:~/sandbox$ python test.py
Hello
how
are
you?

Standalone scripts may also take command-line arguments

In file.py:

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Python Scientific lecture notes, Release 2011

import sys
print sys.argv
$ python file.py test arguments
[file.py, test, arguments]

Note: Dont implement option parsing yourself. Use modules such as optparse.

2.6.2 Importing objects from modules

In [1]: import os
In [2]: os
Out[2]: <module os from / usr / lib / python2.6 / os.pyc >
In [3]: os.listdir(.)
Out[3]:
[conf.py,
basic_types.rst,
control_flow.rst,
functions.rst,
python_language.rst,
reusing.rst,
file_io.rst,
exceptions.rst,
workflow.rst,
index.rst]

And also:
In [4]: from os import listdir

Importing shorthands:
In [5]: import numpy as np

Warning:
from os import *

Do not do it.
Makes the code harder to read and understand: where do symbols come from?
Makes it impossible to guess the functionality by the context and the name (hint: os.name is the name
of the OS), and to profit usefully from tab completion.
Restricts the variable names you can use: os.name might override name, or vise-versa.
Creates possible name clashes between modules.
Makes the code impossible to statically check for undefined symbols.
Modules are thus a good way to organize code in a hierarchical way. Actually, all the scientific computing tools
we are going to use are modules:
>>> import numpy as np # data arrays
>>> np.linspace(0, 10, 6)
array([ 0.,
2.,
4.,
6.,
8., 10.])
>>> import scipy # scientific computing

In Python(x,y) software, Ipython(x,y) execute the following imports at startup:

>>> import numpy
>>> import numpy as np

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>>> from pylab import *

>>> import scipy

and it is not necessary to re-import these modules.

2.6.3 Creating modules

If we want to write larger and better organized programs (compared to simple scripts), where some objects are
defined, (variables, functions, classes) and that we want to reuse several times, we have to create our own modules.
Let us create a module demo contained in the file demo.py:
"A demo module."
def print_b():
"Prints b."
print b
def print_a():
"Prints a."
print a

c = 2
d = 2

In this file, we defined two functions print_a and print_b. Suppose we want to call the print_a function
from the interpreter. We could execute the file as a script, but since we just want to have access to the function
print_a, we are rather going to import it as a module. The syntax is as follows.
In [1]: import demo

In [2]: demo.print_a()
a
In [3]: demo.print_b()
b

Importing the module gives access to its objects, using the module.object syntax. Dont forget to put the
modules name before the objects name, otherwise Python wont recognize the instruction.
Introspection
In [4]: demo ?
Type:
module
Base Class: <type module>
String Form:
<module demo from demo.py>
Namespace: Interactive
File:
/home/varoquau/Projects/Python_talks/scipy_2009_tutorial/source/demo.py
Docstring:
A demo module.

In [5]: who
demo
In [6]: whos
Variable
Type
Data/Info
-----------------------------demo
module
<module demo from demo.py>
In [7]: dir(demo)

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Python Scientific lecture notes, Release 2011

Out[7]:
[__builtins__,
__doc__,
__file__,
__name__,
__package__,
c,
d,
print_a,
print_b]

In [8]: demo.
demo.__builtins__
demo.__class__
demo.__delattr__
demo.__dict__
demo.__doc__
demo.__file__
demo.__format__
demo.__getattribute__
demo.__hash__

demo.__init__
demo.__name__
demo.__new__
demo.__package__
demo.__reduce__
demo.__reduce_ex__
demo.__repr__
demo.__setattr__
demo.__sizeof__

demo.__str__
demo.__subclasshook__
demo.c
demo.d
demo.print_a
demo.print_b
demo.py
demo.pyc

Importing objects from modules into the main namespace

In [9]: from demo import print_a, print_b
In [10]: whos
Variable
Type
Data/Info
-------------------------------demo
module
<module demo from demo.py>
print_a
function
<function print_a at 0xb7421534>
print_b
function
<function print_b at 0xb74214c4>
In [11]: print_a()
a

Warning: Module caching

Modules are cached: if you modify demo.py and re-import it in the old session, you will get the
old one.
Solution:
In [10]: reload(demo)

2.6.4 __main__ and module loading

File demo2.py:
import sys
def print_a():
"Prints a."
print a
print sys.argv
if __name__ == __main__:
print_a()

Importing it:

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In [11]: import demo2

b
In [12]: import demo2

Running it:
In [13]: %run demo2
b
a

2.6.5 Scripts or modules? How to organize your code

Note: Rule of thumb
Sets of instructions that are called several times should be written inside functions for better code reusability.
Functions (or other bits of code) that are called from several scripts should be written inside a module,
so that only the module is imported in the different scripts (do not copy-and-paste your functions in the
different scripts!).
Note: How to import a module from a remote directory?
Many solutions exist, depending mainly on your operating system. When the import mymodule statement is
executed, the module mymodule is searched in a given list of directories. This list includes a list of installationdependent default path (e.g., /usr/lib/python) as well as the list of directories specified by the environment
variable PYTHONPATH.
The list of directories searched by Python is given by the sys.path variable
In [1]: import sys
In [2]: sys.path
Out[2]:
[,
/usr/bin,
/usr/local/include/enthought.traits-1.1.0,
/usr/lib/python2.6,
/usr/lib/python2.6/plat-linux2,
/usr/lib/python2.6/lib-tk,
/usr/lib/python2.6/lib-old,
/usr/lib/python2.6/lib-dynload,
/usr/lib/python2.6/dist-packages,
/usr/lib/pymodules/python2.6,
/usr/lib/pymodules/python2.6/gtk-2.0,
/usr/lib/python2.6/dist-packages/wx-2.8-gtk2-unicode,
/usr/local/lib/python2.6/dist-packages,
/usr/lib/python2.6/dist-packages,
/usr/lib/pymodules/python2.6/IPython/Extensions,
u/home/gouillar/.ipython]

Modules must be located in the search path, therefore you can:

write your own modules within directories already defined in the search path (e.g.
/usr/local/lib/python2.6/dist-packages). You may use symbolic links (on Linux) to keep the code
somewhere else.
modify the environment variable PYTHONPATH to include the directories containing the user-defined
modules. On Linux/Unix, add the following line to a file read by the shell at startup (e.g. /etc/profile,
.profile)
export PYTHONPATH=$PYTHONPATH:/home/emma/user_defined_modules

On Windows, http://support.microsoft.com/kb/310519 explains how to handle environment variables.

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or modify the sys.path variable itself within a Python script.

import sys
new_path = /home/emma/user_defined_modules
if new_path not in sys.path:
sys.path.append(new_path)

This method is not very robust, however, because it makes the code less portable (user-dependent path) and because
you have to add the directory to your sys.path each time you want to import from a module in this directory.
See http://docs.python.org/tutorial/modules.html for more information about modules.

2.6.6 Packages
A directory that contains many modules is called a package. A package is a module with submodules (which can
have submodules themselves, etc.). A special file called __init__.py (which may be empty) tells Python that
the directory is a Python package, from which modules can be imported.
sd-2116 /usr/lib/python2.6/dist-packages/scipy $ ls
[17:07]
cluster/
io/
README.txt@
stsci/
__config__.py@ LATEST.txt@ setup.py@
__svn_version__.py@
__config__.pyc lib/
setup.pyc
__svn_version__.pyc
constants/
linalg/
setupscons.py@ THANKS.txt@
fftpack/
linsolve/
setupscons.pyc TOCHANGE.txt@
__init__.py@
maxentropy/ signal/
version.py@
__init__.pyc
misc/
sparse/
version.pyc
INSTALL.txt@
ndimage/
spatial/
weave/
integrate/
odr/
special/
interpolate/
optimize/
stats/
sd-2116 /usr/lib/python2.6/dist-packages/scipy $ cd ndimage
[17:07]
sd-2116 /usr/lib/python2.6/dist-packages/scipy/ndimage $ ls
[17:07]
doccer.py@
fourier.pyc
interpolation.py@ morphology.pyc
doccer.pyc
info.py@
interpolation.pyc _nd_image.so
setupscons.py@
filters.py@ info.pyc
measurements.py@
_ni_support.py@
setupscons.pyc
filters.pyc __init__.py@ measurements.pyc
_ni_support.pyc
fourier.py@ __init__.pyc morphology.py@
setup.py@

setup.pyc

tests/

From Ipython:
In [1]: import scipy
In [2]: scipy.__file__
Out[2]: /usr/lib/python2.6/dist-packages/scipy/__init__.pyc
In [3]: import scipy.version
In [4]: scipy.version.version
Out[4]: 0.7.0
In [5]: import scipy.ndimage.morphology
In [6]: from scipy.ndimage import morphology
In [17]: morphology.binary_dilation ?
Type:
function
Base Class: <type function>
String Form:
<function binary_dilation at 0x9bedd84>

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Namespace: Interactive
File:
/usr/lib/python2.6/dist-packages/scipy/ndimage/morphology.py
Definition: morphology.binary_dilation(input, structure=None,
iterations=1, mask=None, output=None, border_value=0, origin=0,
brute_force=False)
Docstring:
Multi-dimensional binary dilation with the given structure.
An output array can optionally be provided. The origin parameter
controls the placement of the filter. If no structuring element is
provided an element is generated with a squared connectivity equal
to one. The dilation operation is repeated iterations times. If
iterations is less than 1, the dilation is repeated until the
result does not change anymore. If a mask is given, only those
elements with a true value at the corresponding mask element are
modified at each iteration.

2.6.7 Good practices

Note: Good practices
Indentation: no choice!
Indenting is compulsory in Python. Every commands block following a colon bears an additional indentation level
with respect to the previous line with a colon. One must therefore indent after def f(): or while:. At the
end of such logical blocks, one decreases the indentation depth (and re-increases it if a new block is entered, etc.)
Strict respect of indentation is the price to pay for getting rid of { or ; characters that delineate logical blocks in
other languages. Improper indentation leads to errors such as
-----------------------------------------------------------IndentationError: unexpected indent (test.py, line 2)

All this indentation business can be a bit confusing in the beginning. However, with the clear indentation, and in
the absence of extra characters, the resulting code is very nice to read compared to other languages.
Indentation depth:
Inside your text editor, you may choose to indent with any positive number of spaces (1, 2, 3, 4, ...). However,
it is considered good practice to indent with 4 spaces. You may configure your editor to map the Tab key to a
4-space indentation. In Python(x,y), the editor Scite is already configured this way.
Style guidelines
Long lines: you should not write very long lines that span over more than (e.g.) 80 characters. Long lines can be
broken with the \ character
>>> long_line = "Here is a very very long line \
... that we break in two parts."

Spaces
Write well-spaced code: put whitespaces after commas, around arithmetic operators, etc.:
>>> a = 1 # yes
>>> a=1 # too cramped

A certain number of rules for writing beautiful code (and more importantly using the same conventions as
anybody else!) are given in the Style Guide for Python Code.
Use meaningful object names

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2.7 Input and Output

To be exhaustive, here are some information about input and output in Python. Since we will use the Numpy
methods to read and write files, you may skip this chapter at first reading.
We write or read strings to/from files (other types must be converted to strings). To write in a file:
>>> f = open(workfile, w) # opens the workfile file
>>> type(f)
<type file>
>>> f.write(This is a test \nand another test)
>>> f.close()

To read from a file

In [1]: f = open(workfile, r)
In [2]: s = f.read()
In [3]: print(s)
This is a test
and another test
In [4]: f.close()

For more details: http://docs.python.org/tutorial/inputoutput.html

2.7.1 Iterating over a file

In [6]: f = open(workfile, r)
In [7]: for line in f:
...:
print line
...:
...:
This is a test
and another test
In [8]: f.close()

File modes
Read-only: r
Write-only: w
Note: Create a new file or overwrite existing file.
Append a file: a
Read and Write: r+
Binary mode: b
Note: Use for binary files, especially on Windows.

2.8 Standard Library

Note: Reference document for this section:

2.7. Input and Output

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The Python Standard Library documentation: http://docs.python.org/library/index.html

Python Essential Reference, David Beazley, Addison-Wesley Professional

2.8.1 os module: operating system functionality

A portable way of using operating system dependent functionality.
Directory and file manipulation
Current directory:
In [17]: os.getcwd()
Out[17]: /Users/cburns/src/scipy2009/scipy_2009_tutorial/source

List a directory:
In [31]: os.listdir(os.curdir)
Out[31]:
[.index.rst.swo,
.python_language.rst.swp,
.view_array.py.swp,
_static,
_templates,
basic_types.rst,
conf.py,
control_flow.rst,
debugging.rst,
...

Make a directory:
In [32]: os.mkdir(junkdir)
In [33]: junkdir in os.listdir(os.curdir)
Out[33]: True

Rename the directory:

In [36]: os.rename(junkdir, foodir)
In [37]: junkdir in os.listdir(os.curdir)
Out[37]: False
In [38]: foodir in os.listdir(os.curdir)
Out[38]: True
In [41]: os.rmdir(foodir)
In [42]: foodir in os.listdir(os.curdir)
Out[42]: False

Delete a file:
In [44]: fp = open(junk.txt, w)
In [45]: fp.close()
In [46]: junk.txt in os.listdir(os.curdir)
Out[46]: True
In [47]: os.remove(junk.txt)

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In [48]: junk.txt in os.listdir(os.curdir)

Out[48]: False

os.path: path manipulations

os.path provides common operations on pathnames.
In [70]: fp = open(junk.txt, w)
In [71]: fp.close()
In [72]: a = os.path.abspath(junk.txt)
In [73]: a
Out[73]: /Users/cburns/src/scipy2009/scipy_2009_tutorial/source/junk.txt
In [74]: os.path.split(a)
Out[74]: (/Users/cburns/src/scipy2009/scipy_2009_tutorial/source,
junk.txt)
In [78]: os.path.dirname(a)
Out[78]: /Users/cburns/src/scipy2009/scipy_2009_tutorial/source
In [79]: os.path.basename(a)
Out[79]: junk.txt
In [80]: os.path.splitext(os.path.basename(a))
Out[80]: (junk, .txt)
In [84]: os.path.exists(junk.txt)
Out[84]: True
In [86]: os.path.isfile(junk.txt)
Out[86]: True
In [87]: os.path.isdir(junk.txt)
Out[87]: False
In [88]: os.path.expanduser(~/local)
Out[88]: /Users/cburns/local
In [92]: os.path.join(os.path.expanduser(~), local, bin)
Out[92]: /Users/cburns/local/bin

Running an external command

In [8]: os.system(ls *)
conf.py
debug_file.py demo2.py~ demo.py
demo.pyc
conf.py~ demo2.py
demo2.pyc demo.py~ my_file.py

my_file.py~
pi_wallis_image.py

Walking a directory
os.path.walk generates a list of filenames in a directory tree.
In [10]: for dirpath, dirnames, filenames in os.walk(os.curdir):
....:
for fp in filenames:
....:
print os.path.abspath(fp)
....:
....:

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/Users/cburns/src/scipy2009/scipy_2009_tutorial/source/.index.rst.swo
/Users/cburns/src/scipy2009/scipy_2009_tutorial/source/.view_array.py.swp
/Users/cburns/src/scipy2009/scipy_2009_tutorial/source/basic_types.rst
/Users/cburns/src/scipy2009/scipy_2009_tutorial/source/conf.py
/Users/cburns/src/scipy2009/scipy_2009_tutorial/source/control_flow.rst
...

Environment variables:
In [9]: import os
In [11]: os.environ.keys()
Out[11]:
[_,
FSLDIR,
TERM_PROGRAM_VERSION,
FSLREMOTECALL,
USER,
HOME,
PATH,
PS1,
SHELL,
EDITOR,
WORKON_HOME,
PYTHONPATH,
...
In [12]: os.environ[PYTHONPATH]
Out[12]: .:/Users/cburns/src/utils:/Users/cburns/src/nitools:
/Users/cburns/local/lib/python2.5/site-packages/:
/usr/local/lib/python2.5/site-packages/:
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5
In [16]: os.getenv(PYTHONPATH)
Out[16]: .:/Users/cburns/src/utils:/Users/cburns/src/nitools:
/Users/cburns/local/lib/python2.5/site-packages/:
/usr/local/lib/python2.5/site-packages/:
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5

2.8.2 shutil: high-level file operations

The shutil provides useful file operations:
shutil.rmtree: Recursively delete a directory tree.
shutil.move: Recursively move a file or directory to another location.
shutil.copy: Copy files or directories.

2.8.3 glob: Pattern matching on files

The glob module provides convenient file pattern matching.
Find all files ending in .txt:
In [18]: import glob
In [19]: glob.glob(*.txt)
Out[19]: [holy_grail.txt, junk.txt, newfile.txt]

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2.8.4 sys module: system-specific information

System-specific information related to the Python interpreter.
Which version of python are you running and where is it installed:
In [117]: sys.platform
Out[117]: darwin
In [118]: sys.version
Out[118]: 2.5.2 (r252:60911, Feb 22 2008, 07:57:53) \n
[GCC 4.0.1 (Apple Computer, Inc. build 5363)]
In [119]: sys.prefix
Out[119]: /Library/Frameworks/Python.framework/Versions/2.5

List of command line arguments passed to a Python script:

In [100]: sys.argv
Out[100]: [/Users/cburns/local/bin/ipython]

sys.path is a list of strings that specifies the search path for modules. Initialized from PYTHONPATH:
In [121]: sys.path
Out[121]:
[,
/Users/cburns/local/bin,
/Users/cburns/local/lib/python2.5/site-packages/grin-1.1-py2.5.egg,
/Users/cburns/local/lib/python2.5/site-packages/argparse-0.8.0-py2.5.egg,
/Users/cburns/local/lib/python2.5/site-packages/urwid-0.9.7.1-py2.5.egg,
/Users/cburns/local/lib/python2.5/site-packages/yolk-0.4.1-py2.5.egg,
/Users/cburns/local/lib/python2.5/site-packages/virtualenv-1.2-py2.5.egg,
...

2.8.5 pickle: easy persistence

Useful to store arbitrary objects to a file. Not safe or fast!
In [1]: import pickle
In [2]: l = [1, None, Stan]
In [3]: pickle.dump(l, file(test.pkl, w))
In [4]: pickle.load(file(test.pkl))
Out[4]: [1, None, Stan]

Exercise
Write a program to search your PYTHONPATH for the module site.py.
path_site

2.9 Exceptions handling in Python

It is highly unlikely that you havent yet raised Exceptions if you have typed all the previous commands of the
tutorial. For example, you may have raised an exception if you entered a command with a typo.
Exceptions are raised by different kinds of errors arising when executing Python code. In you own code, you may
also catch errors, or define custom error types.
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2.9.1 Exceptions
Exceptions are raised by errors in Python:
In [1]: 1/0
--------------------------------------------------------------------------ZeroDivisionError: integer division or modulo by zero
In [2]: 1 + e
--------------------------------------------------------------------------TypeError: unsupported operand type(s) for +: int and str
In [3]: d = {1:1, 2:2}
In [4]: d[3]
--------------------------------------------------------------------------KeyError: 3
In [5]: l = [1, 2, 3]
In [6]: l[4]
--------------------------------------------------------------------------IndexError: list index out of range
In [7]: l.foobar
--------------------------------------------------------------------------AttributeError: list object has no attribute foobar

Different types of exceptions for different errors.

2.9.2 Catching exceptions

try/except
In [8]: while True:
....:
try:
....:
x = int(raw_input(Please enter a number: ))
....:
break
....:
except ValueError:
....:
print(That was no valid number. Try again...)
....:
....:
Please enter a number: a
That was no valid number. Try again...
Please enter a number: 1
In [9]: x
Out[9]: 1

try/finally
In [10]: try:
....:
x = int(raw_input(Please enter a number: ))
....: finally:
....:
print(Thank you for your input)
....:
....:
Please enter a number: a
Thank you for your input

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--------------------------------------------------------------------------ValueError: invalid literal for int() with base 10: a

Important for resource management (e.g. closing a file)

Easier to ask for forgiveness than for permission
In [11]: def print_sorted(collection):
....:
try:
....:
collection.sort()
....:
except AttributeError:
....:
pass
....:
print(collection)
....:
....:
In [12]: print_sorted([1, 3, 2])
[1, 2, 3]
In [13]: print_sorted(set((1, 3, 2)))
set([1, 2, 3])
In [14]: print_sorted(132)
132

2.9.3 Raising exceptions

Capturing and reraising an exception:
In [15]: def filter_name(name):
....:
try:
....:
name = name.encode(ascii)
....:
except UnicodeError, e:
....:
if name == Gal:
....:
print(OK, Gal)
....:
else:
....:
raise e
....:
return name
....:
In [16]: filter_name(Gal)
OK, Gal
Out[16]: Ga\xc3\xabl

In [17]: filter_name(Stfan)
--------------------------------------------------------------------------UnicodeDecodeError: ascii codec cant decode byte 0xc3 in position 2: ordinal not in rang

Exceptions to pass messages between parts of the code:

In [17]: def achilles_arrow(x):
....:
if abs(x - 1) < 1e-3:
....:
raise StopIteration
....:
x = 1 - (1-x)/2.
....:
return x
....:
In [18]: x = 0
In [19]: while True:
....:
try:

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....:
....:
....:
....:
....:

x = achilles_arrow(x)
except StopIteration:
break

In [20]: x
Out[20]: 0.9990234375

Use exceptions to notify certain conditions are met (e.g. StopIteration) or not (e.g. custom error raising)

2.10 Object-oriented programming (OOP)

Python supports object-oriented programming (OOP). The goals of OOP are:
to organize the code, and
to re-use code in similar contexts.
Here is a small example: we create a Student class, which is an object gathering several custom functions
(methods) and variables (attributes), we will be able to use:
>>>
...
...
...
...
...
...
...
>>>
>>>
>>>

class Student(object):
def __init__(self, name):
self.name = name
def set_age(self, age):
self.age = age
def set_major(self, major):
self.major = major
anna = Student(anna)
anna.set_age(21)
anna.set_major(physics)

In the previous example, the Student class has __init__, set_age and set_major methods. Its attributes are name, age and major. We can call these methods and attributes with the following notation:
classinstance.method or classinstance.attribute. The __init__ constructor is a special
method we call with: MyClass(init parameters if any).
Now, suppose we want to create a new class MasterStudent with the same methods and attributes as the previous
one, but with an additional internship attribute. We wont copy the previous class, but inherit from it:
>>> class MasterStudent(Student):
...
internship = mandatory, from March to June
...
>>> james = MasterStudent(james)
>>> james.internship
mandatory, from March to June
>>> james.set_age(23)
>>> james.age
23

The MasterStudent class inherited from the Student attributes and methods.
Thanks to classes and object-oriented programming, we can organize code with different classes corresponding to
different objects we encounter (an Experiment class, an Image class, a Flow class, etc.), with their own methods
and attributes. Then we can use inheritance to consider variations around a base class and re-use code. Ex : from
a Flow base class, we can create derived StokesFlow, TurbulentFlow, PotentialFlow, etc.

2.10. Object-oriented programming (OOP)

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CHAPTER 3

NumPy: creating and manipulating

numerical data

authors Emmanuelle Gouillart, Didrik Pinte, Gal Varoquaux, and Pauli Virtanen

3.1 Intro
3.1.1 What is Numpy
Python has:
built-in: lists, integers, floating point
for numerics more is needed (efficiency, convenience)
Numpy is:
extension package to Python for multidimensional arrays
closer to hardware (efficiency)
designed for scientific computation (convenience)
For example:
An array containing
discretized time of an experiment/simulation
signal recorded by a measurement device
pixels of an image
...

3.2 1. Basics I
3.2.1 Getting started
>>> import numpy as np
>>> a = np.array([0, 1, 2, 3])
>>> a
array([0, 1, 2, 3])

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3.2.2 Reference documentation

On the web: http://docs.scipy.org/
Interactive help:
>>> help(np.array)
array(object, dtype=None, copy=True, order=None, subok=False, ndmin=0)
Create an array.
Parameters
---------object : array_like
...
Examples
------->>> np.array([1, 2, 3])
array([1, 2, 3])
...

Looking for something:

>>> np.lookfor(create array)
Search results for create array
--------------------------------numpy.array
Create an array.
numpy.memmap
Create a memory-map to an array stored in a *binary* file on disk.
...
>>> help(np.lookfor)
...

3.2.3 Creating arrays

1-D
>>> a = np.array([0, 1, 2, 3])
>>> a
array([0, 1, 2, 3])
>>> a.ndim
1
>>> a.shape
(4,)
>>> len(a)
4

2-D, 3-D, ...

>>> b = np.array([[0, 1, 2], [3, 4, 5]])
# 2 x 3 array
>>> b
array([[ 0, 1, 2],
[ 3, 4, 5]])
>>> b.ndim
2
>>> b.shape
(2, 3)
>>> len(b)
# returns the size of the first dimension
2

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>>> c = np.array([[[1], [2]], [[3], [4]]])

>>> c
array([[[1],
[2]],
[[3],
[4]]])
>>> c.shape
(2, 2, 1)

In practice, we rarely enter items one by one...

Evenly spaced:
>>> import numpy as np
>>> a = np.arange(10) # 0 .. n-1 (!)
>>> a
array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
>>> b = np.arange(1, 9, 2) # start, end (exlusive), step
>>> b
array([1, 3, 5, 7])

or by number of points:
>>> c =
>>> c
array([
>>> d =
>>> d
array([

np.linspace(0, 1, 6)

# start, end, num-points

0. , 0.2, 0.4, 0.6, 0.8, 1. ])

np.linspace(0, 1, 5, endpoint=False)
0. ,

0.2,

0.4,

0.6,

0.8])

Common arrays:
>>> a = np.ones((3, 3)) # reminder: (3, 3) is a tuple
>>> a
array([[ 1., 1., 1.],
[ 1., 1., 1.],
[ 1., 1., 1.]])
>>> b = np.zeros((2, 2))
>>> b
array([[ 0., 0.],
[ 0., 0.]])
>>> c = np.eye(3)
>>> c
array([[ 1., 0., 0.],
[ 0., 1., 0.],
[ 0., 0., 1.]])
>>> d = np.diag(np.array([1, 2, 3, 4, 5]))
>>> d
array([[1, 0, 0, 0, 0],
[0, 2, 0, 0, 0],
[0, 0, 3, 0, 0],
[0, 0, 0, 4, 0],
[0, 0, 0, 0, 5]])

Random numbers (Mersenne Twister PRNG):

>>> a = np.random.rand(4)
>>> a
array([ 0.58597729, 0.86110455,

# uniform in [0, 1]
0.9401114 ,

0.54264348])

>>> b = np.random.randn(4)
# gaussian
>>> b
array([-2.56844807, 0.06798064, -0.36823781, 0.86966886])

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>>> c = np.random.rand(3, 3)
>>> c
array([[ 0.31976645, 0.64807526,
[ 0.8280203 , 0.8669403 ,
[ 0.11527489, 0.11494884,

0.74770801],
0.07663683],
0.13503285]])

>>> d = np.random.zipf(1.5, size=(2, 8)) # Zipf distribution (s=1.5)

>>> d
array([[5290,
1,
6,
9,
1,
1,
1,
2],
[
1,
5,
1,
13,
1,
1,
2,
1]])
>>> np.random.seed(1234)
>>> np.random.rand(3)
array([ 0.19151945, 0.62210877,
>>> np.random.seed(1234)
>>> np.random.rand(5)
array([ 0.19151945, 0.62210877,

# Setting the random seed

0.43772774])

0.43772774,

0.78535858,

0.77997581])

3.2.4 Basic data types

You probably noted the 1 and 1. above. These are different data types:
>>> a = np.array([1, 2, 3])
>>> a.dtype
dtype(int64)
>>> b = np.array([1., 2., 3.])
>>> b.dtype
dtype(float64)

Much of the time you dont necessarily need to care, but remember they are there.

You can also choose which one you want:

>>> c = np.array([1, 2, 3], dtype=float)
>>> c.dtype
dtype(float64)

The default data type is floating point:

>>> a = np.ones((3, 3))
>>> a.dtype
dtype(float64)
>>> b = np.linspace(0, 1, 6)
>>> b.dtype
dtype(float64)

There are also other types:

>>> d = np.array([1+2j, 3+4j, 5+6*1j])
>>> d.dtype
dtype(complex128)
>>> e = np.array([True, False, False, True])
>>> e.dtype
dtype(bool)
>>> f = np.array([Bonjour, Hello, Hallo, Terve, Hej])
>>> f.dtype
dtype(S7)
# <--- strings containing max. 7 letters

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3.2.5 Basic visualization

Now that we have our first data arrays, we are going to visualize them.
Matplotlib is a 2D plotting package. We can import its functions as below:
>>> import matplotlib.pyplot as plt
>>> # ... or ...
>>> from matplotlib.pyplot import *

# the tidy way

# imports everything in the namespace

If you launched Ipython with python(x,y), or with ipython -pylab (under Linux), both of the above commands have been run. In the remainder of this tutorial, we assume you have run
>>> import matplotlib.pyplot as plt

or are using ipython -pylab which does it automatically.

1D plotting
>>>
>>>
>>>
>>>
>>>

x = np.linspace(0, 3, 20)
y = np.linspace(0, 9, 20)
plt.plot(x, y)
# line plot
plt.plot(x, y, o) # dot plot
plt.show()
# <-- shows the plot (not needed with Ipython)

9
8
7
6
5
4
3
2
1
00.0

0.5

1.0

1.5

2.0

2.5

3.0

2D arrays (such as images)

>>>
>>>
>>>
>>>

image = np.random.rand(30, 30)

plt.imshow(image)
plt.gray()
plt.show()

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0
5
10
15
20
25
0
>>>
>>>
>>>
>>>

10

15

20

25

plt.pcolor(image)
plt.hot()
plt.colorbar()
plt.show()

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30
0.9
25

0.8
0.7

20

0.6
0.5

15

0.4
10

0.3
0.2

0.1
00

10

15

20

25

30

0.0

See Also:
More on matplotlib in the tutorial by Mike Mller tomorrow!
3D plotting
For 3D visualization, we can use another package: Mayavi. A quick example: start with relaunching iPython
with these options: ipython -pylab -wthread (or ipython pylab=wx in IPython >= 0.10).
In [59]: from enthought.mayavi import mlab
In [60]: mlab.figure()
get fences failed: -1
param: 6, val: 0
Out[60]: <enthought.mayavi.core.scene.Scene object at 0xcb2677c>
In [61]: mlab.surf(image)
Out[61]: <enthought.mayavi.modules.surface.Surface object at 0xd0862fc>
In [62]: mlab.axes()
Out[62]: <enthought.mayavi.modules.axes.Axes object at 0xd07892c>

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The mayavi/mlab window that opens is interactive : by clicking on the left mouse button you can rotate the image,
zoom with the mouse wheel, etc.
For more information on Mayavi : http://code.enthought.com/projects/mayavi/docs/development/html/mayavi/index.html

3.2.6 Indexing and slicing

The items of an array can be accessed and assigned to the same way as other Python sequences (list, tuple)
>>> a = np.arange(10)
>>> a
array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
>>> a[0], a[2], a[-1]
(0, 2, 9)

Warning: Indices begin at 0, like other Python sequences (and C/C++). In contrast, in Fortran or Matlab,
indices begin at 1.
For multidimensional arrays, indexes are tuples of integers:
>>> a = np.diag(np.arange(5))
>>> a
array([[0, 0, 0, 0, 0],
[0, 1, 0, 0, 0],
[0, 0, 2, 0, 0],
[0, 0, 0, 3, 0],
[0, 0, 0, 0, 4]])
>>> a[1,1]
1
>>> a[2,1] = 10 # third line, second column
>>> a
array([[ 0, 0, 0, 0, 0],
[ 0, 1, 0, 0, 0],
[ 0, 10, 2, 0, 0],
[ 0, 0, 0, 3, 0],
[ 0, 0, 0, 0, 4]])
>>> a[1]
array([0, 1, 0, 0, 0])

Note that:
In 2D, the first dimension corresponds to rows, the second to columns.
for multidimensional a,a[0] is interpreted by taking all elements in the unspecified dimensions.

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Slicing
Arrays, like other Python sequences can also be sliced:
>>> a = np.arange(10)
>>> a
array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
>>> a[2:9:3] # [start:end:step]
array([2, 5, 8])

Note that the last index is not included!:

>>> a[:4]
array([0, 1, 2, 3])

start:end:step is a slice object which represents the set of indexes range(start, end, step). A
slice can be explicitly created:
>>> sl = slice(1, 9, 2)
>>> a = np.arange(10)
>>> b = np.arange(1, 20, 2)
>>> a, b
(array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9]), array([ 1,
>>> a[sl], b[sl]
(array([1, 3, 5, 7]), array([ 3, 7, 11, 15]))

3,

5,

7,

9, 11, 13, 15, 17, 19]))

All three slice components are not required: by default, start is 0, end is the last and step is 1:
>>> a[1:3]
array([1, 2])
>>> a[::2]
array([0, 2, 4, 6, 8])
>>> a[3:]
array([3, 4, 5, 6, 7, 8, 9])

Of course, it works with multidimensional arrays:

>>> a = np.eye(5)
>>> a
array([[ 1., 0., 0., 0., 0.],
[ 0., 1., 0., 0., 0.],
[ 0., 0., 1., 0., 0.],
[ 0., 0., 0., 1., 0.],
[ 0., 0., 0., 0., 1.]])
>>> a[2:4,:3] # 3rd and 4th rows, 3 first columns
array([[ 0., 0., 1.],
[ 0., 0., 0.]])

All elements specified by a slice can be easily modified:

>>> a[:3,:3] = 4
>>> a
array([[ 4., 4.,
[ 4., 4.,
[ 4., 4.,
[ 0., 0.,
[ 0., 0.,

4.,
4.,
4.,
0.,
0.,

0.,
0.,
0.,
1.,
0.,

0.],
0.],
0.],
0.],
1.]])

A small illustrated summary of Numpy indexing and slicing...

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3.2.7 Copies and views

A slicing operation creates a view on the original array, which is just a way of accessing array data. Thus the
original array is not copied in memory.
When modifying the view, the original array is modified as well:
>>> a = np.arange(10)
>>> a
array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
>>> b = a[::2]; b
array([0, 2, 4, 6, 8])
>>> b[0] = 12
>>> b
array([12, 2, 4, 6, 8])
>>> a
# (!)
array([12, 1, 2, 3, 4, 5, 6, 7,

8,

9])

>>> a = np.arange(10)
>>> b = a[::2].copy() # force a copy
>>> b[0] = 12
>>> a
array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])

This behavior can be surprising at first sight... but it allows to save both memory and time.

3.2.8 Data files

Text files
Example: populations.txt:
1900
1901
1902
...

30e3
47.2e3
70.2e3

3.2. 1. Basics I

4e3
6.1e3
9.8e3

51300
48200
41500

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>>> data = np.loadtxt(populations.txt)

# if in current directory
>>> data
array([[ 1900., 30000.,
4000., 51300.],
[ 1901., 47200.,
6100., 48200.],
[ 1902., 70200.,
9800., 41500.],
...
>>> np.savetxt(pop2.txt, data)
>>> data2 = np.loadtxt(pop2.txt)

Note: If you have a complicated text file, what you can try are:
np.genfromtxt
Using Pythons I/O functions and e.g. regexps for parsing (Python is quite well suited for this)
Navigating the filesystem in Python shells
Ipython
In [1]: pwd
# show current directory
/home/user/stuff/2011-numpy-tutorial
In [2]: cd ex
/home/user/stuff/2011-numpy-tutorial/ex
In [3]: ls
populations.txt species.txt

Python (heres yet one reason to use Ipython for interactive use :)
>>> import os
>>> os.getcwd()
/home/user/stuff/2011-numpy-tutorial
>>> os.chdir(ex)
>>> os.getcwd()
/home/user/stuff/2011-numpy-tutorial/ex
>>> os.listdir(.)
[populations.txt,
species.txt,
...

Images
>>> img = plt.imread(../../data/elephant.png)
>>> img.shape, img.dtype
((200, 300, 3), dtype(float32))
>>> plt.imshow(img)
>>> plt.savefig(plot.png)
>>> plt.show()

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50

100

150

50

100

150

200

250

>>> plt.imsave(red_elephant, img[:,:,0], cmap=plt.cm.gray)

This saved only one channel (of RGB)

>>> plt.imshow(plt.imread(red_elephant.png))
>>> plt.show()

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50

100

150

50

100

150

200

250

Other libraries:
>>>
>>>
>>>
>>>

from scipy.misc import imsave

imsave(tiny_elephant.png, img[::6,::6])
plt.imshow(plt.imread(tiny_elephant.png), interpolation=nearest)
plt.show()

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0
5
10
15
20
25
30
0

10

20

30

40

Numpys own format

>>> np.save(pop.npy, data)
>>> data3 = np.load(pop.npy)

Well-known (& more obscure) file formats

HDF5: h5py, PyTables
NetCDF: scipy.io.netcdf_file, netcdf4-python, ...
Matlab: scipy.io.loadmat, scipy.io.savemat
MatrixMarket: scipy.io.mmread, scipy.io.mmread
... if somebody uses it, theres probably also a Python library for it.

3.2.9 Summary & Exercises

Creating arrays: array, linspace, arange, zeros, ones, rand
Data types: integers, floats, complex floats, and strings
Simple plotting with Matplotlib: plot(x, y)
Indexing, slicing, and assignment into arrays slicing creates views
Reading data from files: loadtxt, savetxt, et al.

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Worked example: Prime number sieve

Compute prime numbers in 099, with a sieve

Construct a shape (100,) boolean array is_prime, filled with True in the beginning:
>>> is_prime = np.ones((100,), dtype=bool)

Cross out 0 and 1 which are not primes

>>> is_prime[:2] = 0

For each integer j starting from 2, cross out its higher multiples
>>> N_max = int(np.sqrt(len(is_prime)))
>>> for j in range(2, N_max):
...
is_prime[2*j::j] = False

Skim through help(np.nonzero), and print the prime numbers

Follow-up:
Move the above code into a script file named prime_sieve.py
Run it to check it works
Convert the simple sieve to the sieve of Eratosthenes:
1. Skip j which are already known to not be primes
2. The first number to cross out is j 2

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Reminder Python scripts:

A very basic script file contains:
import numpy as np
import matplotlib.pyplot as plt

# <- if you use it

# any numpy-using commands follow

a = np.array([1, 2, 3, 4])
print a

Run on command line:

python my_script_1_2.py

Or, in Python shell:

In [10]: %run my_script_1_2.py
>>> execfile(2_2_data_statistics.py)

Exercise 1.1: Certain arrays

Create the following arrays (with correct data types):
[[
[
[
[

1
1
1
1

1
1
1
6

1
1
1
1

[[0.
[2.
[0.
[0.
[0.
[0.

0.
0.
3.
0.
0.
0.

0.
0.
0.
4.
0.
0.

1]
1]
2]
1]]
0.
0.
0.
0.
5.
0.

0.]
0.]
0.]
0.]
0.]
6.]]

Par on course: 3 statements for each (53 & 54 characters)

Exercise 1.2: Text data files

Write a Python script that loads data from populations.txt and drop the last column and the first 5 rows.
Save the smaller dataset to pop2.txt.

Exercise 1.3: Tiling

Skim through the documentation for np.tile, and use this function to construct the array:
[[4
[2
[4
[2

3
1
3
1

4
2
4
2

3
1
3
1

4
2
4
2

3]
1]
3]
1]]

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3.3 2. Basics II
3.3.1 Elementwise operations
With scalars:
>>> a = np.array([1, 2, 3, 4])
>>> a + 1
array([2, 3, 4, 5])
>>> 2**a
array([ 2, 4, 8, 16])

All arithmetic operates elementwise:

>>> b = np.ones(4) + 1
>>> a - b
array([-1., 0., 1., 2.])
>>> a * b
array([ 2., 4., 6., 8.])
>>> j = np.arange(5)
>>> 2**(j + 1) - j
array([ 2, 3, 6, 13, 28])

Warning: ... including multiplication

>>> c = np.ones((3, 3))
>>> c * c
array([[ 1., 1., 1.],
[ 1., 1., 1.],
[ 1., 1., 1.]])

# NOT matrix multiplication!

Note: Matrix multiplication:

>>> c.dot(c)
array([[ 3.,
[ 3.,
[ 3.,

3.,
3.,
3.,

3.],
3.],
3.]])

Comparisons:
>>> a = np.array([1, 2, 3, 4])
>>> b = np.array([4, 2, 2, 4])
>>> a == b
array([False, True, False, True], dtype=bool)
>>> a > b
array([False, False, True, False], dtype=bool)

Logical operations:
>>> a =
>>> b =
>>> a |
array([
>>> a &
array([

np.array([1, 1, 0, 0], dtype=bool)

np.array([1, 0, 1, 0], dtype=bool)
b
True, True, True, False], dtype=bool)
b
True, False, False, False], dtype=bool)

Note: For arrays: & and | for logical operations, not and and or.
Shape mismatches:

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>>> a
array([1, 2, 3, 4])
>>> a + np.array([1, 2])
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ValueError: shape mismatch: objects cannot be broadcast to a single shape

Broadcast? Well return to that later.

3.3.2 Basic linear algebra

Matrix multiplication:
>>> a = np.triu(np.ones((3, 3)), 1)
>>> a
array([[ 0., 1., 1.],
[ 0., 0., 1.],
[ 0., 0., 0.]])
>>> b = np.diag([1, 2, 3])
>>> a.dot(b)
array([[ 0., 2., 3.],
[ 0., 0., 3.],
[ 0., 0., 0.]])
>>> np.dot(a, a)
array([[0, 0, 1],
[0, 0, 0],
[0, 0, 0]])

# see help(np.triu)

Transpose:
>>> a.T
array([[ 0.,
[ 1.,
[ 1.,

0.,
0.,
1.,

0.],
0.],
0.]])

Inverses and linear equation systems:

>>> A = a + b
>>> A
array([[ 1., 1., 1.],
[ 0., 2., 1.],
[ 0., 0., 3.]])
>>> B = np.linalg.inv(A)
>>> B.dot(A)
array([[ 1., 0., 0.],
[ 0., 1., 0.],
[ 0., 0., 1.]])
>>> x = np.linalg.solve(A, [1, 2, 3])
>>> x
array([-0.5, 0.5, 1. ])
>>> A.dot(x)
array([ 1., 2., 3.])

Eigenvalues:
>>> np.linalg.eigvals(A)
array([ 1., 2., 3.])

... and so on, see help(np.linalg)

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3.3.3 Basic reductions

Computing sums:
>>> x = np.array([1, 2, 3, 4])
>>> np.sum(x)
10
>>> x.sum()
10

Sum by rows and by columns:

>>> x = np.array([[1, 1], [2, 2]])

>>> x
array([[1, 1],
[2, 2]])
>>> x.sum(axis=0)
# columns (first dimension)
array([3, 3])
>>> x[:,0].sum(), x[:,1].sum()
(3, 3)
>>> x.sum(axis=1)
# rows (second dimension)
array([2, 4])
>>> x[0,:].sum(), x[1,:].sum()
(2, 4)

Same idea in higher dimensions:

>>> x = np.random.rand(2, 2, 2)
>>> x.sum(axis=2)[0,1]
1.1600112273698793
>>> x[0,1,:].sum()
1.1600112273698793

Other reductions works the same way (and take axis=)

Statistics:
>>> x = np.array([1, 2, 3, 1])
>>> y = np.array([[1, 2, 3], [5, 6, 1]])
>>> x.mean()
1.75
>>> np.median(x)
1.5
>>> np.median(y, axis=-1) # last axis
array([ 2., 5.])

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>>> x.std()
0.82915619758884995
>>> x.std(ddof=1)
0.9574271077563381

# full population standard dev.

# sample std (with N-1 in divisor)

Extrema:
>>> x = np.array([1, 3, 2])
>>> x.min()
1
>>> x.max()
3
>>> x.argmin()
0
>>> x.argmax()
1

# index of minimum
# index of maximum

Logical operations:
>>> np.all([True, True, False])
False
>>> np.any([True, True, False])
True

Note: Can be used for array comparisons:

>>> a = np.zeros((100, 100))
>>> np.any(a != 0)
False
>>> np.all(a == a)
True
>>> a =
>>> b =
>>> c =
>>> ((a
True

np.array([1, 2, 3, 2])
np.array([2, 2, 3, 2])
np.array([6, 4, 4, 5])
<= b) & (b <= c)).all()

... and many more (best to learn as you go).

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Example: data statistics

Data in populations.txt describes the populations of hares and lynxes (and carrots) in northern Canada
during 20 years.
We can first plot the data:
>>> data = np.loadtxt(../../data/populations.txt)
>>> year, hares, lynxes, carrots = data.T # trick: columns to variables
>>>
>>>
>>>
>>>

plt.axes([0.2, 0.1, 0.5, 0.8])

plt.plot(year, hares, year, lynxes, year, carrots)
plt.legend((Hare, Lynx, Carrot), loc=(1.05, 0.5))
plt.show()

80000
70000
60000

Hare
Lynx
Carrot

50000
40000
30000
20000
10000
0
1900

1905

1910

1915

1920

42400.

])

The mean populations over time:

>>> populations = data[:,1:]
>>> populations.mean(axis=0)
array([ 34080.95238095, 20166.66666667,

The sample standard deviations:

>>> populations.std(axis=0, ddof=1)
array([ 21413.98185877, 16655.99991995,

3404.55577132])

Which species has the highest population each year?

>>> np.argmax(populations, axis=1)
array([2, 2, 0, 0, 1, 1, 2, 2, 2, 2, 2, 2, 0, 0, 0, 1, 2, 2, 2, 2, 2])

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Example: diffusion simulation using a random walk algorithm

What is the typical distance from the origin of a random walker after t left or right jumps?

>>> n_stories = 1000 # number of walkers

>>> t_max = 200
# time during which we follow the walker

We randomly choose all the steps 1 or -1 of the walk

>>> t = np.arange(t_max)
>>> steps = 2 * np.random.random_integers(0, 1, (n_stories, t_max)) - 1
>>> np.unique(steps) # Verification: all steps are 1 or -1
array([-1, 1])

We build the walks by summing steps along the time

>>> positions = np.cumsum(steps, axis=1) # axis = 1: dimension of time
>>> sq_distance = positions**2

We get the mean in the axis of the stories

>>> mean_sq_distance = np.mean(sq_distance, axis=0)

Plot the results:

plt.figure(figsize=(4, 3))
plt.plot(t, np.sqrt(mean_sq_distance), g., t, np.sqrt(t), y-)
plt.xlabel(r"$t$")
plt.ylabel(r"$\sqrt{\langle (\delta x)^2 \rangle}$")
plt.show()

16
14
12
10
8
6
4
2
00

(x)2

>>>
>>>
>>>
>>>
>>>

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The RMS distance grows as the square root of the time!

3.3.4 Broadcasting
Basic operations on numpy arrays (addition, etc.) are elementwise
This works on arrays of the same size.
Nevertheless, Its also possible to do operations on arrays of different
sizes if Numpy can transform these arrays so that they all have
the same size: this conversion is called broadcasting.
The image below gives an example of broadcasting:

Lets verify:
>>> a = np.tile(np.arange(0, 40, 10), (3, 1)).T
>>> a
array([[ 0, 0, 0],
[10, 10, 10],
[20, 20, 20],
[30, 30, 30]])
>>> b = np.array([0, 1, 2])
>>> a + b
array([[ 0, 1, 2],
[10, 11, 12],
[20, 21, 22],
[30, 31, 32]])

An useful trick:
>>> a = np.arange(0, 40, 10)
>>> a.shape

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(4,)
>>> a = a[:,np.newaxis]
>>> a.shape
(4, 1)
>>> a
array([[ 0],
[10],
[20],
[30]])
>>> a + b
array([[ 0, 1, 2],
[10, 11, 12],
[20, 21, 22],
[30, 31, 32]])

# adds a new axis -> 2D array

We have already used broadcasting without knowing it!:

>>> a = np.ones((4,5))
>>> a[0] = 2 # we assign an array of dimension 0 to an array of dimension 1
array([[ 2., 2., 2., 2., 2.],
[ 1., 1., 1., 1., 1.],
[ 1., 1., 1., 1., 1.],
[ 1., 1., 1., 1., 1.]])

Broadcasting seems a bit magical, but it is actually quite natural to use it when we want to solve a problem whose
output data is an array with more dimensions than input data.
Example
Lets construct an array of distances (in miles) between cities of Route 66: Chicago, Springfield, Saint-Louis,
Tulsa, Oklahoma City, Amarillo, Santa Fe, Albuquerque, Flagstaff and Los Angeles.
>>> mileposts = np.array([0, 198, 303, 736, 871, 1175, 1475, 1544,
...
1913, 2448])
>>> distance_array = np.abs(mileposts - mileposts[:,np.newaxis])
>>> distance_array
array([[
0, 198, 303, 736, 871, 1175, 1475, 1544, 1913, 2448],
[ 198,
0, 105, 538, 673, 977, 1277, 1346, 1715, 2250],
[ 303, 105,
0, 433, 568, 872, 1172, 1241, 1610, 2145],
[ 736, 538, 433,
0, 135, 439, 739, 808, 1177, 1712],
[ 871, 673, 568, 135,
0, 304, 604, 673, 1042, 1577],
[1175, 977, 872, 439, 304,
0, 300, 369, 738, 1273],
[1475, 1277, 1172, 739, 604, 300,
0,
69, 438, 973],
[1544, 1346, 1241, 808, 673, 369,
69,
0, 369, 904],
[1913, 1715, 1610, 1177, 1042, 738, 438, 369,
0, 535],
[2448, 2250, 2145, 1712, 1577, 1273, 973, 904, 535,
0]])

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Good practices
Explicit variable names (no need of a comment to explain what is in the variable)
Style: spaces after commas, around =, etc.
A certain number of rules for writing beautiful code (and, more importantly, using the same conventions as everybody else!) are given in the Style Guide for Python Code and the Docstring Conventions
page (to manage help strings).
Except some rare cases, variable names and comments in English.
A lot of grid-based or network-based problems can also use broadcasting. For instance, if we want to compute the
distance from the origin of points on a 10x10 grid, we can do:
>>> x, y = np.arange(5), np.arange(5)
>>> distance = np.sqrt(x**2 + y[:, np.newaxis]**2)
>>> distance
array([[ 0.
, 1.
, 2.
, 3.
,
[ 1.
, 1.41421356, 2.23606798, 3.16227766,
[ 2.
, 2.23606798, 2.82842712, 3.60555128,
[ 3.
, 3.16227766, 3.60555128, 4.24264069,
[ 4.
, 4.12310563, 4.47213595, 5.
,

4.
],
4.12310563],
4.47213595],
5.
],
5.65685425]])

Or in color:
>>>
>>>
>>>
>>>

plt.pcolor(distance)
plt.colorbar()
plt.axis(equal)
plt.show()

# <-- again, not needed in interactive Python

5.4

4.8

4.2
3.6

3.0

2.4
1.8

1.2
0
1 1

0.6
0

0.0

Remark : the numpy.ogrid function allows to directly create vectors x and y of the previous example, with
two significant dimensions:

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>>> x, y = np.ogrid[0:5, 0:5]

>>> x, y
(array([[0],
[1],
[2],
[3],
[4]]), array([[0, 1, 2, 3, 4]]))
>>> x.shape, y.shape
((5, 1), (1, 5))
>>> distance = np.sqrt(x**2 + y**2)

So, np.ogrid is very useful as soon as we have to handle computations on a grid. On the other hand, np.mgrid
directly provides matrices full of indices for cases where we cant (or dont want to) benefit from broadcasting:
>>> x, y =
>>> x
array([[0,
[1,
[2,
[3,
>>> y
array([[0,
[0,
[0,
[0,

np.mgrid[0:4, 0:4]
0,
1,
2,
3,

0,
1,
2,
3,

0],
1],
2],
3]])

1,
1,
1,
1,

2,
2,
2,
2,

3],
3],
3],
3]])

However, in practice, this is rarely needed!

3.3.5 Array shape manipulation

Flattening
>>> a = np.array([[1, 2, 3], [4, 5, 6]])
>>> a.ravel()
array([1, 2, 3, 4, 5, 6])
>>> a.T
array([[1, 4],
[2, 5],
[3, 6]])
>>> a.T.ravel()
array([1, 4, 2, 5, 3, 6])

Higher dimensions: last dimensions ravel out first.

Reshaping
The inverse operation to flattening:
>>> a.shape
(2, 3)
>>> b = a.ravel()
>>> b.reshape((2, 3))
array([[1, 2, 3],
[4, 5, 6]])

Creating an array with a different shape, from another array:

>>> a = np.arange(36)
>>> b = a.reshape((6, 6))
>>> b

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array([[ 0,
[ 6,
[12,
[18,
[24,
[30,

1,
7,
13,
19,
25,
31,

2,
8,
14,
20,
26,
32,

3,
9,
15,
21,
27,
33,

4,
10,
16,
22,
28,
34,

5],
11],
17],
23],
29],
35]])

Or,
>>> b = a.reshape((6, -1))

# unspecified (-1) value is inferred

Copies or views
ndarray.reshape may return a view (cf help(np.reshape))), not a copy:
>>> b[0,0] = 99
>>> a
array([99, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
34, 35])

Beware!
>>> a = np.zeros((3,2))
>>> b = a.T.reshape(3*2)
>>> b[0] = 9
>>> a
array([[ 0., 0.],
[ 0., 0.],
[ 0., 0.]])

To understand, see Under the hood below.

Dimension shuffling
>>>
>>>
(4,
>>>
5
>>>
>>>
(3,
>>>
5

a = np.arange(4*3*2).reshape(4, 3, 2)
a.shape
3, 2)
a[0,2,1]
b = a.transpose(1, 2, 0)
b.shape
2, 4)
b[2,1,0]

Also creates a view:

>>> b[2,1,0] = -1
>>> a[0,2,1]
-1

Resizing
Size of an array can be changed with ndarray.resize:
>>> a = np.arange(4)
>>> a.resize((8,))

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>>> a
array([0, 1, 2, 3, 0, 0, 0, 0])

However, it must not be referred to somewhere else:

>>> b = a
>>> a.resize((4,))
...
ValueError: cannot resize an array references or is referenced
by another array in this way. Use the resize function

Some examples of real-world use cases

Case 2.a: Calling (legacy) Fortran code

Shape-preserving functions with elementwise non-Python routines. For instance, Fortran
! 2_a_fortran_module.f90
subroutine some_function(n, a, b)
integer :: n
double precision, dimension(n), intent(in) :: a
double precision, dimension(n), intent(out) :: b
b = a + 1
end subroutine some_function

f2py -c -m fortran_module 2_a_fortran_module.f90

import numpy as np
import fortran_module
def some_function(input):
"""
Call a Fortran routine, and preserve input shape
"""
input = np.asarray(input)
# fortran_module.some_function() takes 1-D arrays!
output = fortran_module.some_function(input.ravel())
return output.reshape(input.shape)
print some_function(np.array([1, 2, 3]))
print some_function(np.array([[1, 2], [3, 4]]))
# ->
# [ 2. 3. 4.]
# [[ 2. 3.]
# [ 4. 5.]]

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Case 2.b: Block matrices and vectors (and tensors)

Vector space: quantum level spin
 

= 1 ,
2

1 =

1
1

2 =



2
2

In short: for block matrices and vectors, it can be useful to preserve the block structure.
In Numpy:
>>> psi = np.zeros((2, 2))
# dimensions: level, spin
>>> psi[0,1] # <-- psi_{1,downarrow}

Linear operators on such block vectors have similar block structure:





11 V
h
1,
0

,
h11 =
,
H =
0
1,
V
h22

...

>>> H = np.zeros((2, 2, 2, 2)) # dimensions: level1, level2, spin1, spin2

>>> h_11 = H[0,0,:,:]
>>> V = H[0,1]

Doing the matrix product: get rid of the block structure, do the 4x4 matrix product, then put it back

H

>>> def mdot(operator, psi):

...
return operator.transpose(0, 2, 1, 3).reshape(4, 4).dot(
...
psi.reshape(4)).reshape(2, 2)

I.e., reorder dimensions first to level1, spin1, level2, spin2 and then reshape => correct matrix
product.

3.3.6 Fancy indexing

Numpy arrays can be indexed with slices, but also with boolean or integer arrays (masks). This method is called
fancy indexing.

Masks
>>> np.random.seed(3)
>>> a = np.random.random_integers(0, 20, 15)
>>> a
array([10, 3, 8, 0, 19, 10, 11, 9, 10, 6, 0, 20, 12, 7, 14])
>>> (a % 3 == 0)
array([False, True, False, True, False, False, False, True, False,
True, True, False, True, False, False], dtype=bool)
>>> mask = (a % 3 == 0)
>>> extract_from_a = a[mask] # or, a[a%3==0]
>>> extract_from_a
# extract a sub-array with the mask
array([ 3, 0, 9, 6, 0, 12])

Extracting a sub-array using a mask produces a copy of this sub-array, not a view like slicing:
>>> extract_from_a[0] = -1
>>> a
array([10, 3, 8, 0, 19, 10, 11,

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9, 10,

6,

0, 20, 12,

7, 14])

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Indexing with a mask can be very useful to assign a new value to a sub-array:
>>> a[a % 3 == 0] = -1
>>> a
array([10, -1, 8, -1, 19, 10, 11, -1, 10, -1, -1, 20, -1,

7, 14])

Indexing with an array of integers

>>> a = np.arange(10)
>>> a[::2] += 3 # to avoid having always the same np.arange(10)...
>>> a
array([ 3, 1, 5, 3, 7, 5, 9, 7, 11, 9])
>>> a[[2, 5, 1, 8]] # or, a[np.array([2, 5, 1, 8])]
array([ 5, 5, 1, 11])

Indexing can be done with an array of integers, where the same index is repeated several time:
>>> a[[2, 3, 2, 4, 2]]
array([5, 3, 5, 7, 5])

# note: [2, 3, 2, 4, 2] is a Python list

New values can be assigned with this kind of indexing:

>>> a[[9, 7]] = -10
>>> a
array([ 3,
1,
5,
3,
>>> a[[2, 3, 2, 4, 2]] += 1
>>> a
array([ 3,
1,
6,
4,

7,

5,

9, -10,

11, -10])

8,

5,

9, -10,

11, -10])

When a new array is created by indexing with an array of integers, the new array has the same shape than the array
of integers:
>>> a = np.arange(10)
>>> idx = np.array([[3, 4], [9, 7]])
>>> a[idx]
array([[3, 4],
[9, 7]])
>>> b = np.arange(10)
>>> a = np.arange(12).reshape(3, 4)
>>> a
array([[ 0, 1, 2, 3],
[ 4, 5, 6, 7],
[ 8, 9, 10, 11]])
>>> i = np.array([0, 1, 1, 2])
>>> j = np.array([2, 1, 3, 3])
>>> a[i, j]
array([ 2, 5, 7, 11])
>>> i = np.array([[0, 1], [1, 2]])
>>> j = np.array([[2, 1], [3, 3]])
>>> i
array([[0, 1],
[1, 2]])
>>> j
array([[2, 1],
[3, 3]])
>>> a[i, j]
array([[ 2, 5],
[ 7, 11]])

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We can even use fancy indexing and broadcasting at the same time:
>>> a = np.arange(12).reshape(3,4)
>>> a
array([[ 0, 1, 2, 3],
[ 4, 5, 6, 7],
[ 8, 9, 10, 11]])
>>> i = np.array([[0, 1], [1, 2]])
>>> a[i, 2] # same as a[i, 2*np.ones((2,2), dtype=int)]
array([[ 2, 6],
[ 6, 10]])

3.3.7 Sorting data

Sorting along an axis:
>>> a = np.array([[4, 3, 5], [1, 2, 1]])
>>> b = np.sort(a, axis=1)
>>> b
array([[3, 4, 5],
[1, 1, 2]])

Note: Sorts each row separately!

In-place sort:
>>> a.sort(axis=1)
>>> a
array([[3, 4, 5],
[1, 1, 2]])

Sorting with fancy indexing:

>>> a = np.array([4, 3, 1, 2])
>>> j = np.argsort(a)
array([2, 3, 1, 0])
>>> a[j]
array([1, 2, 3, 4])

Finding minima and maxima:

>>>
>>>
>>>
>>>
(0,

a = np.array([4, 3, 1, 2])
j_max = np.argmax(a)
j_min = np.argmin(a)
j_max, j_min
2)

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3.3.8 Summary & Exercises

Arithmetic etc. are elementwise operations
Basic linear algebra, .dot()
Reductions: sum(axis=1), std(), all(), any()
Broadcasting: a = np.arange(4); a[:,np.newaxis] + a[np.newaxis,:]
Shape manipulation: a.ravel(), a.reshape(2, 2)
Fancy indexing: a[a > 3], a[[2, 3]]
Sorting data: .sort(), np.sort, np.argsort, np.argmax

Worked example: Framing Lena

Lets do some manipulations on numpy arrays by starting with the famous image of Lena
(http://www.cs.cmu.edu/~chuck/lennapg/). scipy provides a 2D array of this image with the scipy.lena
function:
>>> import scipy
>>> lena = scipy.lena()

Here are a few images we will be able to obtain with our manipulations: use different colormaps, crop the image,
change some parts of the image.

Lets use the imshow function of pylab to display the image.

In [3]: import pylab as plt
In [4]: lena = scipy.lena()
In [5]: plt.imshow(lena)

Lena is then displayed in false colors. A colormap must be specified for her to be displayed in grey.
In [6]: plt.imshow(lena, plt.cm.gray)
In [7]: # or,
In [7]: plt.gray()

Create an array of the image with a narrower centering : for example, remove 30 pixels from all the borders
of the image. To check the result, display this new array with imshow.
In [9]: crop_lena = lena[30:-30,30:-30]

We will now frame Lenas face with a black locket. For this, we need to
create a mask corresponding to the pixels we want to be black. The mask is defined by this
condition (y-256)**2 + (x-256)**2

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In [15]:
In [16]:
Out[16]:
In [17]:
In [18]:

y, x = np.ogrid[0:512,0:512] # x and y indices of pixels

y.shape, x.shape
((512, 1), (1, 512))
centerx, centery = (256, 256) # center of the image
mask = ((y - centery)**2 + (x - centerx)**2) > 230**2 # circle

then
assign the value 0 to the pixels of the image corresponding to the mask. The syntax is
extremely simple and intuitive:
In [19]: lena[mask] = 0
In [20]: plt.imshow(lena)
Out[20]: <matplotlib.image.AxesImage object at 0xa36534c>

Follow-up: copy all instructions of this exercise in a script called lena_locket.py then execute this
script in IPython with %run lena_locket.py.
Change the circle to an ellipsoid.

Exercise 2.1: Matrix manipulations

1. Form the 2-D array (without typing it in explicitly):
1 6
2 7
3 8
4 9
5 10

11
12
13
14
15

and generate a new array containing its 2nd and 4th rows.
2. Divide each column of the array
>>> a = np.arange(25).reshape(5, 5)

elementwise with the array b = np.array([1., 5, 10, 15, 20]). (Hint: np.newaxis).
3. Harder one: Generate a 10 x 3 array of random numbers (in range [0,1]). For each row, pick the number
closest to 0.5.
Use abs and argsort to find the column j closest for each row.
Use fancy indexing to extract the numbers. (Hint: a[i,j] the array i must contain the row numbers
corresponding to stuff in j.)

Exercise 2.2: Data statistics

The data in populations.txt describes the populations of hares and lynxes (and carrots) in northern Canada
during 20 years:
>>> data = np.loadtxt(../../data/populations.txt)
>>> year, hares, lynxes, carrots = data.T # trick: columns to variables
>>>
>>>
>>>
>>>

plt.axes([0.2, 0.1, 0.5, 0.8])

plt.plot(year, hares, year, lynxes, year, carrots)
plt.legend((Hare, Lynx, Carrot), loc=(1.05, 0.5))
plt.show()

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80000
70000
60000

Hare
Lynx
Carrot

50000
40000
30000
20000
10000
0
1900

1905

1910

1915

1920

Computes and print, based on the data in populations.txt...

1. The mean and std of the populations of each species for the years in the period.
2. Which year each species had the largest population.
3. Which species has the largest population for each year.
np.array([H, L, C]))

(Hint: argsort & fancy indexing of

4. Which years any of the populations is above 50000. (Hint: comparisons and np.any)
5. The top 2 years for each species when they had the lowest populations. (Hint: argsort, fancy indexing)
6. Compare (plot) the change in hare population (see help(np.gradient)) and the number of lynxes.
Check correlation (see help(np.corrcoef)).
... all without for-loops.

Exercise 2.3: Crude integral approximations

Write a function f(a, b, c) that returns ab c. Form a 24x12x6 array containing its values in parameter
ranges [0,1] x [0,1] x [0,1].
Approximate the 3-d integral
Z
0

Z
0

(ab c)da db dc

over this volume with the mean. The exact result is: ln 2
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1
2

0.1931 . . . what is your relative error?

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(Hints: use elementwise operations and broadcasting. You can make np.ogrid give a number of points in given
range with np.ogrid[0:1:20j].)
Reminder Python functions
def f(a, b, c):
return some_result

Exercise 2.4: Mandelbrot set

1.5
1.0
0.5
0.0
0.5
1.0
1.52.0

1.5

1.0

0.5

0.0

0.5

1.0

Write a script that computes the Mandelbrot fractal. The Mandelbrot iteration:
N_max = 50
some_threshold = 50
c = x + 1j*y
for j in xrange(N_max):
z = z**2 + c

Point (x, y) belongs to the Mandelbrot set if |c| < some_threshold.

Do this computation by:
1. Construct a grid of c = x + 1j*y values in range [-2, 1] x [-1.5, 1.5]
2. Do the iteration

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3. Form the 2-d boolean mask indicating which points are in the set
4. Save the result to an image with:
>>>
>>>
>>>
>>>

import matplotlib.pyplot as plt

plt.imshow(mask.T, extent=[-2, 1, -1.5, 1.5])
plt.gray()
plt.savefig(mandelbrot.png)

Exercise 2.5: Markov chain

Markov chain transition matrix P, and probability distribution on the states p:

1. 0 <= P[i,j] <= 1: probability to go from state i to state j
2. Transition rule: pnew = P T pold
3. all(sum(P, axis=1) == 1), p.sum() == 1: normalization
Write a script that works with 5 states, and:
Constructs a random matrix, and normalizes each row so that it is a transition matrix.
Starts from a random (normalized) probability distribution p and takes 50 steps => p_50
Computes the stationary distribution: the eigenvector of P.T with eigenvalue 1 (numerically: closest to 1)
=> p_stationary
Remember to normalize the eigenvector I didnt...
Checks if p_50 and p_stationary are equal to tolerance 1e-5
Toolbox: np.random.rand, .dot(), np.linalg.eig, reductions, abs(), argmin, comparisons, all,
np.linalg.norm, etc.

3.3.9 Conclusions
What do you need to know to get started?
Know how to create arrays : array, arange, ones, zeros.
Know the shape of the array with array.shape, then use slicing to obtain different views of the array:
array[::2], etc. Adjust the shape of the array using reshape or flatten it with ravel.
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Obtain a subset of the elements of an array and/or modify their values with masks:
>>> a[a < 0] = 0

Know miscellaneous operations on arrays, such as finding the mean or max (array.max(),
array.mean()). No need to retain everything, but have the reflex to search in the documentation (online
docs, help(), lookfor())!!
For advanced use: master the indexing with arrays of integers, as well as broadcasting. Know more Numpy
functions to handle various array operations.

3.4 3. Moving on
3.4.1 More data types
Casting
Bigger type wins in mixed-type operations:
>>> np.array([1, 2, 3]) + 1.5
array([ 2.5, 3.5, 4.5])

Assignment never changes the type!

>>> a = np.array([1, 2, 3])
>>> a.dtype
dtype(int64)
>>> a[0] = 1.9
# <-- float is truncated to integer
>>> a
array([1, 2, 3])

Forced casts:
>>> a = np.array([1.7, 1.2, 1.6])
>>> b = a.astype(int) # <-- truncates to integer
>>> b
array([1, 1, 1])

Rounding:
>>> a = np.array([1.7, 1.2, 1.6])
>>> b = np.around(a)
>>> b
# still floating-point
array([ 2., 1., 2.])
>>> c = np.around(a).astype(int)
>>> c
array([2, 1, 2])

Different data type sizes

Integers (signed):
int8
int16
int32
int64

8 bits
16 bits
32 bits (same as int on 32-bit platform)
64 bits (same as int on 64-bit platform)

>>> np.array([1], dtype=int).dtype

dtype(int64)
>>> np.iinfo(np.int32).max, 2**31 - 1

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(2147483647, 2147483647)
>>> np.iinfo(np.int64).max, 2**63 - 1
(9223372036854775807, 9223372036854775807L)

Unsigned integers:
8 bits
16 bits
32 bits
64 bits

uint8
uint16
uint32
uint64

>>> np.iinfo(np.uint32).max, 2**32 - 1

(2147483647, 2147483647)
>>> np.iinfo(np.uint64).max, 2**64 - 1
(9223372036854775807, 9223372036854775807L)

Floating-point numbers:
float16
float32
float64
float96
float128

16 bits
32 bits
64 bits (same as float)
96 bits, platform-dependent (same as np.longdouble)
128 bits, platform-dependent (same as np.longdouble)

>>> np.finfo(np.float32).eps
1.1920929e-07
>>> np.finfo(np.float64).eps
2.2204460492503131e-16
>>> np.float32(1e-8) + np.float32(1) == 1
True
>>> np.float64(1e-8) + np.float64(1) == 1
False

Complex floating-point numbers:

complex64
complex128
complex192
complex256

two 32-bit floats

two 64-bit floats
two 96-bit floats, platform-dependent
two 128-bit floats, platform-dependent

Smaller data types

If you dont know you need special data types, then you probably dont.
Comparison on using float32 instead of float64:
Half the size in memory and on disk
Half the memory bandwidth required (may be a bit faster in some operations)
In [1]: a = np.zeros((1e6,), dtype=np.float64)
In [2]: b = np.zeros((1e6,), dtype=np.float32)
In [3]: %timeit a*a
1000 loops, best of 3: 1.78 ms per loop
In [4]: %timeit b*b
1000 loops, best of 3: 1.07 ms per loop

But: bigger rounding errors sometimes in surprising places (i.e., dont use them unless you really
need them)

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3.4.2 Structured data types

Composite data types
sensor_code (4-character string)
position (float)
value (float)
>>> samples = np.zeros((6,), dtype=[(sensor_code, S4),
...
(position, float), (value, float)])
>>> samples.ndim
1
>>> samples.shape
(6,)
>>> samples.dtype.names
(sensor_code, position, value)
>>> samples[:] = [(ALFA, 1, 0.35), (BETA, 1, 0.11), (TAU, 1, 0.39),
...
(ALFA, 1.5, 0.35), (ALFA, 2.1, 0.11), (TAU, 1.2, 0.39)]
>>> samples
array([(ALFA, 1.0, 0.35), (BETA, 1.0, 0.11), (TAU, 1.0, 0.39),
(ALFA, 1.5, 0.35), (ALFA, 2.1, 0.11), (TAU, 1.2, 0.39)],
dtype=[(sensor_code, |S4), (position, <f8), (value, <f8)])

Field access works by indexing with field names:

>>> samples[sensor_code]
array([ALFA, BETA, TAU, ALFA, ALFA, TAU],
dtype=|S4)
>>> samples[value]
array([ 0.35, 0.11, 0.39, 0.35, 0.11, 0.39])
>>> samples[0]
(ALFA, 1.0, 0.35)
>>> samples[0][sensor_code] = TAU
>>> samples[0]
(TAU, 1.0, 0.35)

Multiple fields at once:

>>> samples[[position, value]]
array([(1.0, 0.35), (1.0, 0.11), (1.0, 0.39), (1.5, 0.35), (2.1, 0.11),
(1.2, 0.39)],
dtype=[(position, <f8), (value, <f8)])

Fancy indexing works, as usually:

>>> samples[samples[sensor_code] == ALFA]
array([(ALFA, 1.0, 0.35), (ALFA, 1.5, 0.35), (ALFA, 2.1, 0.11)],
dtype=[(sensor_code, |S4), (position, <f8), (value, <f8)])

Note: There are a bunch of other syntaxes for constructing structured arrays, see here and here.

3.4.3 Fourier transforms

Numpy contains 1-D, 2-D, and N-D fast discrete Fourier transform routines, which compute:
Ak =

3.4. 3. Moving on

n1
X



mk
am exp 2i
n
m=0

k = 0, . . . , n 1.

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Full details of what for you can use such standard routines is beyond this tutorial. Neverheless, there they are, if
you need them:
>>> a = np.exp(2j*np.pi*np.arange(10))
>>> fa = np.fft.fft(a)
>>> np.set_printoptions(suppress=True) # print small number as 0
>>> fa
array([ 10.-0.j,
0.+0.j,
0.+0.j,
0.+0.j,
0.+0.j,
0.+0.j,
-0.+0.j, -0.+0.j, -0.+0.j, -0.+0.j])
>>> a = np.exp(2j*np.pi*np.arange(3))
>>> b = a[:,np.newaxis] + a[np.newaxis,:]
>>> np.fft.fftn(b)
array([[ 18.-0.j,
0.+0.j, -0.+0.j],
[ 0.+0.j,
0.+0.j,
0.+0.j],
[ -0.+0.j,
0.+0.j,
0.+0.j]])

See help(np.fft) and help(np.fft.fft) for more. These functions in general take the axes argument,
and you can additionally specify padding etc.

Worked example: Crude periodicity finding

"""
Discover the periods in ../../../data/populations.txt
"""
import numpy as np
import matplotlib.pyplot as plt
data = np.loadtxt(../../../data/populations.txt)
years = data[:,0]
populations = data[:,1:]
ft_populations = np.fft.fft(populations, axis=0)
frequencies = np.fft.fftfreq(populations.shape[0], years[1] - years[0])
plt.figure()
plt.plot(years, populations)
plt.figure()
plt.plot(1/frequencies, abs(ft_populations), o)
plt.xlim(0, 20)
plt.show()

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80000
70000
60000
50000
40000
30000
20000
10000
0
1900

1905

1910

1915

1920

10

15

20

300000
250000
200000
150000
100000
50000
00

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# Theres probably a period of around 10 years (obvious from the

# plot), but for this crude a method, theres not enough data to say
# much more.

Worked example: Gaussian image blur

Convolution:
Z
f1 (t) =

dt0 K(t t0 )f0 (t0 )

f1 () = K()
f0 ()

"""
Simple image blur by convolution with a Gaussian kernel
"""
import numpy as np
from numpy import newaxis
import matplotlib.pyplot as plt
# read image
img = plt.imread(../../../data/elephant.png)
# prepare an 1-D Gaussian convolution kernel
t = np.linspace(-10, 10, 30)
bump = np.exp(-0.1*t**2)
bump /= np.trapz(bump) # normalize the integral to 1
# make a 2-D kernel out of it
kernel = bump[:,newaxis] * bump[newaxis,:]
# padded fourier transform, with the same shape as the image
kernel_ft = np.fft.fft2(kernel, s=img.shape[:2], axes=(0, 1))
# convolve
img_ft = np.fft.fft2(img, axes=(0, 1))
img2_ft = kernel_ft[:,:,newaxis] * img_ft
img2 = np.fft.ifft2(img2_ft, axes=(0, 1)).real
# clip values to range
img2 = np.clip(img2, 0, 1)
# plot output
plt.imshow(img2)
plt.show()

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50

100

150

#
#
#
#
#
#

50

100

150

200

250

Further exercise (only if you are familiar with this stuff):

A "wrapped border" appears in the upper left and top edges of the
image. This is because the padding is not done correctly, and does
not take the kernel size into account (so the convolution "flows out
of bounds of the image"). Try to remove this artifact.

3.4.4 Masked arrays

Masked arrays are arrays that may have missing or invalid entries.
For example, suppose we have an array where the fourth entry is invalid:
>>> x = np.array([1, 2, 3, -99, 5])

One way to describe this is to create a masked array:

>>> mx = ma.masked_array(x, mask=[0, 0, 0, 1, 0])
>>> mx
masked_array(data = [1 2 3 -- 5],
mask = [False False False True False],
fill_value = 999999)

Masked mean ignores masked data:

>>> mx.mean()
2.75
>>> np.mean(mx)
2.75

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Warning: Not all Numpy functions respect masks, for instance np.dot, so check the return types.
The masked_array returns a view to the original array:
>>> mx[1] = 9
>>> x
array([ 1,
9,

3, -99,

5])

The mask
You can modify the mask by assigning:
>>> mx[1] = np.ma.masked
>>> mx
masked_array(data = [1 -- 3 -- 5],
mask = [False True False
fill_value = 999999)

True False],

The mask is cleared on assignment:

>>> mx[1] = 9
>>> mx
masked_array(data = [1 9 3 -- 5],
mask = [False False False
fill_value = 999999)

True False],

The mask is also available directly:

>>> mx.mask
array([False, False, False,

True, False], dtype=bool)

The masked entries can be filled with a given value to get an usual array back:
>>> x2 = mx.filled(-1)
>>> x2
array([ 1, 9, 3, -1,

5])

The mask can also be cleared:

>>> mx.mask = np.ma.nomask
>>> mx
masked_array(data = [1 9 3 -99 5],
mask = [False False False False False],
fill_value = 999999)

Domain-aware functions
The masked array package also contains domain-aware functions:
>>> np.ma.log(np.array([1, 2, -1, -2, 3, -5]))
masked_array(data = [0.0 0.69314718056 -- -- 1.09861228867 --],
mask = [False False True True False True],
fill_value = 1e+20)

Note: Streamlined and more seamless support for dealing with missing data in arrays is making its way into
Numpy 1.7. Stay tuned!

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Example: Masked statistics

Canadian rangers were distracted when counting hares and lynxes in 1903-1910 and 1917-1918, and got
the numbers are wrong. (Carrot farmers stayed alert, though.) Compute the mean populations over time,
ignoring the invalid numbers.
>>> data = np.loadtxt(../../data/populations.txt)
>>> populations = np.ma.masked_array(data[:,1:])
>>> year = data[:,0]
>>> bad_years = (((year >= 1903) & (year <= 1910))
...
| ((year >= 1917) & (year <= 1918)))
>>> populations[bad_years,0] = np.ma.masked
>>> populations[bad_years,1] = np.ma.masked
>>> populations.mean(axis=0)
masked_array(data = [40472.7272727 18627.2727273 42400.0],
mask = [False False False],
fill_value = 1e+20)
>>> populations.std(axis=0)
masked_array(data = [21087.656489 15625.7998142 3322.50622558],
mask = [False False False],
fill_value = 1e+20)

Note that Matplotlib knows about masked arrays:

>>> plt.plot(year, populations, o-)
>>> plt.show()

80000
70000
60000
50000
40000
30000
20000
10000
0
1900

3.4. 3. Moving on

1905

1910

1915

1920

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3.4.5 Polynomials
Numpy also contains polynomials in different bases:
For example, 3x2 + 2x 1
>>> p = np.poly1d([3, 2, -1])
>>> p(0)
-1
>>> p.roots
array([-1.
, 0.33333333])
>>> p.order
2
>>> x = np.linspace(0, 1, 20)
>>> y = np.cos(x) + 0.3*np.random.rand(20)
>>> p = np.poly1d(np.polyfit(x, y, 3))
>>> t = np.linspace(0, 1, 200)
>>> plt.plot(x, y, o, t, p(t), -)
>>> plt.show()

1.3
1.2
1.1
1.0
0.9
0.8
0.7
0.60.0

0.2

0.4

0.6

0.8

1.0

See http://docs.scipy.org/doc/numpy/reference/routines.polynomials.poly1d.html for more.

More polynomials (with more bases)

Numpy also has a more sophisticated polynomial interface, which supports e.g. the Chebyshev basis.
3x2 + 2x 1

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>>> p = np.polynomial.Polynomial([-1, 2, 3]) # coefs in different order!

>>> p(0)
-1.0
>>> p.roots()
array([-1.
, 0.33333333])
>>> p.order
2

Example using polynomials in Chebyshev basis, for polynomials in range [-1, 1]:
>>> x = np.linspace(-1, 1, 2000)
>>> y = np.cos(x) + 0.3*np.random.rand(2000)
>>> p = np.polynomial.Chebyshev.fit(x, y, 90)
>>>
>>>
>>>
>>>

t = np.linspace(-1, 1, 200)
plt.plot(x, y, r.)
plt.plot(t, p(t), k-, lw=3)
plt.show()

1.3
1.2
1.1
1.0
0.9
0.8
0.7
0.6
0.51.0

0.5

0.0

0.5

1.0

The Chebyshev polynomials have some advantages in interpolation.

3.4.6 Summary & Exercises

There is a number of data types with different precisions. In some special cases you may need to care about
this.
Structured arrays contain data of a composite type. Lumping pieces of data together this way has various
possible uses.
Fourier transform routines are under np.fft
Masked arrays can be used for missing data
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Polynomials are available in various bases

3.5 4. Under the hood

3.5.1 Its...
ndarray =
block of memory + indexing scheme + data type descriptor
raw data
how to locate an element
how to interpret an element

3.5.2 Block of memory

>>> x = np.array([1, 2, 3, 4], dtype=np.int32)
>>> x.data
<read-write buffer for 0xa37bfd8, size 16, offset 0 at 0xa4eabe0>
>>> str(x.data)
\x01\x00\x00\x00\x02\x00\x00\x00\x03\x00\x00\x00\x04\x00\x00\x00

Memory address of the data:

>>> x.__array_interface__[data][0]
159755776

Reminder: two ndarrays may share the same memory:

>>> x = np.array([1,2,3,4])
>>> y = x[:]
>>> x[0] = 9
>>> y
array([9, 2, 3, 4])
>>> y.base is x
True

Memory does not need to be owned by an ndarray:

>>> x = \x01\x02\x03\x04
>>> y = np.frombuffer(x, dtype=np.int8)
>>> y
array([1, 2, 3, 4], dtype=int8)
>>> y.data

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<read-only buffer for 0xa588ba8, size 4, offset 0 at 0xa55cd60>

>>> y.base is x
True
>>> y.flags
C_CONTIGUOUS : True
F_CONTIGUOUS : True
OWNDATA : False
WRITEABLE : False
ALIGNED : True
UPDATEIFCOPY : False

The owndata and writeable flags indicate status of the memory block.

3.5.3 Indexing scheme: strides

The question
>>> x = np.array([[1, 2, 3],
[4, 5, 6],
[7, 8, 9]], dtype=np.int8)
>>> str(x.data)
\x01\x02\x03\x04\x05\x06\x07\x08\x09

At which byte in x.data does the item x[1,2] begin?

The answer (in Numpy)
strides: the number of bytes to jump to find the next element
1 stride per dimension
>>> x.strides
(3, 1)
>>> byte_offset = 3*1 + 1*2
>>> x.data[byte_offset]
\x06
>>> x[1,2]
6

# to find x[1,2]

simple, flexible

C and Fortran order

>>> x = np.array([[1, 2, 3],
[4, 5, 6],
[7, 8, 9]], dtype=np.int16, order=C)
>>> x.strides
(6, 2)
>>> str(x.data)
\x01\x00\x02\x00\x03\x00\x04\x00\x05\x00\x06\x00\x07\x00\x08\x00\t\x00

Need to jump 6 bytes to find the next row

Need to jump 2 bytes to find the next column
>>> y = np.array(x, order=F)
>>> y.strides
(2, 6)
>>> str(y.data)
\x01\x00\x04\x00\x07\x00\x02\x00\x05\x00\x08\x00\x03\x00\x06\x00\t\x00

Need to jump 2 bytes to find the next row

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Need to jump 6 bytes to find the next column

Similarly to higher dimensions:
C: last dimensions vary fastest (= smaller strides)
F: first dimensions vary fastest
shape = (d1 , d2 , ..., dn )
strides = (s1 , s2 , ..., sn )
sC
j = dj+1 dj+2 ...dn itemsize
sF
j = d1 d2 ...dj1 itemsize

Slicing
Everything can be represented by changing only shape, strides, and possibly adjusting the data
pointer!
Never makes copies of the data
>>> x = np.array([1, 2, 3, 4, 5, 6], dtype=np.int32)
>>> y = x[::-1]
>>> y
array([6, 5, 4, 3, 2, 1])
>>> y.strides
(-4,)
>>> y = x[2:]
>>> y.__array_interface__[data][0] - x.__array_interface__[data][0]
8
>>> x = np.zeros((10, 10, 10), dtype=np.float)
>>> x.strides
(800, 80, 8)
>>> x[::2,::3,::4].strides
(1600, 240, 32)

Similarly, transposes never make copies (it just swaps strides)

>>> x = np.zeros((10, 10, 10), dtype=np.float)
>>> x.strides
(800, 80, 8)
>>> x.T.strides
(8, 80, 800)

Reshaping
But: not all reshaping operations can be represented by playing with strides.
>>>
>>>
>>>
(1,

a = np.arange(6, dtype=np.int8).reshape(3, 2)
b = a.T
b.strides
2)

So far, so good. However:

>>> str(a.data)
\x00\x01\x02\x03\x04\x05
>>> b
array([[0, 2, 4],

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[1, 3, 5]], dtype=int8)

>>> c = b.reshape(3*2)
>>> c
array([0, 2, 4, 1, 3, 5], dtype=int8)

Here, there is no way to represent the array c given one stride and the block of memory for a. Therefore, the
reshape operation needs to make a copy here.

3.5.4 Summary
Numpy array: block of memory + indexing scheme + data type description
Indexing: strides
byte_position = np.sum(arr.strides * indices)
Various tricks can you do by playing with the strides (stuff for an advanced tutorial it is)

3.5. 4. Under the hood

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CHAPTER 4

Getting help and finding

documentation

author Emmanuelle Gouillart

Rather than knowing all functions in Numpy and Scipy, it is important to find rapidly information throughout the
documentation and the available help. Here are some ways to get information:
In Ipython, help function opens the docstring of the function. Only type the beginning of the functions name and use tab completion to display the matching functions.
In [204]: help np.v
np.vander
np.vdot
np.var
np.vectorize

np.version
np.void

np.void0
np.vsplit

np.vstack

In [204]: help np.vander

In Ipython it is not possible to open a separated window for help and documentation; however one can always
open a second Ipython shell just to display help and docstrings...
Numpys and Scipys documentations can be browsed online on http://docs.scipy.org/doc.
The search button is quite useful inside the reference documentation of the two packages
(http://docs.scipy.org/doc/numpy/reference/ and http://docs.scipy.org/doc/scipy/reference/).
Tutorials on various topics as well as the complete API with all docstrings are found on this website.

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Numpys and Scipys documentation is enriched and updated on a regular basis by users on a wiki
http://docs.scipy.org/numpy/. As a result, some docstrings are clearer or more detailed on the wiki, and
you may want to read directly the documentation on the wiki instead of the official documentation website.
Note that anyone can create an account on the wiki and write better documentation; this is an easy way to
contribute to an open-source project and improve the tools you are using!

Scipys cookbook http://www.scipy.org/Cookbook gives recipes on many common problems frequently encountered, such as fitting data points, solving ODE, etc.
Matplotlibs website http://matplotlib.sourceforge.net/ features a very nice gallery with a large number of
plots, each of them shows both the source code and the resulting plot. This is very useful for learning by
example. More standard documentation is also available.

Mayavis website http://code.enthought.com/projects/mayavi/docs/development/html/mayavi/ also has a

very nice gallery of examples http://code.enthought.com/projects/mayavi/docs/development/html/mayavi/auto/examples.html
in which one can browse for different visualization solutions.

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Finally, two more technical possibilities are useful as well:

In Ipython, the magical function %psearch search for objects matching patterns. This is useful if, for
example, one does not know the exact name of a function.
In [3]: import numpy as np
In [4]: %psearch np.diag*
np.diag
np.diagflat
np.diagonal

numpy.lookfor looks for keywords inside the docstrings of specified modules.

In [45]: numpy.lookfor(convolution)
Search results for convolution
-------------------------------numpy.convolve
Returns the discrete, linear convolution of two one-dimensional
sequences.
numpy.bartlett
Return the Bartlett window.
numpy.correlate
Discrete, linear correlation of two 1-dimensional sequences.
In [46]: numpy.lookfor(remove, module=os)
Search results for remove
--------------------------os.remove
remove(path)
os.removedirs
removedirs(path)
os.rmdir
rmdir(path)
os.unlink
unlink(path)
os.walk
Directory tree generator.

If everything listed above fails (and Google doesnt have the answer)... dont despair! Write to the mailinglist suited to your problem: you should have a quick answer if you describe your problem well. Experts on
scientific python often give very enlightening explanations on the mailing-list.
Numpy discussion ([email protected]): all about numpy arrays, manipulating them, indexation questions, etc.

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SciPy Users List ([email protected]): scientific computing with Python, high-level data processing, in particular with the scipy package.
[email protected] for plotting with matplotlib.

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CHAPTER 5

Matplotlib

author Mike Mller

5.1 Introduction
matplotlib is probably the single most used Python package for 2D-graphics. It provides both a very quick
way to visualize data from Python and publication-quality figures in many formats. We are going to explore
matplotlib in interactive mode covering most common cases. We also look at the class library which is provided
with an object-oriented interface.

5.2 IPython
IPython is an enhanced interactive Python shell that has lots of interesting features including named inputs and
outputs, access to shell commands, improved debugging and many more. When we start it with the command line
argument -pylab, it allows interactive matplotlib sessions that has Matlab/Mathematica-like functionality.

5.3 pylab
pylab provides a procedural interface to the matplotlib object-oriented plotting library. It is modeled closely
after Matlab(TM). Therefore, the majority of plotting commands in pylab has Matlab(TM) analogs with similar
arguments. Important commands are explained with interactive examples.

5.4 Simple Plots

Lets start an interactive session:
$ ipython -pylab

This brings us to the IPython prompt:

IPython
?
%magic
help
object?

0.8.1 -- An enhanced Interactive Python.

-> Introduction to IPythons features.
-> Information about IPythons magic % functions.
-> Pythons own help system.
-> Details about object. ?object also works, ?? prints more.

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Welcome to pylab, a matplotlib-based Python environment.

For more information, type help(pylab).
In [1]:

Now we can make our first, really simple plot:

In [1]: plot(range(10))
Out[1]: [<matplotlib.lines.Line2D instance at 0x01AA26E8>]
In [2]:

The numbers form 0 through 9 are plotted:

Now we can interactively add features to or plot:

In [2]: xlabel(measured)
Out[2]: <matplotlib.text.Text instance at 0x01A9D210>
In [3]: ylabel(calculated)
Out[3]: <matplotlib.text.Text instance at 0x01A9D918>
In [4]: title(Measured vs. calculated)
Out[4]: <matplotlib.text.Text instance at 0x01A9DF80>
In [5]: grid(True)
In [6]:

We get a reference to our plot:

In [6]: my_plot = gca()

and to our line we plotted, which is the first in the plot:

In [7]: line = my_plot.lines[0]

Now we can set properties using set_something methods:

In [8]: line.set_marker(o)

or the setp function:

In [9]: setp(line, color=g)
Out[9]: [None]

To apply the new properties we need to redraw the screen:

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In [10]: draw()

We can also add several lines to one plot:

In [1]: x = arange(100)
In [2]: linear = arange(100)
In [3]: square = [v * v for v in arange(0, 10, 0.1)]
In [4]: lines = plot(x, linear, x, square)

Lets add a legend:

In [5]: legend((linear, square))
Out[5]: <matplotlib.legend.Legend instance at 0x01BBC170>

This does not look particularly nice. We would rather like to have it at the left. So we clean the old graph:
In [6]: clf()

and print it anew providing new line styles (a green dotted line with crosses for the linear and a red dashed line
with circles for the square graph):
In [7]: lines = plot(x, linear, g:+, x, square, r--o)

Now we add the legend at the upper left corner:

In [8]: l = legend((linear, square), loc=upper left)

The result looks like this:

5.4.1 Exercises
1. Plot a simple graph of a sinus function in the range 0 to 3 with a step size of 0.01.
2. Make the line red. Add diamond-shaped markers with size of 5.
3. Add a legend and a grid to the plot.

5.5 Properties
So far we have used properties for the lines. There are three possibilities to set them:

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1) as keyword arguments at creation time: plot(x, linear, g:+, x, square, r--o).

2. with the function setp: setp(line, color=g).
3. using the set_something methods: line.set_marker(o)
Lines have several properties as shown in the following table:
Property
alpha
antialiased
color
data_clipping
label
linestyle
linewidth
marker
markeredgewidth
markeredgecolor
markerfacecolor
markersize

Value
alpha transparency on 0-1 scale
True or False - use antialised rendering
matplotlib color arg
whether to use numeric to clip data
string optionally used for legend
one of - : -. float, the line width in points
one of + , o . s v x > <, etc
line width around the marker symbol
edge color if a marker is used
face color if a marker is used
size of the marker in points

There are many line styles that can be specified with symbols:
Symbol
--.
:
.
,
o
^
v
<
>
s
+
x
D
d
1
2
3
4
h
H
p
|
_
steps

Description
solid line
dashed line
dash-dot line
dotted line
points
pixels
circle symbols
triangle up symbols
triangle down symbols
triangle left symbols
triangle right symbols
square symbols
plus symbols
cross symbols
diamond symbols
thin diamond symbols
tripod down symbols
tripod up symbols
tripod left symbols
tripod right symbols
hexagon symbols
rotated hexagon symbols
pentagon symbols
vertical line symbols
horizontal line symbols
use gnuplot style steps # kwarg only

Colors can be given in many ways: one-letter abbreviations, gray scale intensity from 0 to 1, RGB in hex and tuple
format as well as any legal html color name.
The one-letter abbreviations are very handy for quick work. With following you can get quite a few things done:

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Abbreviation
b
g
r
c
m
y
k
w

Color
blue
green
red
cyan
magenta
yellow
black
white

Other objects also have properties. The following table list the text properties:
Property
alpha
color
family
fontangle
horizontalalignment
multialignment
name
position
variant
rotation
size
style
text
verticalalignment
weight

Value
alpha transparency on 0-1 scale
matplotlib color arg
set the font family, eg sans-serif, cursive, fantasy
the font slant, one of normal, italic, oblique
left, right or center
left, right or center only for multiline strings
font name, eg, Sans, Courier, Helvetica
x,y location
font variant, eg normal, small-caps
angle in degrees for rotated text
fontsize in points, eg, 8, 10, 12
font style, one of normal, italic, oblique
set the text string itself
top, bottom or center
font weight, e.g. normal, bold, heavy, light

5.5.1 Exercise
1. Apply different line styles to a plot. Change line color and thickness as well as the size and the kind of the
marker. Experiment with different styles.

5.6 Text
Weve already used some commands to add text to our figure: xlabel ylabel, and title.
There are two functions to put text at a defined position. text adds the text with data coordinates:
In [2]: plot(arange(10))
In [3]: t1 = text(5, 5, Text in the middle)

figtext uses figure coordinates form 0 to 1:

In [4]: t2 = figtext(0.8, 0.8, Upper right text)

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matplotlib supports TeX mathematical expression. So r$\pi$ will show up as:

If you want to get more control over where the text goes, you use annotations:
In [4]: ax = gca()
In [5]: ax.annotate(Here is something special, xy = (1, 1))

We will write the text at the position (1, 1) in terms of data. There are many optional arguments that help to
customize the position of the text. The arguments textcoords and xycoords specifies what x and y mean:
argument
figure points
figure pixels
figure fraction
axes points
axes pixels
axes fraction
data

coordinate system
points from the lower left corner of the figure
pixels from the lower left corner of the figure
0,0 is lower left of figure and 1,1 is upper, right
points from lower left corner of axes
pixels from lower left corner of axes
0,1 is lower left of axes and 1,1 is upper right
use the axes data coordinate system

If we do not supply xycoords, the text will be written at xy.

Furthermore, we can use an arrow whose appearance can also be described in detail:
In [14]: plot(arange(10))
Out[14]: [<matplotlib.lines.Line2D instance at 0x01BB15D0>]
In [15]: ax = gca()
In [16]: ax.annotate(Here is something special, xy = (2, 1), xytext=(1,5))
Out[16]: <matplotlib.text.Annotation instance at 0x01BB1648>
In [17]: ax.annotate(Here is something special, xy = (2, 1), xytext=(1,5),
....: arrowprops={facecolor: r})

5.6.1 Exercise
1. Annotate a line at two places with text. Use green and red arrows and align it according to figure
points and data.

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5.7 Ticks
5.7.1 Where and What
Well formatted ticks are an important part of publishing-ready figures. matplotlib provides a totally configurable system for ticks. There are tick locators to specify where ticks should appear and tick formatters to
make ticks look like the way you want. Major and minor ticks can be located and formatted independently from
each other. Per default minor ticks are not shown, i.e. there is only an empty list for them because it is as
NullLocator (see below).

5.7.2 Tick Locators

There are several locators for different kind of requirements:
Class
NullLocator
IndexLocator
LinearLocator
LogLocator
MultipleLocator
AutoLocator

Description
no ticks
locator for index plots (e.g. where x = range(len(y))
evenly spaced ticks from min to max
logarithmically ticks from min to max
ticks and range are a multiple of base; either integer or float
choose a MultipleLocator and dynamically reassign

All of these locators derive from the base class matplotlib.ticker.Locator. You can make your own
locator deriving from it.
Handling dates as ticks can be especially tricky.
matplotlib.dates:
Class
MinuteLocator
HourLocator
DayLocator
WeekdayLocator
MonthLocator
YearLocator
RRuleLocator

Therefore, matplotlib provides special locators in

Description
locate minutes
locate hours
locate specified days of the month
locate days of the week, e.g. MO, TU
locate months, e.g. 10 for October
locate years that are multiples of base
locate using a matplotlib.dates.rrule

5.7.3 Tick Formatters

Similarly to locators, there are formatters:
Class
NullFormatter
FixedFormatter
FuncFormatter
FormatStrFormatter
IndexFormatter
ScalarFormatter
LogFormatter
DateFormatter

Description
no labels on the ticks
set the strings manually for the labels
user defined function sets the labels
use a sprintf format string
cycle through fixed strings by tick position
default formatter for scalars; autopick the fmt string
formatter for log axes
use an strftime string to format the date

All of these formatters derive from the base class matplotlib.ticker.Formatter. You can make your
own formatter deriving from it.
Now we set our major locator to 2 and the minor locator to 1. We also format the numbers as decimals using the
FormatStrFormatter:

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In [5]: major_locator = MultipleLocator(2)

In [6]: major_formatter = FormatStrFormatter(%5.2f)
In [7]: minor_locator = MultipleLocator(1)
In [8]: ax.xaxis.set_major_locator(major_locator)
In [9]: ax.xaxis.set_minor_locator(minor_locator)
In [10]: ax.xaxis.set_major_formatter(major_formatter)
In [10]: draw()

After we redraw the figure our x axis should look like this:

5.7.4 Exercises
1. Plot a graph with dates for one year with daily values at the x axis using the built-in module datetime.
2. Format the dates in such a way that only the first day of the month is shown.
3. Display the dates with and without the year. Show the month as number and as first three letters of the
month name.

5.8 Figures, Subplots, and Axes

5.8.1 The Hierarchy
So far we have used implicit figure and axes creation. This is handy for fast plots. We can have more control
over the display using figure, subplot, and axes explicitly. A figure in matplotlib means the whole
window in the user interface. Within this figure there can be subplots. While subplot positions the plots in
a regular grid, axes allows free placement within the figure. Both can be useful depending on your intention.
Weve already work with figures and subplots without explicitly calling them. When we call plot matplotlib
calls gca() to get the current axes and gca in turn calls gcf() to get the current figure. If there is none it calls
figure() to make one, strictly speaking, to make a subplot(111). Lets look at the details.

5.8.2 Figures
A figure is the windows in the GUI that has Figure # as title. Figures are numbered starting from 1 as
opposed to the normal Python way starting from 0. This is clearly MATLAB-style. There are several parameters
that determine how the figure looks like:
Argument
num
figsize
dpi
facecolor
edgecolor
frameon

Default
1
figure.figsize
figure.dpi
figure.facecolor
figure.edgecolor
True

Description
number of figure
figure size in in inches (width, height)
resolution in dots per inch
color of the drawing background
color of edge around the drawing background
draw figure frame or not

The defaults can be specified in the resource file and will be used most of the time. Only the number of the figure
is frequently changed.

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When you work with the GUI you can close a figure by clicking on the x in the upper right corner. But you can
close a figure programmatically by calling close. Depending on the argument it closes (1) the current figure
(no argument), (2) a specific figure (figure number or figure instance as argument), or (3) all figures (all as
argument).
As with other objects, you can set figure properties also setp or with the set_something methods.

5.8.3 Subplots
With subplot you can arrange plots in regular grid. You need to specify the number of rows and columns and
the number of the plot.
A plot with two rows and one column is created with subplot(211) and subplot(212). The result looks
like this:

If you want two plots side by side, you create one row and two columns with subplot(121) and
subplot(112). The result looks like this:

You can arrange as many figures as you want. A two-by-two arrangement can be created with subplot(221),
subplot(222), subplot(223), and subplot(224). The result looks like this:

Frequently, you dont want all subplots to have ticks or labels. You can set the xticklabels or the
yticklabels to an empty list ([]). Every subplot defines the methods is_first_row, is_first_col,
is_last_row, is_last_col. These can help to set ticks and labels only for the outer pots.

5.8.4 Axes
Axes are very similar to subplots but allow placement of plots at any location in the figure. So if we want to put a
smaller plot inside a bigger one we do so with axes:
In [22]: plot(x)
Out[22]: [<matplotlib.lines.Line2D instance at 0x02C9CE90>]
In [23]: a = axes([0.2, 0.5, 0.25, 0.25])

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In [24]: plot(x)

The result looks like this:

5.8.5 Exercises
1. Draw two figures, one 5 by 5, one 10 by 10 inches.
2. Add four subplots to one figure. Add labels and ticks only to the outermost axes.
3. Place a small plot in one bigger plot.

5.9 Other Types of Plots

5.9.1 Many More
So far we have used only line plots. matplotlib offers many more types of plots. We will have a brief look at
some of them. All functions have many optional arguments that are not shown here.

5.9.2 Bar Charts

The function bar creates a new bar chart:
bar([1, 2, 3], [4, 3, 7])

Now we have three bars starting at 1, 2, and 3 with height of 4, 3, 7 respectively:

The default column width is 0.8. It can be changed with common methods by setting width. As it can be color
and bottom, we can also set an error bar with yerr or xerr.

5.9.3 Horizontal Bar Charts

The function barh creates an vertical bar chart. Using the same data:
barh([1, 2, 3], [4, 3, 7])

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We get:

5.9.4 Broken Horizontal Bar Charts

We can also have discontinuous vertical bars with broken_barh. We specify start and width of the range in
y-direction and all start-width pairs in x-direction:
yrange = (2, 1)
xranges = ([0, 0.5], [1, 1], [4, 1])
broken_barh(xranges, yrange)

We changes the extension of the y-axis to make plot look nicer:

ax = gca()
ax.set_ylim(0, 5)
(0, 5)
draw()

and get this:

5.9.5 Box and Whisker Plots

We can draw box and whisker plots:
boxplot((arange(2, 10), arange(1, 5)))

We want to have the whiskers well within the plot and therefore increase the y axis:
ax = gca()
ax.set_ylim(0, 12)
draw()

Our plot looks like this:

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The range of the whiskers can be determined with the argument whis, which defaults to 1.5. The range of the
whiskers is between the most extreme data point within whis*(75%-25%) of the data.

5.9.6 Contour Plots

We can also do contour plots. We define arrays for the x and y coordinates:
x = y = arange(10)

and also a 2D array for z:

z = ones((10,
z[5,5] = 7
z[2,1] = 3
z[8,7] = 4
z
array([[ 1.,
[ 1.,
[ 1.,
[ 1.,
[ 1.,
[ 1.,
[ 1.,
[ 1.,
[ 1.,
[ 1.,

10))

1.,
1.,
3.,
1.,
1.,
1.,
1.,
1.,
1.,
1.,

1.,
1.,
1.,
1.,
1.,
1.,
1.,
1.,
1.,
1.,

1.,
1.,
1.,
1.,
1.,
1.,
1.,
1.,
1.,
1.,

1.,
1.,
1.,
1.,
1.,
1.,
1.,
1.,
1.,
1.,

1.,
1.,
1.,
1.,
1.,
7.,
1.,
1.,
1.,
1.,

1.,
1.,
1.,
1.,
1.,
1.,
1.,
1.,
1.,
1.,

1.,
1.,
1.,
1.,
1.,
1.,
1.,
1.,
4.,
1.,

1.,
1.,
1.,
1.,
1.,
1.,
1.,
1.,
1.,
1.,

1.],
1.],
1.],
1.],
1.],
1.],
1.],
1.],
1.],
1.]])

Now we can make a simple contour plot:

contour(x, x, z)

Our plot looks like this:

We can also fill the area. We just use numbers form 0 to 9 for the values v:
v = x
contourf(x, x, z, v)

Now our plot area is filled:

5.9.7 Histograms
We can make histograms. Lets get some normally distributed random numbers from numpy:

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import numpy as N
r_numbers = N.random.normal(size= 1000)

Now we make a simple histogram:

hist(r_numbers)

With 100 numbers our figure looks pretty good:

5.9.8 Loglog Plots

Plots with logarithmic scales are easy:
loglog(arange(1000))

We set the mayor and minor grid:

grid(True)
grid(True, which=minor)

Now we have loglog plot:

If we want only one axis with a logarithmic scale we can use semilogx or semilogy.

5.9.9 Pie Charts

Pie charts can also be created with a few lines:
data = [500, 700, 300]
labels = [cats, dogs, other]
pie(data, labels=labels)

The result looks as expected:

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5.9.10 Polar Plots

Polar plots are also possible. Lets define our r from 0 to 360 and our theta from 0 to 360 degrees. We need to
convert them to radians:
r = arange(360)
theta = r / (180/pi)

Now plot in polar coordinates:

polar(theta, r)

We get a nice spiral:

5.9.11 Arrow Plots

Plotting arrows in 2D plane can be achieved with quiver. We define the x and y coordinates of the arrow shafts:
x = y = arange(10)

The x and y components of the arrows are specified as 2D arrays:

u = ones((10, 10))
v = ones((10, 10))
u[4, 4] = 3
v[1, 1] = -1

Now we can plot the arrows:

quiver(x, y, u, v)

All arrows point to the upper right, except two. The one at the location (4, 4) has 3 units in x-direction and the
other at location (1, 1) has -1 unit in y direction:

5.9.12 Scatter Plots

Scatter plots print x vs. y diagrams. We define x and y and make some point in y random:
x = arange(10)
y = arange(10)
y[1] = 7
y[4] = 2
y[8] = 3

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Now make a scatter plot:

scatter(x, y)

The three different values for y break out of the line:

5.9.13 Sparsity Pattern Plots

Working with sparse matrices, it is often of interest as how the matrix looks like in terms of sparsity. We take an
identity matrix as an example:
i = identity(10)
i
array([[1, 0, 0,
[0, 1, 0,
[0, 0, 1,
[0, 0, 0,
[0, 0, 0,
[0, 0, 0,
[0, 0, 0,
[0, 0, 0,
[0, 0, 0,
[0, 0, 0,

0,
0,
0,
1,
0,
0,
0,
0,
0,
0,

0,
0,
0,
0,
1,
0,
0,
0,
0,
0,

0,
0,
0,
0,
0,
1,
0,
0,
0,
0,

0,
0,
0,
0,
0,
0,
1,
0,
0,
0,

0,
0,
0,
0,
0,
0,
0,
1,
0,
0,

0,
0,
0,
0,
0,
0,
0,
0,
1,
0,

0],
0],
0],
0],
0],
0],
0],
0],
0],
1]])

Now we look at it more visually:

spy(i)

5.9.14 Stem Plots

Stem plots vertical lines at the given x location up to the specified y location. Lets reuse x and y from our scatter
(see above):
stem(x, y)

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5.9.15 Date Plots

There is a function for creating date plots. Lets define 10 dates starting at January 1st 2000 at 15.day intervals:
import datetime
d1 = datetime.datetime(2000, 1, 1)
delta = datetime.timedelta(15)
dates = [d1 + x * delta for x in range(1
dates
[datetime.datetime(2000, 1, 1, 0, 0),
datetime.datetime(2000, 1, 16, 0, 0),
datetime.datetime(2000, 1, 31, 0, 0),
datetime.datetime(2000, 2, 15, 0, 0),
datetime.datetime(2000, 3, 1, 0, 0),
datetime.datetime(2000, 3, 16, 0, 0),
datetime.datetime(2000, 3, 31, 0, 0),
datetime.datetime(2000, 4, 15, 0, 0),
datetime.datetime(2000, 4, 30, 0, 0),
datetime.datetime(2000, 5, 15, 0, 0)]

We reuse our data from the scatter plot (see above):

y
array([0, 7, 2, 3, 2, 5, 6, 7, 3, 9])

Now we can plot the dates at the x axis:

plot_date(dates, y)

5.10 The Class Library

So far we have used the pylab interface only. As the name suggests it is just wrapper around the class library.
All pylab commands can be invoked via the class library using an object-oriented approach.

5.10.1 The Figure Class

The class Figure lives in the module matplotlib.figure. Its constructor takes these arguments:
figsize=None, dpi=None, facecolor=None, edgecolor=None,
linewidth=1.0, frameon=True, subplotpars=None

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Comparing this with the arguments of figure in pylab shows significant overlap:
num=None, figsize=None, dpi=None, facecolor=None
edgecolor=None, frameon=True

Figure provides lots of methods, many of them have equivalents in pylab. The methods add_axes and
add_subplot are called if new axes or subplot are created with axes or subplot in pylab. Also the
method gca maps directly to pylab as do legend, text and many others.
There are also several set_something method such as set_facecolor or set_edgecolor that will be
called through pylab to set properties of the figure. Figure also implements get_something methods such
as get_axes or get_facecolor to get properties of the figure.

5.10.2 The Classes Axes and Subplot

In the class Axes we find most of the figure elements such as Axis, Tick, Line2D, or Text. It also sets the
coordinate system. The class Subplot inherits from Axes and adds some more functionality to arrange the plots
in a grid.
Analogous to Figure, it has methods to get and set properties and methods already encountered as functions in
pylab such as annotate. In addition, Axes has methods for all types of plots shown in the previous section.

5.10.3 Other Classes

Other classes such as text, Legend or Ticker are setup very similarly. They can be understood mostly by
comparing to the pylab interface.

5.10.4 Example
Lets look at an example for using the object-oriented API:
#file matplotlib/oo.py
from matplotlib.figure import Figure

#1

figsize = (8, 5)
fig = Figure(figsize=figsize)
ax = fig.add_subplot(111)
line = ax.plot(range(10))[0]
ax.set_title(Plotted with OO interface)
ax.set_xlabel(measured)
ax.set_ylabel(calculated)
ax.grid(True)
line.set_marker(o)

#2
#3
#4
#5
#6

#7
#8

from matplotlib.backends.backend_agg import FigureCanvasAgg #9

canvas = FigureCanvasAgg(fig)
#10
canvas.print_figure("oo.png", dpi=80)
#11

import Tkinter as Tk
#12
from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg #13
root = Tk.Tk()
#14
canvas2 = FigureCanvasTkAgg(fig, master=root) #15
canvas2.show()
#16
canvas2.get_tk_widget().pack(side=Tk.TOP, fill=Tk.BOTH, expand=1) #17
Tk.mainloop()
#18
from matplotlib import _pylab_helpers

5.10. The Class Library

#19

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import pylab

#20

pylab_fig = pylab.figure(1, figsize=figsize)

figManager = _pylab_helpers.Gcf.get_active()
figManager.canvas.figure = fig
pylab.show()

#21
#22
#23
#24

Since we are not in the interactive pylab-mode, we need to import the class Figure explicitly (#1).
We set the size of our figure to be 8 by 5 inches (#2). Now we initialize a new figure (#3) and add a subplot to the
figure (#4). The 111 says one plot at position 1, 1 just as in MATLAB. We create a new plot with the numbers
from 0 to 9 and at the same time get a reference to our line (#5). We can add several things to our plot. So we set
a title and labels for the x and y axis (#6).
We also want to see the grid (#7) and would like to have little filled circles as markers (#8).
There are many different backends for rendering our figure. We use the Anti-Grain Geometry toolkit
(http://www.antigrain.com) to render our figure. First, we import the backend (#9), then we create a new canvas that renders our figure (#10). We save our figure in a png-file with a resolution of 80 dpi (#11).
We can use several GUI toolkits directly. So we import Tkinter (#12) as well as the corresponding backend (#13).
Now we have to do some basic GUI programming work. We make a root object for our GUI (#14) and feed it
together with our figure to the backend to get our canvas (15). We call the show method (#16), pack our widget
(#17), and call the Tkinter mainloop to start the application (#18). You should see GUI window with the figure
on your screen. After closing the screen, the next part, the script, will be executed.
We would like to create a screen display just as we would use pylab. Therefore we import a helper (#19) and
pylab itself (#20). We create a normal figure with pylab (21) and get the corresponding figure manager
(#22). Now lets set our figure we created above to be the current figure (#23) and let pylab show the result
(#24). The lower part of the figure might be cover by the toolbar. If so, please adjust the figsize for pylab
accordingly.

5.10.5 Exercises
1. Use the object-oriented API of matplotlib to create a png-file with a plot of two lines, one linear and square
with a legend in it.

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CHAPTER 6

Scipy : high-level scientific computing

authors Adrien Chauve, Andre Espaze, Emmanuelle Gouillart, Gal Varoquaux

Scipy
The scipy package contains various toolboxes dedicated to common issues in scientific computing. Its
different submodules correspond to different applications, such as interpolation, integration, optimization,
image processing, statistics, special functions, etc.
scipy can be compared to other standard scientific-computing libraries, such as the GSL (GNU Scientific
Library for C and C++), or Matlabs toolboxes. scipy is the core package for scientific routines in Python;
it is meant to operate efficiently on numpy arrays, so that numpy and scipy work hand in hand.
Before implementing a routine, if is worth checking if the desired data processing is not already implemented in Scipy. As non-professional programmers, scientists often tend to re-invent the wheel, which
leads to buggy, non-optimal, difficult-to-share and unmaintainable code. By contrast, Scipys routines are
optimized and tested, and should therefore be used when possible.
Warning: This tutorial is far from an introduction to numerical computing. As enumerating the different
submodules and functions in scipy would be very boring, we concentrate instead on a few examples to give a
general idea of how to use scipy for scientific computing.
To begin with
>>> import numpy as np
>>> import scipy

scipy is mainly composed of task-specific sub-modules:

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cluster
fftpack
integrate
interpolate
io
linalg
maxentropy
ndimage
odr
optimize
signal
sparse
spatial
special
stats

Vector quantization / Kmeans

Fourier transform
Integration routines
Interpolation
Data input and output
Linear algebra routines
Routines for fitting maximum entropy models
n-dimensional image package
Orthogonal distance regression
Optimization
Signal processing
Sparse matrices
Spatial data structures and algorithms
Any special mathematical functions
Statistics

6.1 Scipy builds upon Numpy

Numpy is required for running Scipy but also for using it. The most important type introduced to Python is the N
dimensional array, and it can be seen that Scipy uses the same:
>>> scipy.ndarray is np.ndarray
True

Moreover most of the Scipy usual functions are provided by Numpy:

>>> scipy.cos is np.cos
True

If you would like to know the objects used from Numpy, have a look at the scipy.__file__[:-1] file. On
version 0.6.0, the whole Numpy namespace is imported by the line from numpy import *.

6.2 File input/output: scipy.io

Loading and saving matlab files:
>>> from scipy import io
>>> struct = io.loadmat(file.mat, struct_as_record=True)
>>> io.savemat(file.mat, struct)

See also:
Load text files:
np.loadtxt/np.savetxt

Clever loading of text/csv files:

np.genfromtxt/np.recfromcsv

Fast an efficient, but numpy-specific, binary format:

np.save/np.load

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6.3 Signal processing: scipy.signal

>>> from scipy import signal

Detrend: remove linear trend from signal:

t = np.linspace(0, 5, 100)
x = t + np.random.normal(size=100)
pl.plot(t, x, linewidth=3)
pl.plot(t, signal.detrend(x), linewidth=3)
import numpy as np
import pylab as pl
from scipy import signal
t = np.linspace(0, 5, 100)
x = t + np.random.normal(size=100)
pl.plot(t, x, linewidth=3)
pl.plot(t, signal.detrend(x), linewidth=3)

8
6
4
2
0
2
40

Resample: resample a signal to n points using FFT.

t = np.linspace(0, 5, 100)
x = np.sin(t)
pl.plot(t, x, linewidth=3)
pl.plot(t[::2], signal.resample(x, 50), ko)
import numpy as np
import pylab as pl
from scipy import signal
t = np.linspace(0, 5, 100)
x = np.sin(t)

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pl.plot(t, x, linewidth=3)
pl.plot(t[::2], signal.resample(x, 50), ko)

1.5
1.0
0.5
0.0
0.5
1.0
1.50

Notice how on the side of the window the resampling is less accurate and has a rippling effect.
Signal has many window function: hamming, bartlett, blackman...
Signal has filtering (Gaussian, median filter, Wiener), but we will discuss this in the image paragraph.

6.4 Special functions: scipy.special

Special functions are transcendal functions. The docstring of the module is well-written and we will not list them.
Frequently used ones are:
Bessel function, such as special.jn (nth integer order Bessel function)
Elliptic function (special.ellipj for the Jacobian elliptic function, ...)
Gamma function: special.gamma, also note special.gammaln which will give the log of Gamma
to a higher numerical precision.
Erf, the area under a Gaussian curve: special.erf

6.5 Statistics and random numbers: scipy.stats

The module scipy.stats contains statistical tools and probabilistic description of random processes. Random
number generators for various random process can be found in numpy.random.

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6.5.1 Histogram and probability density function

Given observations of a random process, their histogram is an estimator of the random processs PDF (probability
density function):
>>> a = np.random.normal(size=1000)
>>> bins = np.arange(-4, 5)
>>> bins
array([-4, -3, -2, -1, 0, 1, 2, 3, 4])
>>> histogram = np.histogram(a, bins=bins, normed=True)[0]
>>> bins = 0.5*(bins[1:] + bins[:-1])
>>> bins
array([-3.5, -2.5, -1.5, -0.5, 0.5, 1.5, 2.5, 3.5])
>>> from scipy import stats
>>> b = stats.norm.pdf(bins)
In [1]: pl.plot(bins, histogram)
In [2]: pl.plot(bins, b)
from scipy import stats
import numpy as np
import pylab as pl
a = np.random.normal(size=10000)
bins = np.linspace(-5, 5, 30)
histogram, bins = np.histogram(a, bins=bins, normed=True)
bins = 0.5*(bins[1:] + bins[:-1])
from scipy import stats
b = stats.norm.pdf(bins)
pl.plot(bins, histogram)
pl.plot(bins, b)

0.45
0.40
0.35
0.30
0.25
0.20
0.15
0.10
0.05
0.00 6

If we know that the random process belongs to a given family of random processes, such as normal processes,

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we can do a maximum-likelihood fit of the observations to estimate the parameters of the underlying distribution.
Here we fit a normal process to the observed data:
>>> loc, std = stats.norm.fit(a)
>>> loc
0.003738964114102075
>>> std
0.97450996668871193

6.5.2 Percentiles
The median is the value with half of the observations below, and half above:
>>> np.median(a)
0.0071645570292782519

It is also called the percentile 50, because 50% of the observation are below it:
>>> stats.scoreatpercentile(a, 50)
0.0071645570292782519

Similarly, we can calculate the percentile 90:

>>> stats.scoreatpercentile(a, 90)
1.2729556087871292

The percentile is an estimator of the CDF: cumulative distribution function.

6.5.3 Statistical tests

A statistical test is a decision indicator. For instance, if we have 2 sets of observations, that we assume are generated from Gaussian processes, we can use a T-test to decide whether the two sets of observations are significantly
different:
>>> a = np.random.normal(0, 1, size=100)
>>> b = np.random.normal(1, 1, size=10)
>>> stats.ttest_ind(a, b)
(-2.389876434401887, 0.018586471712806949)

The resulting output is composed of:

The T statistic value: it is a number the sign of which is proportional to the difference between the two
random processes and the magnitude is related to the significance of this difference.
the p value: the probability of both process being identical. If it is close to 1, the two process are almost
certainly identical. The closer it is to zero, the more likely it is that the processes have different mean.

6.6 Linear algebra operations: scipy.linalg

First, the linalg module provides standard linear algebra operations. The det function computes the determinant
of a square matrix:
>>> from scipy import linalg
>>> arr = np.array([[1, 2],
...
[3, 4]])
>>> linalg.det(arr)
-2.0
>>> arr = np.array([[3, 2],
...
[6, 4]])
>>> linalg.det(arr)

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0.0
>>> linalg.det(np.ones((3, 4)))
Traceback (most recent call last):
...
ValueError: expected square matrix

The inv function computes the inverse of a square matrix:

>>> arr = np.array([[1, 2],
...
[3, 4]])
>>> iarr = linalg.inv(arr)
>>> iarr
array([[-2. , 1. ],
[ 1.5, -0.5]])
>>> np.allclose(np.dot(arr, iarr), np.eye(2))
True

Note that in case you use the matrix type, the inverse is computed when requesting the I attribute:
>>> ma = np.matrix(arr, copy=False)
>>> np.allclose(ma.I, iarr)
True

Finally computing the inverse of a singular matrix (its determinant is zero) will raise LinAlgError:
>>> arr = np.array([[3, 2],
...
[6, 4]])
>>> linalg.inv(arr)
Traceback (most recent call last):
...
LinAlgError: singular matrix

More advanced operations are available like singular-value decomposition (SVD):

>>> arr = np.arange(12).reshape((3, 4)) + 1
>>> uarr, spec, vharr = linalg.svd(arr)

The resulting array spectrum is:

>>> spec
array([ 2.54368356e+01,

1.72261225e+00,

5.14037515e-16])

For the recomposition, an alias for manipulating matrix will first be defined:
>>> asmat = np.asmatrix

then the steps are:

>>> sarr = np.zeros((3, 4))
>>> sarr.put((0, 5, 10), spec)
>>> svd_mat = asmat(uarr) * asmat(sarr) * asmat(vharr)
>>> np.allclose(svd_mat, arr)
True

SVD is commonly used in statistics or signal processing. Many other standard decompositions (QR, LU, Cholesky,
Schur), as well as solvers for linear systems, are available in scipy.linalg.

6.7 Numerical integration: scipy.integrate

The most generic integration routine is scipy.integrate.quad:
>>> from scipy.integrate import quad
>>> res, err = quad(np.sin, 0, np.pi/2)

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>>> np.allclose(res, 1)
True
>>> np.allclose(err, 1 - res)
True

Others integration schemes are available with fixed_quad, quadrature, romberg.

scipy.integrate also features routines for Ordinary differential equations (ODE) integration. In particular,
scipy.integrate.odeint is a general-purpose integrator using LSODA (Livermore solver for ordinary differential equations with automatic method switching for stiff and non-stiff problems), see the ODEPACK Fortran
library for more details.
odeint solves first-order ODE systems of the form:
dy/dt = rhs(y1, y2, .., t0,...)

As an introduction, let us solve the ODE dy/dt = -2y between t = 0..4, with the initial condition y(t=0)
= 1. First the function computing the derivative of the position needs to be defined:
>>> def calc_derivative(ypos, time, counter_arr):
...
counter_arr += 1
...
return -2*ypos
...

An extra argument counter_arr has been added to illustrate that the function may be called several times for
a single time step, until solver convergence. The counter array is defined as:
>>> counter = np.zeros((1,), np.uint16)

The trajectory will now be computed:

>>> from scipy.integrate import odeint
>>> time_vec = np.linspace(0, 4, 40)
>>> yvec, info = odeint(calc_derivative, 1, time_vec,
...
args=(counter,), full_output=True)

Thus the derivative function has been called more than 40 times:
>>> counter
array([129], dtype=uint16)

and the cumulative iterations number for the 10 first convergences can be obtained by:
>>> info[nfe][:10]
array([31, 35, 43, 49, 53, 57, 59, 63, 65, 69], dtype=int32)

The solver requires more iterations at start. The final trajectory is seen on the Matplotlib figure:
"""Solve the ODE dy/dt = -2y between t = 0..4, with the
initial condition y(t=0) = 1.
"""
import numpy as np
from scipy.integrate import odeint
import pylab as pl
def calc_derivative(ypos, time):
return -2*ypos
time_vec = np.linspace(0, 4, 40)
yvec = odeint(calc_derivative, 1, time_vec)
pl.plot(time_vec, yvec)
pl.xlabel(Time [s])
pl.ylabel(y position [m])

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1.0

y position [m]

0.8
0.6
0.4
0.2
0.00.0

0.5

1.0

1.5

2.0
Time [s]

2.5

3.0

3.5

4.0

Another example with odeint will be a damped spring-mass oscillator (2nd order oscillator). The position of
a mass attached to a spring obeys the 2nd order ODE y + 2 eps wo y + wo^2 y = 0 with wo^2 =
k/m being k the spring constant, m the mass and eps=c/(2 m wo) with c the damping coefficient. For a
computing example, the parameters will be:
>>> mass = 0.5 # kg
>>> kspring = 4 # N/m
>>> cviscous = 0.4 # N s/m

so the system will be underdamped because:

>>> eps = cviscous / (2 * mass * np.sqrt(kspring/mass))
>>> eps < 1
True

For the odeint solver the 2nd order equation needs to be transformed in a system of two first-order equations
for the vector Y=(y, y). It will be convenient to define nu = 2 eps wo = c / m and om = wo^2 =
k/m:
>>> nu_coef = cviscous/mass
>>> om_coef = kspring/mass

Thus the function will calculate the velocity and acceleration by:
>>> def calc_deri(yvec, time, nuc, omc):
...
return (yvec[1], -nuc * yvec[1] - omc * yvec[0])
...
>>> time_vec = np.linspace(0, 10, 100)
>>> yarr = odeint(calc_deri, (1, 0), time_vec, args=(nu_coef, om_coef))

The final position and velocity are shown on the following Matplotlib figure:
"""Damped spring-mass oscillator
"""
import numpy as np

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from scipy.integrate import odeint

import pylab as pl
mass = 0.5
kspring = 4
cviscous = 0.4
nu_coef = cviscous / mass
om_coef = kspring / mass
def calc_deri(yvec, time, nuc, omc):
return (yvec[1], -nuc * yvec[1] - omc * yvec[0])
time_vec = np.linspace(0, 10, 100)
yarr = odeint(calc_deri, (1, 0), time_vec, args=(nu_coef, om_coef))
pl.plot(time_vec, yarr[:, 0], label=y)
pl.plot(time_vec, yarr[:, 1], label="y")
pl.legend()

1.5

y
y'

1.0
0.5
0.0
0.5
1.0
1.5
2.0
2.50

10

There is no Partial Differential Equations (PDE) solver in scipy. Some PDE packages are written in Python, such
as fipy or SfePy.

6.8 Fast Fourier transforms: scipy.fftpack

The fftpack module allows to compute fast Fourier transforms. As an illustration, an input signal may look
like:
>>> time_step = 0.1
>>> period = 5.

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>>> time_vec = np.arange(0, 20, time_step)

>>> sig = np.sin(2 * np.pi / period * time_vec) + \
...
np.cos(10 * np.pi * time_vec)

However the observer does not know the signal frequency, only the sampling time step of the signal sig. But
the signal is supposed to come from a real function so the Fourier transform will be symmetric. The fftfreq
function will generate the sampling frequencies and fft will compute the fast Fourier transform:
>>> from scipy import fftpack
>>> sample_freq = fftpack.fftfreq(sig.size, d=time_step)
>>> sig_fft = fftpack.fft(sig)

Nevertheless only the positive part will be used for finding the frequency because the resulting power is symmetric:
>>> pidxs = np.where(sample_freq > 0)
>>> freqs = sample_freq[pidxs]
>>> power = np.abs(sig_fft)[pidxs]
import numpy as np
from scipy import fftpack
import pylab as pl
time_step = 0.1
period = 5.
time_vec = np.arange(0, 20, time_step)
sig = np.sin(2 * np.pi / period * time_vec) + np.cos(10 * np.pi * time_vec)
sample_freq = fftpack.fftfreq(sig.size, d=time_step)
sig_fft = fftpack.fft(sig)
pidxs = np.where(sample_freq > 0)
freqs, power = sample_freq[pidxs], np.abs(sig_fft)[pidxs]
freq = freqs[power.argmax()]
pl.figure()
pl.plot(freqs, power)
pl.ylabel(plower)
pl.xlabel(Frequency [Hz])
axes = pl.axes([0.3, 0.3, 0.5, 0.5])
pl.title(Peak frequency)
pl.plot(freqs[:8], power[:8])
pl.setp(axes, yticks=[])

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100

Peak frequency
80

plower

60
40
20
00

0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45

2
3
Frequency [Hz]

Thus the signal frequency can be found by:

>>> freq = freqs[power.argmax()]
>>> np.allclose(freq, 1./period)
True

Now only the main signal component will be extracted from the Fourier transform:
>>> sig_fft[np.abs(sample_freq) > freq] = 0

The resulting signal can be computed by the ifft function:

>>> main_sig = fftpack.ifft(sig_fft)

The result is shown on the Matplotlib figure:

import numpy as np
from scipy import fftpack
import pylab as pl
time_step = 0.1
period = 5.
time_vec = np.arange(0, 20, time_step)
sig = np.sin(2 * np.pi / period * time_vec) + np.cos(10 * np.pi * time_vec)
sample_freq = fftpack.fftfreq(sig.size, d=time_step)
sig_fft = fftpack.fft(sig)
pidxs = np.where(sample_freq > 0)
freqs, power = sample_freq[pidxs], np.abs(sig_fft)[pidxs]
freq = freqs[power.argmax()]
sig_fft[np.abs(sample_freq) > freq] = 0

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main_sig = fftpack.ifft(sig_fft)
pl.figure()
pl.plot(time_vec, sig)
pl.plot(time_vec, main_sig, linewidth=3)
pl.ylabel(Amplitude)
pl.xlabel(Time [s])

2.0
1.5
1.0
Amplitude

0.5
0.0
0.5
1.0
1.5
2.00

10
Time [s]

15

20

6.9 Interpolation: scipy.interpolate

The scipy.interpolate is useful for fitting a function from experimental data and thus evaluating points
where no measure exists. The module is based on the FITPACK Fortran subroutines from the netlib project.
By imagining experimental data close to a sinus function:
>>> measured_time = np.linspace(0, 1, 10)
>>> noise = (np.random.random(10)*2 - 1) * 1e-1
>>> measures = np.sin(2 * np.pi * measured_time) + noise

The interp1d class can built a linear interpolation function:

>>> from scipy.interpolate import interp1d
>>> linear_interp = interp1d(measured_time, measures)

Then the linear_interp instance needs to be evaluated on time of interest:

>>> computed_time = np.linspace(0, 1, 50)
>>> linear_results = linear_interp(computed_time)

A cubic interpolation can also be selected by providing the kind optional keyword argument:

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>>> cubic_interp = interp1d(measured_time, measures, kind=cubic)

>>> cubic_results = cubic_interp(computed_time)

The results are now gathered on the following Matplotlib figure:

"""Generate the interpolation.png image for the interpolate
section of the Scipy tutorial
"""
import numpy as np
from scipy.interpolate import interp1d
import pylab as pl
measured_time = np.linspace(0, 1, 10)
noise = (np.random.random(10)*2 - 1) * 1e-1
measures = np.sin(2 * np.pi * measured_time) + noise
linear_interp = interp1d(measured_time, measures)
computed_time = np.linspace(0, 1, 50)
linear_results = linear_interp(computed_time)
cubic_interp = interp1d(measured_time, measures, kind=cubic)
cubic_results = cubic_interp(computed_time)
pl.plot(measured_time, measures, o, ms=6, label=measures)
pl.plot(computed_time, linear_results, label=linear interp)
pl.plot(computed_time, cubic_results, label=cubic interp)
pl.legend()

1.0

measures
linear interp
cubic interp

0.5

0.0

0.5

1.00.0

0.2

0.4

0.6

0.8

1.0

scipy.interpolate.interp2d is similar to interp1d, but for 2-D arrays. Note that for the interp
family, the computed time must stay within the measured time range. See the summary exercise on Maximum
wind speed prediction at the Sprog station (page 133) for a more advance spline interpolation example.

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6.10 Optimization and fit: scipy.optimize

Optimization is the problem of finding a numerical solution to a minimization or equality.
The scipy.optimize module provides useful algorithms for function minimization (scalar or multidimensional), curve fitting and root finding.
Example: Minimizing a scalar function using different algorithms
Lets define the following function:
>>> def f(x):
...
return x**2 + 10*np.sin(x)

and plot it:

>>> x = np.arange(-10,10,0.1)
>>> plt.plot(x, f(x))
>>> plt.show()

This function has a global minimum around -1.3 and a local minimum around 3.8.

6.10.1 Local (convex) optimization

The general and efficient way to find a minimum for this function is to conduct a gradient descent starting from a
given initial point. The BFGS algorithm is a good way of doing this:
>>> optimize.fmin_bfgs(f, 0)
Optimization terminated successfully.
Current function value: -7.945823
Iterations: 5
Function evaluations: 24
Gradient evaluations: 8
array([-1.30644003])

This resolution takes 4.11ms on our computer.

The problem with this approach is that, if the function has local minima (is not convex), the algorithm may
find these local minima instead of the global minimum depending on the initial point. If we dont know the
neighborhood of the global minima to choose the initial point, we need to resort to costlier global optimization.

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6.10.2 Global optimization

To find the global minimum, the simplest algorithm is the brute force algorithm, in which the function is evaluated
on each point of a given grid:
>>> from scipy import optimize
>>> grid = (-10, 10, 0.1)
>>> optimize.brute(f, (grid,))
array([-1.30641113])

This approach take 20 ms on our computer.

This simple algorithm becomes very slow as the size of the grid grows, so you should use optimize.brent
instead for scalar functions:
>>> optimize.brent(f)
-1.3064400120612139

To find the local minimum, lets add some constraints on the variable using optimize.fminbound:
>>> # search the minimum only between 0 and 10
>>> optimize.fminbound(f, 0, 10)
array([ 3.83746712])

You can find algorithms with the same functionalities for multi-dimensional problems in scipy.optimize.
See the summary exercise on Non linear least squares curve fitting: application to point extraction in topographical lidar data (page 138) for a more advanced example.

6.11 Image processing: scipy.ndimage

The submodule dedicated to image processing in scipy is scipy.ndimage.
>>> from scipy import ndimage

Image processing routines may be sorted according to the category of processing they perform.

6.11.1 Geometrical transformations on images

Changing orientation, resolution, ..
>>> import scipy
>>> lena = scipy.lena()
>>> shifted_lena = ndimage.shift(lena, (50, 50))
>>> shifted_lena2 = ndimage.shift(lena, (50, 50), mode=nearest)
>>> rotated_lena = ndimage.rotate(lena, 30)
>>> cropped_lena = lena[50:-50, 50:-50]
>>> zoomed_lena = ndimage.zoom(lena, 2)
>>> zoomed_lena.shape
(1024, 1024)

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In [35]: subplot(151)
Out[35]: <matplotlib.axes.AxesSubplot object at 0x925f46c>
In [36]: imshow(shifted_lena, cmap=cm.gray)
Out[36]: <matplotlib.image.AxesImage object at 0x9593f6c>
In [37]: axis(off)
Out[37]: (-0.5, 511.5, 511.5, -0.5)
In [39]: # etc.

6.11.2 Image filtering

>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>

lena = scipy.lena()
import numpy as np
noisy_lena = np.copy(lena)
noisy_lena += lena.std()*0.5*np.random.standard_normal(lena.shape)
blurred_lena = ndimage.gaussian_filter(noisy_lena, sigma=3)
median_lena = ndimage.median_filter(blurred_lena, size=5)
import scipy.signal
wiener_lena = scipy.signal.wiener(blurred_lena, (5,5))

And many other filters in scipy.ndimage.filters and scipy.signal can be applied to images
Exercise
Compare histograms for the different filtered images.

6.11.3 Mathematical morphology

Mathematical morphology is a mathematical theory that stems from set theory. It characterizes and transforms
geometrical structures. Binary (black and white) images, in particular, can be transformed using this theory:
the sets to be transformed are the sets of neighboring non-zero-valued pixels. The theory was also extended to
gray-valued images.

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Elementary mathematical-morphology operations use a structuring element in order to modify other geometrical
structures.
Let us first generate a structuring element
>>> el = ndimage.generate_binary_structure(2, 1)
>>> el
array([[False, True, False],
[ True, True, True],
[False, True, False]], dtype=bool)
>>> el.astype(np.int)
array([[0, 1, 0],
[1, 1, 1],
[0, 1, 0]])

Erosion
>>> a = np.zeros((7,7), dtype=np.int)
>>> a[1:6, 2:5] = 1
>>> a
array([[0, 0, 0, 0, 0, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0]])
>>> ndimage.binary_erosion(a).astype(a.dtype)
array([[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 1, 0, 0, 0],
[0, 0, 0, 1, 0, 0, 0],
[0, 0, 0, 1, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0]])
>>> #Erosion removes objects smaller than the structure
>>> ndimage.binary_erosion(a, structure=np.ones((5,5))).astype(a.dtype)
array([[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0]])

Dilation
>>> a = np.zeros((5, 5))
>>> a[2, 2] = 1
>>> a
array([[ 0., 0., 0., 0.,

0.],

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[ 0., 0., 0., 0., 0.],

[ 0., 0., 1., 0., 0.],
[ 0., 0., 0., 0., 0.],
[ 0., 0., 0., 0., 0.]])
>>> ndimage.binary_dilation(a).astype(a.dtype)
array([[ 0., 0., 0., 0., 0.],
[ 0., 0., 1., 0., 0.],
[ 0., 1., 1., 1., 0.],
[ 0., 0., 1., 0., 0.],
[ 0., 0., 0., 0., 0.]])

Opening
>>> a = np.zeros((5,5), dtype=np.int)
>>> a[1:4, 1:4] = 1; a[4, 4] = 1
>>> a
array([[0, 0, 0, 0, 0],
[0, 1, 1, 1, 0],
[0, 1, 1, 1, 0],
[0, 1, 1, 1, 0],
[0, 0, 0, 0, 1]])
>>> # Opening removes small objects
>>> ndimage.binary_opening(a, structure=np.ones((3,3))).astype(np.int)
array([[0, 0, 0, 0, 0],
[0, 1, 1, 1, 0],
[0, 1, 1, 1, 0],
[0, 1, 1, 1, 0],
[0, 0, 0, 0, 0]])
>>> # Opening can also smooth corners
>>> ndimage.binary_opening(a).astype(np.int)
array([[0, 0, 0, 0, 0],
[0, 0, 1, 0, 0],
[0, 1, 1, 1, 0],
[0, 0, 1, 0, 0],
[0, 0, 0, 0, 0]])

Closing: ndimage.binary_closing
Exercise
Check that opening amounts to eroding, then dilating.
An opening operation removes small structures, while a closing operation fills small holes. Such operation can
therefore be used to clean an image.
>>>
>>>
>>>
>>>
>>>
>>>

a = np.zeros((50, 50))
a[10:-10, 10:-10] = 1
a += 0.25*np.random.standard_normal(a.shape)
mask = a>=0.5
opened_mask = ndimage.binary_opening(mask)
closed_mask = ndimage.binary_closing(opened_mask)

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Exercise
Check that the area of the reconstructed square is smaller than the area of the initial square. (The opposite
would occur if the closing step was performed before the opening).
For gray-valued images, eroding (resp. dilating) amounts to replacing a pixel by the minimal (resp. maximal)
value among pixels covered by the structuring element centered on the pixel of interest.
>>> a = np.zeros((7,7), dtype=np.int)
>>> a[1:6, 1:6] = 3
>>> a[4,4] = 2; a[2,3] = 1
>>> a
array([[0, 0, 0, 0, 0, 0, 0],
[0, 3, 3, 3, 3, 3, 0],
[0, 3, 3, 1, 3, 3, 0],
[0, 3, 3, 3, 3, 3, 0],
[0, 3, 3, 3, 2, 3, 0],
[0, 3, 3, 3, 3, 3, 0],
[0, 0, 0, 0, 0, 0, 0]])
>>> ndimage.grey_erosion(a, size=(3,3))
array([[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 3, 2, 2, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0]])

6.11.4 Measurements on images

Let us first generate a nice synthetic binary image.
>>> x, y = np.indices((100, 100))
>>> sig = np.sin(2*np.pi*x/50.)*np.sin(2*np.pi*y/50.)*(1+x*y/50.**2)**2
>>> mask = sig > 1

Now we look for various information about the objects in the image:
>>> labels, nb = ndimage.label(mask)
>>> nb
8
>>> areas = ndimage.sum(mask, labels, xrange(1, labels.max()+1))
>>> areas
[190.0, 45.0, 424.0, 278.0, 459.0, 190.0, 549.0, 424.0]
>>> maxima = ndimage.maximum(sig, labels, xrange(1, labels.max()+1))
>>> maxima
[1.8023823799830032, 1.1352760475048373, 5.5195407887291426,
2.4961181804217221, 6.7167361922608864, 1.8023823799830032,
16.765472169131161, 5.5195407887291426]
>>> ndimage.find_objects(labels==4)
[(slice(30, 48, None), slice(30, 48, None))]
>>> sl = ndimage.find_objects(labels==4)
>>> imshow(sig[sl[0]])

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See the summary exercise on Image processing application: counting bubbles and unmolten grains (page 142) for
a more advanced example.

6.12 Summary exercises on scientific computing

The summary exercises use mainly Numpy, Scipy and Matplotlib. They first aim at providing real life examples
on scientific computing with Python. Once the groundwork is introduced, the interested user is invited to try some
exercises.

6.12.1 Maximum wind speed prediction at the Sprog station

The exercise goal is to predict the maximum wind speed occurring every 50 years even if no measure exists for
such a period. The available data are only measured over 21 years at the Sprog meteorological station located
in Denmark. First, the statistical steps will be given and then illustrated with functions from the scipy.interpolate
module. At the end the interested readers are invited to compute results from raw data and in a slightly different
approach.
Statistical approach
The annual maxima are supposed to fit a normal probability density function. However such function is not going
to be estimated because it gives a probability from a wind speed maxima. Finding the maximum wind speed
occurring every 50 years requires the opposite approach, the result needs to be found from a defined probability.
That is the quantile function role and the exercise goal will be to find it. In the current model, it is supposed that
the maximum wind speed occurring every 50 years is defined as the upper 2% quantile.
By definition, the quantile function is the inverse of the cumulative distribution function. The latter describes the
probability distribution of an annual maxima. In the exercise, the cumulative probability p_i for a given year
i is defined as p_i = i/(N+1) with N = 21, the number of measured years. Thus it will be possible to
calculate the cumulative probability of every measured wind speed maxima. From those experimental points, the
scipy.interpolate module will be very useful for fitting the quantile function. Finally the 50 years maxima is going
to be evaluated from the cumulative probability of the 2% quantile.
Computing the cumulative probabilities
The annual wind speeds maxima have already been computed and saved in the numpy format in the file maxspeeds.npy, thus they will be loaded by using numpy:
>>> import numpy as np
>>> max_speeds = np.load(data/max-speeds.npy)
>>> years_nb = max_speeds.shape[0]

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Following the cumulative probability definition p_i from the previous section, the corresponding values will be:
>>> cprob = (np.arange(years_nb, dtype=np.float32) + 1)/(years_nb + 1)

and they are assumed to fit the given wind speeds:

>>> sorted_max_speeds = np.sort(max_speeds)

Prediction with UnivariateSpline

In this section the quantile function will be estimated by using the UnivariateSpline class which can
represent a spline from points. The default behavior is to build a spline of degree 3 and points can have
different weights according to their reliability. Variants are InterpolatedUnivariateSpline and
LSQUnivariateSpline on which errors checking is going to change. In case a 2D spline is wanted, the
BivariateSpline class family is provided. All those classes for 1D and 2D splines use the FITPACK Fortran subroutines, thats why a lower library access is available through the splrep and splev functions for
respectively representing and evaluating a spline. Moreover interpolation functions without the use of FITPACK
parameters are also provided for simpler use (see interp1d, interp2d, barycentric_interpolate
and so on).
For the Sprog maxima wind speeds, the UnivariateSpline will be used because a spline of degree 3 seems
to correctly fit the data:
>>> from scipy.interpolate import UnivariateSpline
>>> quantile_func = UnivariateSpline(cprob, sorted_max_speeds)

The quantile function is now going to be evaluated from the full range of probabilities:
>>> nprob = np.linspace(0, 1, 1e2)
>>> fitted_max_speeds = quantile_func(nprob)

2%
In the current model, the maximum wind speed occurring every 50 years is defined as the upper 2% quantile. As
a result, the cumulative probability value will be:
>>> fifty_prob = 1. - 0.02

So the storm wind speed occurring every 50 years can be guessed by:
>>> fifty_wind = quantile_func(fifty_prob)
>>> fifty_wind
array([ 32.97989825])

The results are now gathered on a Matplotlib figure:

"""Generate the image cumulative-wind-speed-prediction.png
for the interpolate section of scipy.rst.
"""
import numpy as np
from scipy.interpolate import UnivariateSpline
import pylab as pl
# since its called from intro/summary-exercises
# we need to ../
max_speeds = np.load(../data/max-speeds.npy)
years_nb = max_speeds.shape[0]
cprob = (np.arange(years_nb, dtype=np.float32) + 1)/(years_nb + 1)
sorted_max_speeds = np.sort(max_speeds)
speed_spline = UnivariateSpline(cprob, sorted_max_speeds)
nprob = np.linspace(0, 1, 1e2)

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fitted_max_speeds = speed_spline(nprob)
fifty_prob = 1. - 0.02
fifty_wind = speed_spline(fifty_prob)
pl.figure()
pl.plot(sorted_max_speeds, cprob, o)
pl.plot(fitted_max_speeds, nprob, g--)
pl.plot([fifty_wind], [fifty_prob], o, ms=8., mfc=y, mec=y)
pl.text(30, 0.05, $V_{50} = %.2f \, m/s$ % fifty_wind)
pl.plot([fifty_wind, fifty_wind], [pl.axis()[2], fifty_prob], k--)
pl.xlabel(Annual wind speed maxima [$m/s$])
pl.ylabel(Cumulative probability)

1.0

Cumulative probability

0.8
0.6
0.4
0.2
0.020

V50 =32.98 m/s

22

24
26
28
30
Annual wind speed maxima [m/s]

32

34

Exercise with the Gumbell distribution

The interested readers are now invited to make an exercise by using the wind speeds measured over 21 years.
The measurement period is around 90 minutes (the original period was around 10 minutes but the file size has
been reduced for making the exercise setup easier). The data are stored in numpy format inside the file sprogwindspeeds.npy. Do not look at the source code for the plots until you have completed the exercise.
The first step will be to find the annual maxima by using numpy and plot them as a matplotlib bar figure.
"""Generate the exercise results on the Gumbell distribution
"""
import numpy as np
from scipy.interpolate import UnivariateSpline
import pylab as pl

def gumbell_dist(arr):

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return -np.log(-np.log(arr))
years_nb = 21
wspeeds = np.load(../data/sprog-windspeeds.npy)
max_speeds = np.array([arr.max() for arr in np.array_split(wspeeds, years_nb)])
sorted_max_speeds = np.sort(max_speeds)
cprob = (np.arange(years_nb, dtype=np.float32) + 1)/(years_nb + 1)
gprob = gumbell_dist(cprob)
speed_spline = UnivariateSpline(gprob, sorted_max_speeds, k=1)
nprob = gumbell_dist(np.linspace(1e-3, 1-1e-3, 1e2))
fitted_max_speeds = speed_spline(nprob)
fifty_prob = gumbell_dist(49./50.)
fifty_wind = speed_spline(fifty_prob)
pl.figure()
pl.bar(np.arange(years_nb) + 1, max_speeds)
pl.axis(tight)
pl.xlabel(Year)
pl.ylabel(Annual wind speed maxima [$m/s$])

Annual wind speed maxima [m/s]

30
25
20
15
10
5
0

10

Year

15

20

The second step will be to use the Gumbell distribution on cumulative probabilities p_i defined as -log(
-log(p_i) ) for fitting a linear quantile function (remember that you can define the degree of the
UnivariateSpline). Plotting the annual maxima versus the Gumbell distribution should give you
the following figure.
"""Generate the exercise results on the Gumbell distribution
"""
import numpy as np
from scipy.interpolate import UnivariateSpline
import pylab as pl

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def gumbell_dist(arr):
return -np.log(-np.log(arr))
years_nb = 21
wspeeds = np.load(../data/sprog-windspeeds.npy)
max_speeds = np.array([arr.max() for arr in np.array_split(wspeeds, years_nb)])
sorted_max_speeds = np.sort(max_speeds)
cprob = (np.arange(years_nb, dtype=np.float32) + 1)/(years_nb + 1)
gprob = gumbell_dist(cprob)
speed_spline = UnivariateSpline(gprob, sorted_max_speeds, k=1)
nprob = gumbell_dist(np.linspace(1e-3, 1-1e-3, 1e2))
fitted_max_speeds = speed_spline(nprob)
fifty_prob = gumbell_dist(49./50.)
fifty_wind = speed_spline(fifty_prob)
pl.figure()
pl.plot(sorted_max_speeds, gprob, o)
pl.plot(fitted_max_speeds, nprob, g--)
pl.plot([fifty_wind], [fifty_prob], o, ms=8., mfc=y, mec=y)
pl.plot([fifty_wind, fifty_wind], [pl.axis()[2], fifty_prob], k--)
pl.text(35, -1, r$V_{50} = %.2f \, m/s$ % fifty_wind)
pl.xlabel(Annual wind speed maxima [$m/s$])
pl.ylabel(Gumbell cumulative probability)

Gumbell cumulative probability

6
5
4
3
2
1
0
1
220

V50 =34.23 m/s

25

30
35
Annual wind speed maxima [m/s]

40

45

The last step will be to find 34.23 m/s for the maximum wind speed occurring every 50 years.

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6.12.2 Non linear least squares curve fitting: application to point extraction in
topographical lidar data
The goal of this exercise is to fit a model to some data. The data used in this tutorial are lidar data and are described
in details in the following introductory paragraph. If youre impatient and want to practice now, please skip it and
go directly to Loading and visualization (page 138).
Introduction
Lidars systems are optical rangefinders that analyze property of scattered light to measure distances. Most of them
emit a short light impulsion towards a target and record the reflected signal. This signal is then processed to extract
the distance between the lidar system and the target.
Topographical lidar systems are such systems embedded in airborne platforms. They measure distances between
the platform and the Earth, so as to deliver information on the Earths topography (see [Mallet09] (page 287) for
more details).
In this tutorial, the goal is to analyze the waveform recorded by the lidar system 1 . Such a signal contains peaks
whose center and amplitude permit to compute the position and some characteristics of the hit target. When the
footprint of the laser beam is around 1m on the Earth surface, the beam can hit multiple targets during the two-way
propagation (for example the ground and the top of a tree or building). The sum of the contributions of each target
hit by the laser beam then produces a complex signal with multiple peaks, each one containing information about
one target.
One state of the art method to extract information from these data is to decompose them in a sum of Gaussian
functions where each function represents the contribution of a target hit by the laser beam.
Therefore, we use the scipy.optimize module to fit a waveform to one or a sum of Gaussian functions.
Loading and visualization
Load the first waveform using:
>>> import numpy as np
>>> waveform_1 = np.load(data/waveform_1.npy)

and visualize it:

>>>
>>>
>>>
>>>

import matplotlib.pyplot as plt

t = np.arange(len(waveform_1))
plt.plot(t, waveform_1)
plt.show()

1 The data used for this tutorial are part of the demonstration data available for the FullAnalyze software and were kindly provided by the
GIS DRAIX.

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As you can notice, this waveform is a 80-bin-length signal with a single peak.
Fitting a waveform with a simple Gaussian model
The signal is very simple and can be modeled as a single Gaussian function and an offset corresponding to the
background noise. To fit the signal with the function, we must:
define the model
propose an initial solution
call scipy.optimize.leastsq

Model
A Gaussian function defined by
( 
2 )
t
B + A exp

can be defined in python by:

>>> def model(t, coeffs):
...
return coeffs[0] + coeffs[1] * np.exp( - ((t-coeffs[2])/coeffs[3])**2 )

where
coeffs[0] is B (noise)

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coeffs[1] is A (amplitude)
coeffs[2] is (center)
coeffs[3] is (width)

Initial solution
An approximative initial solution that we can find from looking at the graph is for instance:
>>> x0 = np.array([3, 30, 15, 1], dtype=float)

Fit
scipy.optimize.leastsq minimizes the sum of squares of the function given as an argument. Basically,
the function to minimize is the residuals (the difference between the data and the model):
>>> def residuals(coeffs, y, t):
...
return y - model(t, coeffs)

So lets get our solution by calling scipy.optimize.leastsq with the following arguments:
the function to minimize
an initial solution
the additional arguments to pass to the function
>>> from scipy.optimize import leastsq
>>> x, flag = leastsq(residuals, x0, args=(waveform_1, t))
>>> print x
[ 2.70363341 27.82020742 15.47924562
3.05636228]

And visualize the solution:

>>> plt.plot(t, waveform_1, t, model(t, x))
>>> plt.legend([waveform, model])
>>> plt.show()

Remark: from scipy v0.8 and above, you should rather use scipy.optimize.curve_fit which takes the
model and the data as arguments, so you dont need to define the residuals any more.
Going further
Try with a more complex waveform (for instance data/waveform_2.npy) that contains three significant peaks. You must adapt the model which is now a sum of Gaussian functions instead of only one
Gaussian peak.

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In some cases, writing an explicit function to compute the Jacobian is faster than letting leastsq estimate it numerically. Create a function to compute the Jacobian of the residuals and use it as an input for
leastsq.
When we want to detect very small peaks in the signal, or when the initial guess is too far from a good
solution, the result given by the algorithm is often not satisfying. Adding constraints to the parameters of
the model enables to overcome such limitations. An example of a priori knowledge we can add is the sign
of our variables (which are all positive).
With the following initial solution:
>>> x0 = np.array([3, 50, 20, 1], dtype=float)

compare the result of scipy.optimize.leastsq and what

scipy.optimize.fmin_slsqp when adding boundary constraints.

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can

get

with

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6.12.3 Image processing application: counting bubbles and unmolten grains

Statement of the problem

1. Open the image file MV_HFV_012.jpg and display it. Browse through the keyword arguments in the docstring
of imshow to display the image with the right orientation (origin in the bottom left corner, and not the upper
left corner as for standard arrays).
This Scanning Element Microscopy image shows a glass sample (light gray matrix) with some bubbles (on black)
and unmolten sand grains (dark gray). We wish to determine the fraction of the sample covered by these three
phases, and to estimate the typical size of sand grains and bubbles, their sizes, etc.
2. Crop the image to remove the lower panel with measure information.
3. Slightly filter the image with a median filter in order to refine its histogram. Check how the histogram changes.
4. Using the histogram of the filtered image, determine thresholds that allow to define masks for sand pixels, glass
pixels and bubble pixels. Other option (homework): write a function that determines automatically the thresholds
from the minima of the histogram.
5. Display an image in which the three phases are colored with three different colors.
6. Use mathematical morphology to clean the different phases.
7. Attribute labels to all bubbles and sand grains, and remove from the sand mask grains that are smaller than 10
pixels. To do so, use ndimage.sum or np.bincount to compute the grain sizes.
8. Compute the mean size of bubbles.

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Proposed solution

6.12.4 Example of solution for the image processing exercise: unmolten grains
in glass

1. Open the image file MV_HFV_012.jpg and display it. Browse through the keyword arguments in the
docstring of imshow to display the image with the right orientation (origin in the bottom left corner, and
not the upper left corner as for standard arrays).
>>> dat = imread(MV_HFV_012.jpg)

2. Crop the image to remove the lower panel with measure information.
>>> dat = dat[60:]

3. Slightly filter the image with a median filter in order to refine its histogram. Check how the histogram
changes.
>>> filtdat = ndimage.median_filter(dat, size=(7,7))
>>> hi_dat = np.histogram(dat, bins=np.arange(256))
>>> hi_filtdat = np.histogram(filtdat, bins=np.arange(256))

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4. Using the histogram of the filtered image, determine thresholds that allow to define masks for sand pixels,
glass pixels and bubble pixels. Other option (homework): write a function that determines automatically
the thresholds from the minima of the histogram.
>>> void = filtdat <= 50
>>> sand = np.logical_and(filtdat>50, filtdat<=114)
>>> glass = filtdat > 114

5. Display an image in which the three phases are colored with three different colors.
>>> phases = void.astype(np.int) + 2*glass.astype(np.int) +\
3*sand.astype(np.int)

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6. Use mathematical morphology to clean the different phases.

>>> sand_op = ndimage.binary_opening(sand, iterations=2)

7. Attribute labels to all bubbles and sand grains, and remove from the sand mask grains that are smaller than
10 pixels. To do so, use ndimage.sum or np.bincount to compute the grain sizes.
>>>
>>>
...
>>>
>>>

sand_labels, sand_nb = ndimage.label(sand_op)

sand_areas = np.array(ndimage.sum(sand_op, sand_labels,\
np.arange(sand_labels.max()+1)))
mask = sand_areas>100
remove_small_sand = mask[sand_labels.ravel()].reshape(sand_labels.shape)

8. Compute the mean size of bubbles.

>>>
>>>
>>>
>>>

bubbles_labels, bubbles_nb = ndimage.label(void)

bubbles_areas = np.bincount(bubbles_labels.ravel())[1:]
mean_bubble_size = bubbles_areas.mean()
median_bubble_size = np.median(bubbles_areas)

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>>> mean_bubble_size, median_bubble_size

(1699.875, 65.0)

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Part II

Advanced topics

147

CHAPTER 7

Advanced Python Constructs

author Zbigniew Jedrzejewski-Szmek

This chapter is about some features of the Python language which can be considered advanced in the sense that
not every language has them, and also in the sense that they are more useful in more complicated programs or
libraries, but not in the sense of being particularly specialized, or particularly complicated.
It is important to underline that this chapter is purely about the language itself about features supported through
special syntax complemented by functionality of the Python stdlib, which could not be implemented through
clever external modules.
The process of developing the Python programming language, its syntax, is unique because it is very transparent,
proposed changes are evaluated from various angles and discussed on public mailing lists, and the final decision
takes into account the balance between the importance of envisioned use cases, the burden of carrying more
language features, consistency with the rest of the syntax, and whether the proposed variant is the easiest to read,
write, and understand. This process is formalised in Python Enhancement Proposals PEPs. As a result, features
described in this chapter were added after it was shown that they indeed solve real problems and that their use is
as simple as possible.
Chapters contents
Iterators, generator expressions and generators (page 149)
Iterators (page 149)
Generator expressions (page 150)
Generators (page 150)
Bidirectional communication (page 151)
Chaining generators (page 153)
Decorators (page 153)
Replacing or tweaking the original object (page 154)
Decorators implemented as classes and as functions (page 154)
Copying the docstring and other attributes of the original function (page 156)
Examples in the standard library (page 157)
Deprecation of functions (page 159)
A while-loop removing decorator (page 159)
A plugin registration system (page 160)
More examples and reading (page 161)
Context managers (page 161)
Catching exceptions (page 162)
Using generators to define context managers (page 163)

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7.1 Iterators, generator expressions and generators

7.1.1 Iterators
Simplicity
Duplication of effort is wasteful, and replacing the various home-grown approaches with a standard feature
usually ends up making things more readable, and interoperable as well.
Guido van Rossum Adding Optional Static Typing to Python
An iterator is an object adhering to the iterator protocol basically this means that it has a next method,
which, when called, returns the next item in the sequence, and when theres nothing to return, raises the
StopIteration exception.
An iterator object allows to loop just once. It holds the state (position) of a single iteration, or from the other side,
each loop over a sequence requires a single iterator object. This means that we can iterate over the same sequence
more than once concurrently. Separating the iteration logic from the sequence allows us to have more than one
way of iteration.
Calling the __iter__ method on a container to create an iterator object is the most straightforward way to get
hold of an iterator. The iter function does that for us, saving a few keystrokes.
>>> nums = [1,2,3]
# note that ... varies: these are different objects
>>> iter(nums)
<listiterator object at ...>
>>> nums.__iter__()
<listiterator object at ...>
>>> nums.__reversed__()
<listreverseiterator object at ...>
>>> it = iter(nums)
>>> next(it)
# next(obj) simply calls obj.next()
1
>>> it.next()
2
>>> next(it)
3
>>> next(it)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
StopIteration

When used in a loop, StopIteration is swallowed and causes the loop to finish. But with explicit invocation,
we can see that once the iterator is exhausted, accessing it raises an exception.
Using the for..in loop also uses the __iter__ method. This allows us to transparently start the iteration over a
sequence. But if we already have the iterator, we want to be able to use it in an for loop in the same way. In order
to achieve this, iterators in addition to next are also required to have a method called __iter__ which returns
the iterator (self).
Support for iteration is pervasive in Python: all sequences and unordered containers in the standard library allow
this. The concept is also stretched to other things: e.g. file objects support iteration over lines.
>>> f = open(/etc/fstab)
>>> f is f.__iter__()
True

The file is an iterator itself and its __iter__ method doesnt create a separate object: only a single thread of
sequential access is allowed.

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7.1.2 Generator expressions

A second way in which iterator objects are created is through generator expressions, the basis for list comprehensions. To increase clarity, a generator expression must always be enclosed in parentheses or an expression. If
round parentheses are used, then a generator iterator is created. If rectangular parentheses are used, the process is
short-circuited and we get a list.
>>> (i for
<generator
>>> [i for
[1, 2, 3]
>>> list(i
[1, 2, 3]

i in nums)
object <genexpr> at 0x...>
i in nums]
for i in nums)

In Python 2.7 and 3.x the list comprehension syntax was extended to dictionary and set comprehensions. A
set is created when the generator expression is enclosed in curly braces. A dict is created when the generator
expression contains pairs of the form key:value:
>>> {i for i in range(3)}
set([0, 1, 2])
>>> {i:i**2 for i in range(3)}
{0: 0, 1: 1, 2: 4}

If you are stuck at some previous Python version, the syntax is only a bit worse:
>>> set(i for i in abc)
set([a, c, b])
>>> dict((i, ord(i)) for i in abc)
{a: 97, c: 99, b: 98}

Generator expression are fairly simple, not much to say here. Only one gotcha should be mentioned: in old
Pythons the index variable (i) would leak, and in versions >= 3 this is fixed.

7.1.3 Generators
Generators
A generator is a function that produces a sequence of results instead of a single value.
David Beazley A Curious Course on Coroutines and Concurrency
A third way to create iterator objects is to call a generator function. A generator is a function containing the
keyword yield. It must be noted that the mere presence of this keyword completely changes the nature of the
function: this yield statement doesnt have to be invoked, or even reachable, but causes the function to be
marked as a generator. When a normal function is called, the instructions contained in the body start to be
executed. When a generator is called, the execution stops before the first instruction in the body. An invocation
of a generator function creates a generator object, adhering to the iterator protocol. As with normal function
invocations, concurrent and recursive invocations are allowed.
When next is called, the function is executed until the first yield. Each encountered yield statement gives a
value becomes the return value of next. After executing the yield statement, the execution of this function is
suspended.
>>> def f():
...
yield 1
...
yield 2
>>> f()
<generator object f at 0x...>
>>> gen = f()
>>> gen.next()
1

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>>> gen.next()
2
>>> gen.next()
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
StopIteration

Lets go over the life of the single invocation of the generator function.
>>> def f():
...
print("-...
yield 3
...
print("-...
yield 4
...
print("->>> gen = f()
>>> next(gen)
-- start -3
>>> next(gen)
-- middle -4
>>> next(gen)
-- finished -Traceback (most
...
StopIteration

start --")
middle --")
finished --")

recent call last):

Contrary to a normal function, where executing f() would immediately cause the first print to be executed,
gen is assigned without executing any statements in the function body. Only when gen.next() is invoked
by next, the statements up to the first yield are executed. The second next prints -- middle -- and
execution halts on the second yield. The third next prints -- finished -- and falls of the end of the
function. Since no yield was reached, an exception is raised.
What happens with the function after a yield, when the control passes to the caller? The state of each generator
is stored in the generator object. From the point of view of the generator function, is looks almost as if it was
running in a separate thread, but this is just an illusion: execution is strictly single-threaded, but the interpreter
keeps and restores the state in between the requests for the next value.
Why are generators useful? As noted in the parts about iterators, a generator function is just a different way to
create an iterator object. Everything that can be done with yield statements, could also be done with next
methods. Nevertheless, using a function and having the interpreter perform its magic to create an iterator has
advantages. A function can be much shorter than the definition of a class with the required next and __iter__
methods. What is more important, it is easier for the author of the generator to understand the state which is
kept in local variables, as opposed to instance attributes, which have to be used to pass data between consecutive
invocations of next on an iterator object.
A broader question is why are iterators useful? When an iterator is used to power a loop, the loop becomes very
simple. The code to initialise the state, to decide if the loop is finished, and to find the next value is extracted into
a separate place. This highlights the body of the loop the interesting part. In addition, it is possible to reuse the
iterator code in other places.

7.1.4 Bidirectional communication

Each yield statement causes a value to be passed to the caller. This is the reason for the introduction of generators
by PEP 255 (implemented in Python 2.2). But communication in the reverse direction is also useful. One obvious
way would be some external state, either a global variable or a shared mutable object. Direct communication is
possible thanks to PEP 342 (implemented in 2.5). It is achieved by turning the previously boring yield statement
into an expression. When the generator resumes execution after a yield statement, the caller can call a method
on the generator object to either pass a value into the generator, which then is returned by the yield statement,
or a different method to inject an exception into the generator.

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The first of the new methods is send(value), which is similar to next(), but passes value into the generator
to be used for the value of the yield expression. In fact, g.next() and g.send(None) are equivalent.
The second of the new methods is throw(type, value=None, traceback=None) which is equivalent
to:
raise type, value, traceback

at the point of the yield statement.

Unlike raise (which immediately raises an exception from the current execution point), throw() first resumes
the generator, and only then raises the exception. The word throw was picked because it is suggestive of putting
the exception in another location, and is associated with exceptions in other languages.
What happens when an exception is raised inside the generator? It can be either raised explicitly or when executing
some statements or it can be injected at the point of a yield statement by means of the throw() method.
In either case, such an exception propagates in the standard manner: it can be intercepted by an except or
finally clause, or otherwise it causes the execution of the generator function to be aborted and propagates in
the caller.
For completeness sake, its worth mentioning that generator iterators also have a close() method, which can
be used to force a generator that would otherwise be able to provide more values to finish immediately. It allows
the generator __del__ method to destroy objects holding the state of generator.
Lets define a generator which just prints what is passed in through send and throw.
>>> import itertools
>>> def g():
...
print --start--
...
for i in itertools.count():
...
print --yielding {}--.format(i)
...
try:
...
ans = yield i
...
except GeneratorExit:
...
print --closing--
...
raise
...
except Exception as e:
...
print --yield raised {!r}--.format(e)
...
else:
...
print --yield returned {!r}--.format(ans)
>>> it = g()
>>> next(it)
--start---yielding 0-0
>>> it.send(11)
--yield returned 11---yielding 1-1
>>> it.throw(IndexError)
--yield raised IndexError()---yielding 2-2
>>> it.close()
--closing--

Note: next or __next__?

In Python 2.x, the iterator method to retrieve the next value is called next. It is invoked implicitly through the
global function next, which means that it should be called __next__. Just like the global function iter
calls __iter__. This inconsistency is corrected in Python 3.x, where it.next becomes it.__next__.
For other generator methods send and throw the situation is more complicated, because they are not
called implicitly by the interpreter. Nevertheless, theres a proposed syntax extension to allow continue to take
an argument which will be passed to send of the loops iterator. If this extension is accepted, its likely that
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gen.send will become gen.__send__. The last of generator methods, close, is pretty obviously named
incorrectly, because it is already invoked implicitly.

7.1.5 Chaining generators

Note: This is a preview of PEP 380 (not yet implemented, but accepted for Python 3.3).
Lets say we are writing a generator and we want to yield a number of values generated by a second generator,
a subgenerator. If yielding of values is the only concern, this can be performed without much difficulty using a
loop such as
subgen = some_other_generator()
for v in subgen:
yield v

However, if the subgenerator is to interact properly with the caller in the case of calls to send(), throw()
and close(), things become considerably more difficult. The yield statement has to be guarded by a
try..except..finally structure similar to the one defined in the previous section to debug the generator function. Such code is provided in :pep:380#id13, here it suffices to say that new syntax to properly yield from a
subgenerator is being introduced in Python 3.3:
yield from some_other_generator()

This behaves like the explicit loop above, repeatedly yielding values from some_other_generator until it is
exhausted, but also forwards send, throw and close to the subgenerator.

7.2 Decorators
Summary
This amazing feature appeared in the language almost apologetically and with concern that it might not be
that useful.
Bruce Eckel An Introduction to Python Decorators
Since a function or a class are objects, they can be passed around. Since they are mutable objects, they can be
modified. The act of altering a function or class object after it has been constructed but before is is bound to its
name is called decorating.
There are two things hiding behind the name decorator one is the function which does the work of decorating,
i.e. performs the real work, and the other one is the expression adhering to the decorator syntax, i.e. an at-symbol
and the name of the decorating function.
Function can be decorated by using the decorator syntax for functions:
@decorator
def function():
pass

#
#

A function is defined in the standard way.

An expression starting with @ placed before the function definition is the decorator . The part after @ must
be a simple expression, usually this is just the name of a function or class. This part is evaluated first, and
after the function defined below is ready, the decorator is called with the newly defined function object as
the single argument. The value returned by the decorator is attached to the original name of the function.
Decorators can be applied to functions and to classes. For classes the semantics are identical the original class
definition is used as an argument to call the decorator and whatever is returned is assigned under the original name.
Before the decorator syntax was implemented (PEP 318), it was possible to achieve the same effect by assigning
the function or class object to a temporary variable and then invoking the decorator explicitly and then assigning
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the return value to the name of the function. This sound like more typing, and it is, and also the name of the
decorated function dubbling as a temporary variable must be used at least three times, which is prone to errors.
Nevertheless, the example above is equivalent to:
def function():
pass
function = decorator(function)

#
#

Decorators can be stacked the order of application is bottom-to-top, or inside-out. The semantics are such
that the originally defined function is used as an argument for the first decorator, whatever is returned by the first
decorator is used as an argument for the second decorator, ..., and whatever is returned by the last decorator is
attached under the name of the original function.
The decorator syntax was chosen for its readability. Since the decorator is specified before the header of the
function, it is obvious that its is not a part of the function body and its clear that it can only operate on the whole
function. Because the expression is prefixed with @ is stands out and is hard to miss (in your face, according to
the PEP :) ). When more than one decorator is applied, each one is placed on a separate line in an easy to read
way.

7.2.1 Replacing or tweaking the original object

Decorators can either return the same function or class object or they can return a completely different object.
In the first case, the decorator can exploit the fact that function and class objects are mutable and add attributes,
e.g. add a docstring to a class. A decorator might do something useful even without modifying the object, for
example register the decorated class in a global registry. In the second case, virtually anything is possible: when
a something different is substituted for the original function or class, the new object can be completely different.
Nevertheless, such behaviour is not the purpose of decorators: they are intended to tweak the decorated object, not
do something unpredictable. Therefore, when a function is decorated by replacing it with a different function,
the new function usually calls the original function, after doing some preparatory work. Likewise, when a class is
decorated by replacing if with a new class, the new class is usually derived from the original class. When the
purpose of the decorator is to do something every time, like to log every call to a decorated function, only the
second type of decorators can be used. On the other hand, if the first type is sufficient, it is better to use it, because
it is simpler.

7.2.2 Decorators implemented as classes and as functions

The only requirement on decorators is that they can be called with a single argument. This means that decorators
can be implemented as normal functions, or as classes with a __call__ method, or in theory, even as lambda
functions.
Lets compare the function and class approaches. The decorator expression (the part after @) can be either just a
name, or a call. The bare-name approach is nice (less to type, looks cleaner, etc.), but is only possible when no
arguments are needed to customise the decorator. Decorators written as functions can be used in those two cases:
>>> def simple_decorator(function):
...
print "doing decoration"
...
return function
>>> @simple_decorator
... def function():
...
print "inside function"
doing decoration
>>> function()
inside function
>>> def decorator_with_arguments(arg):
...
print "defining the decorator"
...
def _decorator(function):
...
# in this inner function, arg is available too
...
print "doing decoration,", arg
...
return function

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...
return _decorator
>>> @decorator_with_arguments("abc")
... def function():
...
print "inside function"
defining the decorator
doing decoration, abc
>>> function()
inside function

The two trivial decorators above fall into the category of decorators which return the original function. If they
were to return a new function, an extra level of nestedness would be required. In the worst case, three levels of
nested functions.
>>> def replacing_decorator_with_args(arg):
...
print "defining the decorator"
...
def _decorator(function):
...
# in this inner function, arg is available too
...
print "doing decoration,", arg
...
def _wrapper(*args, **kwargs):
...
print "inside wrapper,", args, kwargs
...
return function(*args, **kwargs)
...
return _wrapper
...
return _decorator
>>> @replacing_decorator_with_args("abc")
... def function(*args, **kwargs):
...
print "inside function,", args, kwargs
...
return 14
defining the decorator
doing decoration, abc
>>> function(11, 12)
inside wrapper, (11, 12) {}
inside function, (11, 12) {}
14

The _wrapper function is defined to accept all positional and keyword arguments. In general we cannot know
what arguments the decorated function is supposed to accept, so the wrapper function just passes everything to the
wrapped function. One unfortunate consequence is that the apparent argument list is misleading.
Compared to decorators defined as functions, complex decorators defined as classes are simpler. When an object
is created, the __init__ method is only allowed to return None, and the type of the created object cannot be
changed. This means that when a decorator is defined as a class, it doesnt make much sense to use the argumentless form: the final decorated object would just be an instance of the decorating class, returned by the constructor
call, which is not very useful. Therefore its enough to discuss class-based decorators where arguments are given
in the decorator expression and the decorator __init__ method is used for decorator construction.
>>> class decorator_class(object):
...
def __init__(self, arg):
...
# this method is called in the decorator expression
...
print "in decorator init,", arg
...
self.arg = arg
...
def __call__(self, function):
...
# this method is called to do the job
...
print "in decorator call,", self.arg
...
return function
>>> deco_instance = decorator_class(foo)
in decorator init, foo
>>> @deco_instance
... def function(*args, **kwargs):
...
print "in function,", args, kwargs
in decorator call, foo
>>> function()
in function, () {}

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Contrary to normal rules (PEP 8) decorators written as classes behave more like functions and therefore their
name often starts with a lowercase letter.
In reality, it doesnt make much sense to create a new class just to have a decorator which returns the original
function. Objects are supposed to hold state, and such decorators are more useful when the decorator returns a
new object.
>>> class replacing_decorator_class(object):
...
def __init__(self, arg):
...
# this method is called in the decorator expression
...
print "in decorator init,", arg
...
self.arg = arg
...
def __call__(self, function):
...
# this method is called to do the job
...
print "in decorator call,", self.arg
...
self.function = function
...
return self._wrapper
...
def _wrapper(self, *args, **kwargs):
...
print "in the wrapper,", args, kwargs
...
return self.function(*args, **kwargs)
>>> deco_instance = replacing_decorator_class(foo)
in decorator init, foo
>>> @deco_instance
... def function(*args, **kwargs):
...
print "in function,", args, kwargs
in decorator call, foo
>>> function(11, 12)
in the wrapper, (11, 12) {}
in function, (11, 12) {}

A decorator like this can do pretty much anything, since it can modify the original function object and mangle the
arguments, call the original function or not, and afterwards mangle the return value.

7.2.3 Copying the docstring and other attributes of the original function
When a new function is returned by the decorator to replace the original function, an unfortunate consequence
is that the original function name, the original docstring, the original argument list are lost. Those attributes of
the original function can partially be transplanted to the new function by setting __doc__ (the docstring),
__module__ and __name__ (the full name of the function), and __annotations__ (extra information
about arguments and the return value of the function available in Python 3). This can be done automatically by
using functools.update_wrapper.
functools.update_wrapper(wrapper, wrapped)
Update a wrapper function to look like the wrapped function.
>>>
>>>
...
...
...
...
...
...
...
...
>>>
...
...
...

import functools
def better_replacing_decorator_with_args(arg):
print "defining the decorator"
def _decorator(function):
print "doing decoration,", arg
def _wrapper(*args, **kwargs):
print "inside wrapper,", args, kwargs
return function(*args, **kwargs)
return functools.update_wrapper(_wrapper, function)
return _decorator
@better_replacing_decorator_with_args("abc")
def function():
"extensive documentation"
print "inside function"

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...
return 14
defining the decorator
doing decoration, abc
>>> function
<function function at 0x...>
>>> print function.__doc__
extensive documentation

One important thing is missing from the list of attributes which can be copied to the replacement function: the argument list. The default values for arguments can be modified through the __defaults__,
__kwdefaults__ attributes, but unfortunately the argument list itself cannot be set as an attribute. This means
that help(function) will display a useless argument list which will be confusing for the user of the function.
An effective but ugly way around this problem is to create the wrapper dynamically, using eval. This can be
automated by using the external decorator module. It provides support the decorator decorator, which
takes a wrapper and turns it into a decorator which preserves the function signature.
To sum things up, decorators should always use functools.update_wrapper or some other means of
copying function attributes.

7.2.4 Examples in the standard library

First, it should be mentioned that theres a number of useful decorators available in the standard library. There are
three decorators which really form a part of the language:
classmethod causes a method to become a class method, which means that it can be invoked without
creating an instance of the class. When a normal method is invoked, the interpreter inserts the instance
object as the first positional parameter, self. When a class method is invoked, the class itself is given as
the first parameter, often called cls.
Class methods are still accessible through the class namespace, so they dont pollute the modules namespace. Class methods can be used to provide alternative constructors:
class Array(object):
def __init__(self, data):
self.data = data
@classmethod
def fromfile(cls, file):
data = numpy.load(file)
return cls(data)

This is cleaner then using a multitude of flags to __init__.

staticmethod is applied to methods to make them static, i.e. basically a normal function, but accessible through the class namespace. This can be useful when the function is only needed inside this class (its
name would then be prefixed with _), or when we want the user to think of the method as connected to the
class, despite an implementation which doesnt require this.
property is the pythonic answer to the problem of getters and setters. A method decorated with
property becomes a getter which is automatically called on attribute access.
>>> class A(object):
...
@property
...
def a(self):
...
"an important attribute"
...
return "a value"
>>> A.a
<property object at 0x...>
>>> A().a
a value

In this example, A.a is an read-only attribute. It is also documented: help(A) includes the docstring for
attribute a taken from the getter method. Defining a as a property allows it to be a calculated on the fly, and
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has the side effect of making it read-only, because no setter is defined.

To have a setter and a getter, two methods are required, obviously. Since Python 2.6 the following syntax is
preferred:
class Rectangle(object):
def __init__(self, edge):
self.edge = edge
@property
def area(self):
"""Computed area.
Setting this updates the edge length to the proper value.
"""
return self.edge**2
@area.setter
def area(self, area):
self.edge = area ** 0.5

The way that this works, is that the property decorator replaces the getter method with a property object.
This object in turn has three methods, getter, setter, and deleter, which can be used as decorators.
Their job is to set the getter, setter and deleter of the property object (stored as attributes fget, fset, and
fdel). The getter can be set like in the example above, when creating the object. When defining the setter,
we already have the property object under area, and we add the setter to it by using the setter method.
All this happens when we are creating the class.
Afterwards, when an instance of the class has been created, the property object is special. When the interpreter executes attribute access, assignment, or deletion, the job is delegated to the methods of the property
object.
To make everything crystal clear, lets define a debug example:
>>> class D(object):
...
@property
...
def a(self):
...
print "getting", 1
...
return 1
...
@a.setter
...
def a(self, value):
...
print "setting", value
...
@a.deleter
...
def a(self):
...
print "deleting"
>>> D.a
<property object at 0x...>
>>> D.a.fget
<function a at 0x...>
>>> D.a.fset
<function a at 0x...>
>>> D.a.fdel
<function a at 0x...>
>>> d = D()
# ... varies, this is not the same a function
>>> d.a
getting 1
1
>>> d.a = 2
setting 2
>>> del d.a
deleting
>>> d.a
getting 1
1

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Properties are a bit of a stretch for the decorator syntax. One of the premises of the decorator syntax that
the name is not duplicated is violated, but nothing better has been invented so far. It is just good style to
use the same name for the getter, setter, and deleter methods.
Some newer examples include:
functools.lru_cache memoizes an arbitrary function maintaining a limited cache of arguments:answer pairs (Python 3.2)
functools.total_ordering is a class decorator which fills in missing ordering methods (__lt__,
__gt__, __le__, ...) based on a single available one (Python 2.7).

7.2.5 Deprecation of functions

Lets say we want to print a deprecation warning on stderr on the first invocation of a function we dont like
anymore. If we dont want to modify the function, we can use a decorator:
class deprecated(object):
"""Print a deprecation warning once on first use of the function.
>>> @deprecated()
# doctest: +SKIP
... def f():
...
pass
>>> f()
# doctest: +SKIP
f is deprecated
"""
def __call__(self, func):
self.func = func
self.count = 0
return self._wrapper
def _wrapper(self, *args, **kwargs):
self.count += 1
if self.count == 1:
print self.func.__name__, is deprecated
return self.func(*args, **kwargs)

It can also be implemented as a function:

def deprecated(func):
"""Print a deprecation warning once on first use of the function.
>>> @deprecated
# doctest: +SKIP
... def f():
...
pass
>>> f()
# doctest: +SKIP
f is deprecated
"""
count = [0]
def wrapper(*args, **kwargs):
count[0] += 1
if count[0] == 1:
print func.__name__, is deprecated
return func(*args, **kwargs)
return wrapper

7.2.6 A while-loop removing decorator

Lets say we have function which returns a lists of things, and this list created by running a loop. If we dont know
how many objects will be needed, the standard way to do this is something like:

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def find_answers():
answers = []
while True:
ans = look_for_next_answer()
if ans is None:
break
answers.append(ans)
return answers

This is fine, as long as the body of the loop is fairly compact. Once it becomes more complicated, as often happens
in real code, this becomes pretty unreadable. We could simplify this by using yield statements, but then the user
would have to explicitly call list(find_answers()).
We can define a decorator which constructs the list for us:
def vectorized(generator_func):
def wrapper(*args, **kwargs):
return list(generator_func(*args, **kwargs))
return functools.update_wrapper(wrapper, generator_func)

Our function then becomes:

@vectorized
def find_answers():
while True:
ans = look_for_next_answer()
if ans is None:
break
yield ans

7.2.7 A plugin registration system

This is a class decorator which doesnt modify the class, but just puts it in a global registry. It falls into the category
of decorators returning the original object:
class WordProcessor(object):
PLUGINS = []
def process(self, text):
for plugin in self.PLUGINS:
text = plugin().cleanup(text)
return text
@classmethod
def plugin(cls, plugin):
cls.PLUGINS.append(plugin)
@WordProcessor.plugin
class CleanMdashesExtension(object):
def cleanup(self, text):
return text.replace(&mdash;, u\N{em dash})

Here we use a decorator to decentralise the registration of plugins. We call our decorator with a noun, instead of
a verb, because we use it to declare that our class is a plugin for WordProcessor. Method plugin simply
appends the class to the list of plugins.
A word about the plugin itself: it replaces HTML entity for em-dash with a real Unicode em-dash character. It
exploits the unicode literal notation to insert a character by using its name in the unicode database (EM DASH).
If the Unicode character was inserted directly, it would be impossible to distinguish it from an en-dash in the
source of a program.

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7.2.8 More examples and reading

PEP 318 (function and method decorator syntax)
PEP 3129 (class decorator syntax)
http://wiki.python.org/moin/PythonDecoratorLibrary
http://docs.python.org/dev/library/functools.html
http://pypi.python.org/pypi/decorator
Bruce Eckel
Decorators I: Introduction to Python Decorators
Python Decorators II: Decorator Arguments
Python Decorators III: A Decorator-Based Build System

7.3 Context managers

A context manager is an object with __enter__ and __exit__ methods which can be used in the with statement:
with manager as var:
do_something(var)

is in the simplest case equivalent to

var = manager.__enter__()
try:
do_something(var)
finally:
manager.__exit__()

In other words, the context manager protocol defined in PEP 343 permits the extraction of the boring part of a
try..except..finally structure into a separate class leaving only the interesting do_something block.
1. The __enter__ method is called first. It can return a value which will be assigned to var. The as-part
is optional: if it isnt present, the value returned by __enter__ is simply ignored.
2. The block of code underneath with is executed. Just like with try clauses, it can either execute successfully to the end, or it can break, continue or return, or it can throw an exception. Either way, after the
block is finished, the __exit__ method is called. If an exception was thrown, the information about the
exception is passed to __exit__, which is described below in the next subsection. In the normal case,
exceptions can be ignored, just like in a finally clause, and will be rethrown after __exit__ is finished.
Lets say we want to make sure that a file is closed immediately after we are done writing to it:
>>> class closing(object):
...
def __init__(self, obj):
...
self.obj = obj
...
def __enter__(self):
...
return self.obj
...
def __exit__(self, *args):
...
self.obj.close()
>>> with closing(open(/tmp/file, w)) as f:
...
f.write(the contents\n)

Here we have made sure that the f.close() is called when the with block is exited. Since closing files is such
a common operation, the support for this is already present in the file class. It has an __exit__ method which
calls close and can be used as a context manager itself:

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>>> with open(/tmp/file, a) as f:

...
f.write(more contents\n)

The common use for try..finally is releasing resources. Various different cases are implemented similarly:
in the __enter__ phase the resource is acquired, in the __exit__ phase it is released, and the exception, if
thrown, is propagated. As with files, theres often a natural operation to perform after the object has been used and
it is most convenient to have the support built in. With each release, Python provides support in more places:
all file-like objects:
file automatically closed
fileinput, tempfile (py >= 3.2)
bz2.BZ2File, gzip.GzipFile, tarfile.TarFile, zipfile.ZipFile
ftplib, nntplib close connection (py >= 3.2 or 3.3)
locks
multiprocessing.RLock lock and unlock
multiprocessing.Semaphore
memoryview automatically release (py >= 3.2 and 2.7)
decimal.localcontext modify precision of computations temporarily
_winreg.PyHKEY open and close hive key
warnings.catch_warnings kill warnings temporarily
contextlib.closing the same as the example above, call close
parallel programming
concurrent.futures.ThreadPoolExecutor invoke in parallel then kill thread pool (py
>= 3.2)
concurrent.futures.ProcessPoolExecutor invoke in parallel then kill process pool
(py >= 3.2)
nogil solve the GIL problem temporarily (cython only :( )

7.3.1 Catching exceptions

When an exception is thrown in the with-block, it is passed as arguments to __exit__. Three arguments are
used, the same as returned by sys.exc_info(): type, value, traceback. When no exception is thrown, None
is used for all three arguments. The context manager can swallow the exception by returning a true value from
__exit__. Exceptions can be easily ignored, because if __exit__ doesnt use return and just falls of the
end, None is returned, a false value, and therefore the exception is rethrown after __exit__ is finished.
The ability to catch exceptions opens interesting possibilities. A classic example comes from unit-tests we
want to make sure that some code throws the right kind of exception:
class assert_raises(object):
# based on pytest and unittest.TestCase
def __init__(self, type):
self.type = type
def __enter__(self):
pass
def __exit__(self, type, value, traceback):
if type is None:
raise AssertionError(exception expected)
if issubclass(type, self.type):
return True # swallow the expected exception
raise AssertionError(wrong exception type)

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with assert_raises(KeyError):
{}[foo]

7.3.2 Using generators to define context managers

When discussing generators (page 150), it was said that we prefer generators to iterators implemented as classes
because they are shorter, sweeter, and the state is stored as local, not instance, variables. On the other hand, as
described in Bidirectional communication (page 151), the flow of data between the generator and its caller can
be bidirectional. This includes exceptions, which can be thrown into the generator. We would like to implement
context managers as special generator functions. In fact, the generator protocol was designed to support this use
case.
@contextlib.contextmanager
def some_generator(<arguments>):
<setup>
try:
yield <value>
finally:
<cleanup>

The contextlib.contextmanager helper takes a generator and turns it into a context manager. The generator has to obey some rules which are enforced by the wrapper function most importantly it must yield
exactly once. The part before the yield is executed from __enter__, the block of code protected by the context manager is executed when the generator is suspended in yield, and the rest is executed in __exit__. If
an exception is thrown, the interpreter hands it to the wrapper through __exit__ arguments, and the wrapper
function then throws it at the point of the yield statement. Through the use of generators, the context manager
is shorter and simpler.
Lets rewrite the closing example as a generator:
@contextlib.contextmanager
def closing(obj):
try:
yield obj
finally:
obj.close()

Lets rewrite the assert_raises example as a generator:

@contextlib.contextmanager
def assert_raises(type):
try:
yield
except type:
return
except Exception as value:
raise AssertionError(wrong exception type)
else:
raise AssertionError(exception expected)

Here we use a decorator to turn generator functions into context managers!

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CHAPTER 8

Advanced Numpy

author Pauli Virtanen

Numpy is at the base of Pythons scientific stack of tools. Its purpose is simple: implementing efficient operations
on many items in a block of memory. Understanding how it works in detail helps in making efficient use of its
flexibility, taking useful shortcuts, and in building new work based on it.
This tutorial aims to cover:
Anatomy of Numpy arrays, and its consequences. Tips and tricks.
Universal functions: what, why, and what to do if you want a new one.
Integration with other tools: Numpy offers several ways to wrap any data in an ndarray, without unnecessary
copies.
Recently added features, and whats in them for me: PEP 3118 buffers, generalized ufuncs, ...
Prerequisites

Numpy (>= 1.2; preferably newer...)

Cython (>= 0.12, for the Ufunc example)
PIL (used in a couple of examples)
Source codes:
http://pav.iki.fi/tmp/advnumpy-ex.zip

In this section, numpy will be imported as follows:

>>> import numpy as np

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Life of ndarray (page 165)

Its... (page 165)
Block of memory (page 166)
Data types (page 167)
Indexing scheme: strides (page 171)
Findings in dissection (page 177)
Universal functions (page 177)
What they are? (page 177)
Exercise: building an ufunc from scratch (page 178)
Solution: building an ufunc from scratch (page 181)
Generalized ufuncs (page 184)
Interoperability features (page 186)
Sharing multidimensional, typed data (page 186)
The old buffer protocol (page 186)
The old buffer protocol (page 186)
Array interface protocol (page 187)
The new buffer protocol: PEP 3118 (page 188)
PEP 3118 details (page 189)
Siblings: chararray, maskedarray, matrix (page 193)
Summary (page 194)
Contributing to Numpy/Scipy (page 194)
Why (page 194)
Reporting bugs (page 194)
Contributing to documentation (page 195)
Contributing features (page 196)
How to help, in general (page 197)

8.1 Life of ndarray

8.1.1 Its...
ndarray =
block of memory + indexing scheme + data type descriptor
raw data
how to locate an element
how to interpret an element

typedef struct PyArrayObject {

PyObject_HEAD

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/* Block of memory */
char *data;
/* Data type descriptor */
PyArray_Descr *descr;
/* Indexing scheme */
int nd;
npy_intp *dimensions;
npy_intp *strides;
/* Other stuff */
PyObject *base;
int flags;
PyObject *weakreflist;
} PyArrayObject;

8.1.2 Block of memory

>>> x = np.array([1, 2, 3, 4], dtype=np.int32)
>>> x.data
<read-write buffer for 0xa37bfd8, size 16, offset 0 at 0xa4eabe0>
>>> str(x.data)
\x01\x00\x00\x00\x02\x00\x00\x00\x03\x00\x00\x00\x04\x00\x00\x00

Memory address of the data:

>>> x.__array_interface__[data][0]
159755776

Reminder: two ndarrays may share the same memory:

>>> x = np.array([1,2,3,4])
>>> y = x[:-1]
>>> x[0] = 9
>>> y
array([9, 2, 3])

Memory does not need to be owned by an ndarray:

>>> x = 1234
>>> y = np.frombuffer(x, dtype=np.int8)
>>> y.data
<read-only buffer for 0xa588ba8, size 4, offset 0 at 0xa55cd60>
>>> y.base is x
True
>>> y.flags
C_CONTIGUOUS : True
F_CONTIGUOUS : True
OWNDATA : False
WRITEABLE : False
ALIGNED : True
UPDATEIFCOPY : False

The owndata and writeable flags indicate status of the memory block.

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8.1.3 Data types

The descriptor
dtype describes a single item in the array:
type

itemsize
byteorder
fields
shape

scalar type of the data, one of:

int8, int16, float64, et al. (fixed size)
str, unicode, void (flexible size)
size of the data block
byte order: big-endian > / little-endian < / not applicable |
sub-dtypes, if its a structured data type
shape of the array, if its a sub-array

>>> np.dtype(int).type
<type numpy.int32>
>>> np.dtype(int).itemsize
4
>>> np.dtype(int).byteorder
=

Example: reading .wav files

The .wav file header:
chunk_id
chunk_size
format
fmt_id
fmt_size
audio_fmt
num_channels
sample_rate
byte_rate
block_align
bits_per_sample
data_id
data_size

"RIFF"
4-byte unsigned little-endian integer
"WAVE"
"fmt "
4-byte unsigned little-endian integer
2-byte unsigned little-endian integer
2-byte unsigned little-endian integer
4-byte unsigned little-endian integer
4-byte unsigned little-endian integer
2-byte unsigned little-endian integer
2-byte unsigned little-endian integer
"data"
4-byte unsigned little-endian integer

44-byte block of raw data (in the beginning of the file)

... followed by data_size bytes of actual sound data.
The .wav file header as a Numpy structured data type:
>>> wav_header_dtype = np.dtype([
("chunk_id", (str, 4)),
# flexible-sized scalar type, item size 4
("chunk_size", "<u4"),
# little-endian unsigned 32-bit integer
("format", "S4"),
# 4-byte string
("fmt_id", "S4"),
("fmt_size", "<u4"),
("audio_fmt", "<u2"),
#
("num_channels", "<u2"), # .. more of the same ...
("sample_rate", "<u4"),
#
("byte_rate", "<u4"),
("block_align", "<u2"),
("bits_per_sample", "<u2"),
("data_id", ("S1", (2, 2))), # sub-array, just for fun!
("data_size", "u4"),
#
# the sound data itself cannot be represented here:

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# it does not have a fixed size

])

See Also:
wavreader.py
>>> wav_header_dtype[format]
dtype(|S4)
>>> wav_header_dtype.fields
<dictproxy object at 0x85e9704>
>>> wav_header_dtype.fields[format]
(dtype(|S4), 8)

The first element is the sub-dtype in the structured data, corresponding to the name format
The second one is its offset (in bytes) from the beginning of the item
Note: Mini-exercise, make a sparse dtype by using offsets, and only some of the fields:
>>> wav_header_dtype = np.dtype(dict(
names=[format, sample_rate, data_id],
offsets=[offset_1, offset_2, offset_3], # counted from start of structure in bytes
formats=list of dtypes for each of the fields,
))

and use that to read the sample rate, and data_id (as sub-array).
>>> f = open(test.wav, r)
>>> wav_header = np.fromfile(f, dtype=wav_header_dtype, count=1)
>>> f.close()
>>> print(wav_header)
[ (RIFF, 17402L, WAVE, fmt , 16L, 1, 1, 16000L, 32000L, 2, 16,
[[d, a], [t, a]], 17366L)]
>>> wav_header[sample_rate]
array([16000], dtype=uint32)

Lets try accessing the sub-array:

>>> wav_header[data_id]
array([[[d, a],
[t, a]]],
dtype=|S1)
>>> wav_header.shape
(1,)
>>> wav_header[data_id].shape
(1, 2, 2)

When accessing sub-arrays, the dimensions get added to the end!

Note: There are existing modules such as wavfile, audiolab, etc. for loading sound data...
Casting and re-interpretation/views
casting
on assignment
on array construction
on arithmetic
etc.
and manually: .astype(dtype)
data re-interpretation
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manually: .view(dtype)

Casting
Casting in arithmetic, in nutshell:
only type (not value!) of operands matters
largest safe type able to represent both is picked
scalars can lose to arrays in some situations
Casting in general copies data
>>> x = np.array([1, 2, 3, 4], dtype=np.float)
>>> x
array([ 1., 2., 3., 4.])
>>> y = x.astype(np.int8)
>>> y
array([1, 2, 3, 4], dtype=int8)
>>> y + 1
array([2, 3, 4, 5], dtype=int8)
>>> y + 256
array([1, 2, 3, 4], dtype=int8)
>>> y + 256.0
array([ 257., 258., 259., 260.])
>>> y + np.array([256], dtype=np.int32)
array([258, 259, 260, 261])

Casting on setitem: dtype of the array is not changed on item assignment

>>> y[:] = y + 1.5
>>> y
array([2, 3, 4, 5], dtype=int8)

Note: Exact rules: see documentation: http://docs.scipy.org/doc/numpy/reference/ufuncs.html#casting-rules

Re-interpretation / viewing
Data block in memory (4 bytes)
0x01

||

0x02

||

0x03

||

0x04

4 of uint8, OR,
4 of int8, OR,
2 of int16, OR,
1 of int32, OR,
1 of float32, OR,
...
How to switch from one to another?
1. Switch the dtype:
>>> x = np.array([1, 2, 3, 4], dtype=np.uint8)
>>> x.dtype = "<i2"
>>> x
array([ 513, 1027], dtype=int16)
>>> 0x0201, 0x0403
(513, 1027)

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0x01

0x02

||

0x03

0x04

Note: little-endian: least significant byte is on the left in memory

2. Create a new view:
>>> y = x.view("<i4")
>>> y
array([67305985])
>>> 0x04030201
67305985

0x01

0x02

0x03

0x04

Note:
.view() makes views, does not copy (or alter) the memory block
only changes the dtype (and adjusts array shape)
>>> x[1] = 5
>>> y
array([328193])
>>> y.base is x
True

Mini-exercise: data re-interpretation

See Also:
view-colors.py
You have RGBA data in an array
>>>
>>>
>>>
>>>
>>>

x = np.zeros((10, 10, 4), dtype=np.int8)

x[:,:,0] = 1
x[:,:,1] = 2
x[:,:,2] = 3
x[:,:,3] = 4

where the last three dimensions are the R, B, and G, and alpha channels.
How to make a (10, 10) structured array with field names r, g, b, a without copying data?
>>> y = ...
>>>
>>>
>>>
>>>

assert
assert
assert
assert

(y[r]
(y[g]
(y[b]
(y[a]

==
==
==
==

1).all()
2).all()
3).all()
4).all()

Solution
>>> y = x.view([(r, i1),
(g, i1),
(b, i1),
(a, i1)]
)[:,:,0]

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Warning: Another array taking exactly 4 bytes of memory:

>>> y = np.array([[1, 3], [2, 4]], dtype=np.uint8).transpose()
>>> x = y.copy()
>>> x
array([[1, 2],
[3, 4]], dtype=uint8)
>>> y
array([[1, 2],
[3, 4]], dtype=uint8)
>>> x.view(np.int16)
array([[ 513],
[1027]], dtype=int16)
>>> 0x0201, 0x0403
(513, 1027)
>>> y.view(np.int16)
array([[ 769, 1026]], dtype=int16)

What happened?
... we need to look into what x[0,1] actually means
>>> 0x0301, 0x0402
(769, 1026)

8.1.4 Indexing scheme: strides

Main point
The question
>>> x = np.array([[1, 2, 3],
[4, 5, 6],
[7, 8, 9]], dtype=np.int8)
>>> str(x.data)
\x01\x02\x03\x04\x05\x06\x07\x08\t

At which byte in x.data does the item x[1,2] begin?

The answer (in Numpy)
strides: the number of bytes to jump to find the next element
1 stride per dimension
>>> x.strides
(3, 1)
>>> byte_offset = 3*1 + 1*2
>>> x.data[byte_offset]
\x06
>>> x[1,2]
6

# to find x[1,2]

simple, flexible

C and Fortran order

>>> x = np.array([[1, 2, 3],
[4, 5, 6],
[7, 8, 9]], dtype=np.int16, order=C)

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>>> x.strides
(6, 2)
>>> str(x.data)
\x01\x00\x02\x00\x03\x00\x04\x00\x05\x00\x06\x00\x07\x00\x08\x00\t\x00

Need to jump 6 bytes to find the next row

Need to jump 2 bytes to find the next column
>>> y = np.array(x, order=F)
>>> y.strides
(2, 6)
>>> str(y.data)
\x01\x00\x04\x00\x07\x00\x02\x00\x05\x00\x08\x00\x03\x00\x06\x00\t\x00

Need to jump 2 bytes to find the next row

Need to jump 6 bytes to find the next column
Similarly to higher dimensions:
C: last dimensions vary fastest (= smaller strides)
F: first dimensions vary fastest
shape = (d1 , d2 , ..., dn )
strides = (s1 , s2 , ..., sn )
sC
j = dj+1 dj+2 ...dn itemsize
sF
j = d1 d2 ...dj1 itemsize
Note: Now we can understand the behavior of .view():
>>> y = np.array([[1, 3], [2, 4]], dtype=np.uint8).transpose()
>>> x = y.copy()

Transposition does not affect the memory layout of the data, only strides
>>>
(2,
>>>
(1,

x.strides
1)
y.strides
2)

>>> str(x.data)
\x01\x02\x03\x04
>>> str(y.data)
\x01\x03\x02\x04

the results are different when interpreted as 2 of int16

.copy() creates new arrays in the C order (by default)

Slicing with integers

Everything can be represented by changing only shape, strides, and possibly adjusting the data
pointer!
Never makes copies of the data
>>> x = np.array([1, 2, 3, 4, 5, 6], dtype=np.int32)
>>> y = x[::-1]
>>> y
array([6, 5, 4, 3, 2, 1])

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>>> y.strides
(-4,)
>>> y = x[2:]
>>> y.__array_interface__[data][0] - x.__array_interface__[data][0]
8
>>> x = np.zeros((10, 10, 10), dtype=np.float)
>>> x.strides
(800, 80, 8)
>>> x[::2,::3,::4].strides
(1600, 240, 32)

Example: fake dimensions with strides

Stride manipulation
>>> from numpy.lib.stride_tricks import as_strided
>>> help(as_strided)
as_strided(x, shape=None, strides=None)
Make an ndarray from the given array with the given shape and strides

Warning: as_strided does not check that you stay inside the memory block bounds...
>>> x = np.array([1, 2, 3, 4], dtype=np.int16)
>>> as_strided(x, strides=(2*2,), shape=(2,))
array([1, 3], dtype=int16)
>>> x[::2]
array([1, 3], dtype=int16)

See Also:
stride-fakedims.py
Exercise
array([1, 2, 3, 4], dtype=np.int8)
-> array([[1, 2, 3, 4],
[1, 2, 3, 4],
[1, 2, 3, 4]], dtype=np.int8)

using only as_strided.:

Hint: byte_offset = stride[0]*index[0] + stride[1]*index[1] + ...

Spoiler
Stride can also be 0:
>>> x = np.array([1, 2, 3, 4], dtype=np.int8)
>>> y = as_strided(x, strides=(0, 1), shape=(3, 4))
>>> y
array([[1, 2, 3, 4],
[1, 2, 3, 4],
[1, 2, 3, 4]], dtype=int8)
>>> y.base.base is x
True

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Broadcasting
Doing something useful with it: outer product of [1, 2, 3, 4] and [5, 6, 7]
>>> x = np.array([1, 2, 3, 4], dtype=np.int16)
>>> x2 = as_strided(x, strides=(0, 1*2), shape=(3, 4))
>>> x2
array([[1, 2, 3, 4],
[1, 2, 3, 4],
[1, 2, 3, 4]], dtype=int16)
>>> y = np.array([5, 6, 7], dtype=np.int16)
>>> y2 = as_strided(y, strides=(1*2, 0), shape=(3, 4))
>>> y2
array([[5, 5, 5, 5],
[6, 6, 6, 6],
[7, 7, 7, 7]], dtype=int16)
>>> x2 *
array([[
[
[

y2
5, 10, 15, 20],
6, 12, 18, 24],
7, 14, 21, 28]], dtype=int16)

... seems somehow familiar ...

>>> x = np.array([1, 2, 3, 4], dtype=np.int16)
>>> y = np.array([5, 6, 7], dtype=np.int16)
>>> x[np.newaxis,:] * y[:,np.newaxis]
array([[ 5, 10, 15, 20],
[ 6, 12, 18, 24],
[ 7, 14, 21, 28]], dtype=int16)

Internally, array broadcasting is indeed implemented using 0-strides.

More tricks: diagonals
See Also:
stride-diagonals.py
Challenge
Pick diagonal entries of the matrix: (assume C memory order)
>>> x = np.array([[1, 2, 3],
[4, 5, 6],
[7, 8, 9]], dtype=np.int32)
>>> x_diag = as_strided(x, shape=(3,), strides=(???,))

Pick the first super-diagonal entries [2, 6].

And the sub-diagonals?
(Hint to the last two: slicing first moves the point where striding starts from.)
Solution
Pick diagonals:
>>> x_diag = as_strided(x, shape=(3,), strides=((3+1)*x.itemsize,))
>>> x_diag
array([1, 5, 9])

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Slice first, to adjust the data pointer:

>>> as_strided(x[0,1:], shape=(2,), strides=((3+1)*x.itemsize,))
array([2, 6])
>>> as_strided(x[1:,0], shape=(2,), strides=((3+1)*x.itemsize,))
array([4, 8])

Note:
>>> y = np.diag(x, k=1)
>>> y
array([2, 6])

However,
>>> y.flags.owndata
True

It makes a copy?! Room for improvement... (bug #xxx)

See Also:
stride-diagonals.py
Challenge
Compute the tensor trace
>>> x = np.arange(5*5*5*5).reshape(5,5,5,5)
>>> s = 0
>>> for i in xrange(5):
>>>
for j in xrange(5):
>>>
s += x[j,i,j,i]

by striding, and using sum() on the result.

>>> y = as_strided(x, shape=(5, 5), strides=(TODO, TODO))
>>> s2 = ...
>>> assert s == s2

Solution
>>> y = as_strided(x, shape=(5, 5), strides=((5*5*5+5)*x.itemsize,
(5*5+1)*x.itemsize))
>>> s2 = y.sum()

CPU cache effects

Memory layout can affect performance:
In [1]: x = np.zeros((20000,))
In [2]: y = np.zeros((20000*67,))[::67]
In [3]: x.shape, y.shape
((20000,), (20000,))
In [4]: %timeit x.sum()
100000 loops, best of 3: 0.180 ms per loop
In [5]: %timeit y.sum()
100000 loops, best of 3: 2.34 ms per loop
In [6]: x.strides, y.strides
((8,), (536,))

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Smaller strides are faster?

CPU pulls data from main memory to its cache in blocks

If many array items consecutively operated on fit in a single block (small stride):
fewer transfers needed
faster
See Also:
numexpr is designed to mitigate cache effects in array computing.
Example: inplace operations (caveat emptor)
Sometimes,
>>> a -= b

is not the same as

>>> a -= b.copy()
>>> x = np.array([[1, 2], [3, 4]])
>>> x -= x.transpose()
>>> x
array([[ 0, -1],
[ 4, 0]])
>>> y = np.array([[1, 2], [3, 4]])
>>> y -= y.T.copy()
>>> y
array([[ 0, -1],
[ 1, 0]])

x and x.transpose() share data

x -= x.transpose() modifies the data element-by-element...
because x and x.transpose() have different striding, modified data re-appears on the RHS

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8.1.5 Findings in dissection

memory block: may be shared, .base, .data

data type descriptor: structured data, sub-arrays, byte order, casting, viewing, .astype(), .view()
strided indexing: strides, C/F-order, slicing w/ integers, as_strided, broadcasting, stride tricks, diag,
CPU cache coherence

8.2 Universal functions

8.2.1 What they are?
Ufunc performs and elementwise operation on all elements of an array.
Examples:
np.add, np.subtract, scipy.special.*, ...

Automatically support: broadcasting, casting, ...

The author of an ufunc only has to supply the elementwise operation, Numpy takes care of the rest.
The elementwise operation needs to be implemented in C (or, e.g., Cython)

Parts of an Ufunc
1. Provided by user
void ufunc_loop(void **args, int *dimensions, int *steps, void *data)
{
/*
* int8 output = elementwise_function(int8 input_1, int8 input_2)
*
* This function must compute the ufunc for many values at once,
* in the way shown below.
*/
char *input_1 = (char*)args[0];
char *input_2 = (char*)args[1];
char *output = (char*)args[2];
int i;
for (i = 0; i < dimensions[0]; ++i) {
*output = elementwise_function(*input_1, *input_2);
input_1 += steps[0];

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input_2 += steps[1];
output += steps[2];
}
}

2. The Numpy part, built by

char types[3]
types[0] = NPY_BYTE
types[1] = NPY_BYTE
types[2] = NPY_BYTE

/* type of first input arg */

/* type of second input arg */
/* type of third input arg */

PyObject *python_ufunc = PyUFunc_FromFuncAndData(

ufunc_loop,
NULL,
types,
1, /* ntypes */
2, /* num_inputs */
1, /* num_outputs */
identity_element,
name,
docstring,
unused)

A ufunc can also support multiple different input-output type combinations.

... can be made slightly easier

3. ufunc_loop is of very generic form, and Numpy provides pre-made ones
PyUfunc_f_f float elementwise_func(float input_1)
PyUfunc_ff_ffloat elementwise_func(float input_1, float input_2)
PyUfunc_d_d double elementwise_func(double input_1)
PyUfunc_dd_ddouble elementwise_func(double input_1, double input_2)
PyUfunc_D_D elementwise_func(npy_cdouble *input, npy_cdouble* output)
PyUfunc_DD_Delementwise_func(npy_cdouble *in1, npy_cdouble *in2,
npy_cdouble* out)
Only elementwise_func needs to be supplied
... except when your elementwise function is not in one of the above forms

8.2.2 Exercise: building an ufunc from scratch

The Mandelbrot fractal is defined by the iteration
z z2 + c
where c = x + iy is a complex number. This iteration is repeated if z stays finite no matter how long the iteration
runs, c belongs to the Mandelbrot set.
Make ufunc called mandel(z0, c) that computes:
z = z0
for k in range(iterations):
z = z*z + c

say, 100 iterations or until z.real**2 + z.imag**2 > 1000. Use it to determine which c are in the
Mandelbrot set.
Our function is a simple one, so make use of the PyUFunc_* helpers.
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Write it in Cython
See Also:
mandel.pyx, mandelplot.py
#
# Fix the parts marked by TODO
#
#
# Compile this file by (Cython >= 0.12 required because of the complex vars)
#
#
cython mandel.pyx
#
python setup.py build_ext -i
#
# and try it out with, in this directory,
#
#
>>> import mandel
#
>>> mandel.mandel(0, 1 + 2j)
#
#
# The elementwise function
# -----------------------cdef void mandel_single_point(double complex *z_in,
double complex *c_in,
double complex *z_out) nogil:
#
# The Mandelbrot iteration
#
#
#
#
#
#
#
#
#
#
#
#
#

Some points of note:

- Its *NOT* allowed to call any Python functions here.
The Ufunc loop runs with the Python Global Interpreter Lock released.
Hence, the nogil.
- And so all local variables must be declared with cdef
- Note also that this function receives *pointers* to the data

cdef double complex z = z_in[0]

cdef double complex c = c_in[0]
cdef int k # the integer we use in the for loop
#
# TODO: write the Mandelbrot iteration for one point here,
#
as you would write it in Python.
#
#
Say, use 100 as the maximum number of iterations, and 1000
#
as the cutoff for z.real**2 + z.imag**2.
#
TODO: mandelbrot iteration should go here
# Return the answer for this point
z_out[0] = z

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#
#
#
#
#

Boilerplate Cython definitions

The litany below is particularly long, but you dont really need to
read this part; it just pulls in stuff from the Numpy C headers.
----------------------------------------------------------

cdef extern from "numpy/arrayobject.h":

void import_array()
ctypedef int npy_intp
cdef enum NPY_TYPES:
NPY_DOUBLE
NPY_CDOUBLE
NPY_LONG
cdef extern from "numpy/ufuncobject.h":
void import_ufunc()
ctypedef void (*PyUFuncGenericFunction)(char**, npy_intp*, npy_intp*, void*)
object PyUFunc_FromFuncAndData(PyUFuncGenericFunction* func, void** data,
char* types, int ntypes, int nin, int nout,
int identity, char* name, char* doc, int c)
# List of pre-defined loop functions
void
void
void
void
void
void
void
void
void
void
void
void
void
void
void
void

PyUFunc_f_f_As_d_d(char** args, npy_intp* dimensions, npy_intp* steps, void* func)

PyUFunc_d_d(char** args, npy_intp* dimensions, npy_intp* steps, void* func)
PyUFunc_f_f(char** args, npy_intp* dimensions, npy_intp* steps, void* func)
PyUFunc_g_g(char** args, npy_intp* dimensions, npy_intp* steps, void* func)
PyUFunc_F_F_As_D_D(char** args, npy_intp* dimensions, npy_intp* steps, void* func)
PyUFunc_F_F(char** args, npy_intp* dimensions, npy_intp* steps, void* func)
PyUFunc_D_D(char** args, npy_intp* dimensions, npy_intp* steps, void* func)
PyUFunc_G_G(char** args, npy_intp* dimensions, npy_intp* steps, void* func)
PyUFunc_ff_f_As_dd_d(char** args, npy_intp* dimensions, npy_intp* steps, void* func)
PyUFunc_ff_f(char** args, npy_intp* dimensions, npy_intp* steps, void* func)
PyUFunc_dd_d(char** args, npy_intp* dimensions, npy_intp* steps, void* func)
PyUFunc_gg_g(char** args, npy_intp* dimensions, npy_intp* steps, void* func)
PyUFunc_FF_F_As_DD_D(char** args, npy_intp* dimensions, npy_intp* steps, void* func)
PyUFunc_DD_D(char** args, npy_intp* dimensions, npy_intp* steps, void* func)
PyUFunc_FF_F(char** args, npy_intp* dimensions, npy_intp* steps, void* func)
PyUFunc_GG_G(char** args, npy_intp* dimensions, npy_intp* steps, void* func)

# Required module initialization

# -----------------------------import_array()
import_ufunc()

# The actual ufunc declaration

# ---------------------------cdef PyUFuncGenericFunction loop_func[1]
cdef char input_output_types[3]
cdef void *elementwise_funcs[1]
#
#
#
#
#
#
#
#

Reminder: some pre-made Ufunc loops:

================
PyUfunc_f_f
PyUfunc_ff_f
PyUfunc_d_d
PyUfunc_dd_d

=======================================================
float elementwise_func(float input_1)
float elementwise_func(float input_1, float input_2)
double elementwise_func(double input_1)
double elementwise_func(double input_1, double input_2)

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#
#
#
#
#
#
#
#
#
#
#
#
#
#

PyUfunc_D_D
PyUfunc_DD_D
================

elementwise_func(complex_double *input, complex_double* complex_double)

elementwise_func(complex_double *in1, complex_double *in2, complex_double* o
=======================================================

The full list is above.

Type codes:
NPY_BOOL, NPY_BYTE, NPY_UBYTE, NPY_SHORT, NPY_USHORT, NPY_INT, NPY_UINT,
NPY_LONG, NPY_ULONG, NPY_LONGLONG, NPY_ULONGLONG, NPY_FLOAT, NPY_DOUBLE,
NPY_LONGDOUBLE, NPY_CFLOAT, NPY_CDOUBLE, NPY_CLONGDOUBLE, NPY_DATETIME,
NPY_TIMEDELTA, NPY_OBJECT, NPY_STRING, NPY_UNICODE, NPY_VOID

loop_func[0] = ... TODO: suitable PyUFunc_* ...

input_output_types[0] = ... TODO ...
... TODO: fill in rest of input_output_types ...
# This thing is passed as the data parameter for the generic
# PyUFunc_* loop, to let it know which function it should call.
elementwise_funcs[0] = <void*>mandel_single_point
# Construct the ufunc:
mandel = PyUFunc_FromFuncAndData(
loop_func,
elementwise_funcs,
input_output_types,
1, # number of supported input types
TODO, # number of input args
TODO, # number of output args
0, # identity element, never mind this
"mandel", # function name
"mandel(z, c) -> computes z*z + c", # docstring
0 # unused
)

Reminder: some pre-made Ufunc loops:

PyUfunc_f_f float elementwise_func(float input_1)
PyUfunc_ff_ffloat elementwise_func(float input_1, float input_2)
PyUfunc_d_d double elementwise_func(double input_1)
PyUfunc_dd_ddouble elementwise_func(double input_1, double input_2)
PyUfunc_D_D elementwise_func(complex_double *input, complex_double*
output)
PyUfunc_DD_Delementwise_func(complex_double *in1, complex_double *in2,
complex_double* out)
Type codes:
NPY_BOOL, NPY_BYTE, NPY_UBYTE, NPY_SHORT, NPY_USHORT, NPY_INT, NPY_UINT,
NPY_LONG, NPY_ULONG, NPY_LONGLONG, NPY_ULONGLONG, NPY_FLOAT, NPY_DOUBLE,
NPY_LONGDOUBLE, NPY_CFLOAT, NPY_CDOUBLE, NPY_CLONGDOUBLE, NPY_DATETIME,
NPY_TIMEDELTA, NPY_OBJECT, NPY_STRING, NPY_UNICODE, NPY_VOID

8.2.3 Solution: building an ufunc from scratch

# The elementwise function
# -----------------------cdef void mandel_single_point(double complex *z_in,

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double complex *c_in,

double complex *z_out) nogil:
#
# The Mandelbrot iteration
#
#
#
#
#
#
#
#
#
#
#
#
#
#

Some points of note:

- Its *NOT* allowed to call any Python functions here.
The Ufunc loop runs with the Python Global Interpreter Lock released.
Hence, the nogil.
- And so all local variables must be declared with cdef
- Note also that this function receives *pointers* to the data;
the "traditional" solution to passing complex variables around

cdef double complex z = z_in[0]

cdef double complex c = c_in[0]
cdef int k # the integer we use in the for loop
# Straightforward iteration
for k in range(100):
z = z*z + c
if z.real**2 + z.imag**2 > 1000:
break
# Return the answer for this point
z_out[0] = z

#
#
#
#
#

Boilerplate Cython definitions

You dont really need to read this part, it just pulls in
stuff from the Numpy C headers.
----------------------------------------------------------

cdef extern from "numpy/arrayobject.h":

void import_array()
ctypedef int npy_intp
cdef enum NPY_TYPES:
NPY_CDOUBLE
cdef extern from "numpy/ufuncobject.h":
void import_ufunc()
ctypedef void (*PyUFuncGenericFunction)(char**, npy_intp*, npy_intp*, void*)
object PyUFunc_FromFuncAndData(PyUFuncGenericFunction* func, void** data,
char* types, int ntypes, int nin, int nout,
int identity, char* name, char* doc, int c)
void PyUFunc_DD_D(char**, npy_intp*, npy_intp*, void*)

# Required module initialization

# -----------------------------import_array()
import_ufunc()

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# The actual ufunc declaration

# ---------------------------cdef PyUFuncGenericFunction loop_func[1]
cdef char input_output_types[3]
cdef void *elementwise_funcs[1]
loop_func[0] = PyUFunc_DD_D
input_output_types[0] = NPY_CDOUBLE
input_output_types[1] = NPY_CDOUBLE
input_output_types[2] = NPY_CDOUBLE
elementwise_funcs[0] = <void*>mandel_single_point
mandel = PyUFunc_FromFuncAndData(
loop_func,
elementwise_funcs,
input_output_types,
1, # number of supported input types
2, # number of input args
1, # number of output args
0, # identity element, never mind this
"mandel", # function name
"mandel(z, c) -> computes iterated z*z + c", # docstring
0 # unused
)
import numpy as np
import mandel
x = np.linspace(-1.7, 0.6, 1000)
y = np.linspace(-1.4, 1.4, 1000)
c = x[None,:] + 1j*y[:,None]
z = mandel.mandel(c, c)
import matplotlib.pyplot as plt
plt.imshow(abs(z)**2 < 1000, extent=[-1.7, 0.6, -1.4, 1.4])
plt.gray()
plt.show()

Note: Most of the boilerplate could be automated by these Cython modules:

http://wiki.cython.org/MarkLodato/CreatingUfuncs

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Several accepted input types

E.g. supporting both single- and double-precision versions
cdef void mandel_single_point(double complex *z_in,
double complex *c_in,
double complex *z_out) nogil:
...
cdef void mandel_single_point_singleprec(float complex *z_in,
float complex *c_in,
float complex *z_out) nogil:
...
cdef PyUFuncGenericFunction loop_funcs[2]
cdef char input_output_types[3*2]
cdef void *elementwise_funcs[1*2]
loop_funcs[0] = PyUFunc_DD_D
input_output_types[0] = NPY_CDOUBLE
input_output_types[1] = NPY_CDOUBLE
input_output_types[2] = NPY_CDOUBLE
elementwise_funcs[0] = <void*>mandel_single_point
loop_funcs[1] = PyUFunc_FF_F
input_output_types[3] = NPY_CFLOAT
input_output_types[4] = NPY_CFLOAT
input_output_types[5] = NPY_CFLOAT
elementwise_funcs[1] = <void*>mandel_single_point_singleprec
mandel = PyUFunc_FromFuncAndData(
loop_func,
elementwise_funcs,
input_output_types,
2, # number of supported input types
<---------------2, # number of input args
1, # number of output args
0, # identity element, never mind this
"mandel", # function name
"mandel(z, c) -> computes iterated z*z + c", # docstring
0 # unused
)

8.2.4 Generalized ufuncs

ufunc
output = elementwise_function(input)
Both output and input can be a single array element only.
generalized ufunc
output and input can be arrays with a fixed number of dimensions
For example, matrix trace (sum of diag elements):
input shape = (n, n)
output shape = ()

i.e.

scalar

(n, n) -> ()

Matrix product:

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input_1 shape = (m, n)

input_2 shape = (n, p)
output shape = (m, p)
(m, n), (n, p) -> (m, p)

This is called the signature of the generalized ufunc

The dimensions on which the g-ufunc acts, are core dimensions

Status in Numpy
g-ufuncs are in Numpy already ...
new ones can be created with PyUFunc_FromFuncAndDataAndSignature
... but we dont ship with public g-ufuncs, except for testing, ATM
>>> import numpy.core.umath_tests as ut
>>> ut.matrix_multiply.signature
(m,n),(n,p)->(m,p)
>>> x = np.ones((10, 2, 4))
>>> y = np.ones((10, 4, 5))
>>> ut.matrix_multiply(x, y).shape
(10, 2, 5)

the last two dimensions became core dimensions, and are modified as per the signature
otherwise, the g-ufunc operates elementwise
matrix multiplication this way could be useful for operating on many small matrices at once

Generalized ufunc loop

Matrix multiplication (m,n),(n,p) -> (m,p)
void gufunc_loop(void **args, int *dimensions, int *steps, void *data)
{
char *input_1 = (char*)args[0]; /* these are as previously */
char *input_2 = (char*)args[1];
char *output = (char*)args[2];
int
int
int
int
int
int

input_1_stride_m = steps[3]; /* strides for the core dimensions */

input_1_stride_n = steps[4]; /* are added after the non-core */
input_2_strides_n = steps[5]; /* steps */
input_2_strides_p = steps[6];
output_strides_n = steps[7];
output_strides_p = steps[8];

int m = dimension[1]; /* core dimensions are added after */

int n = dimension[2]; /* the main dimension; order as in */
int p = dimension[3]; /* signature */
int i;
for (i = 0; i < dimensions[0]; ++i) {
matmul_for_strided_matrices(input_1, input_2, output,
strides for each array...);
input_1 += steps[0];
input_2 += steps[1];

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output += steps[2];
}
}

8.3 Interoperability features

8.3.1 Sharing multidimensional, typed data
Suppose you
1. Write a library than handles (multidimensional) binary data,
2. Want to make it easy to manipulate the data with Numpy, or whatever other library,
3. ... but would not like to have Numpy as a dependency.
Currently, 3 solutions:
1. the old buffer interface
2. the array interface
3. the new buffer interface (PEP 3118)

8.3.2 The old buffer protocol

Only 1-D buffers
No data type information
C-level interface; PyBufferProcs tp_as_buffer in the type object
But its integrated into Python (e.g. strings support it)
Mini-exercise using PIL (Python Imaging Library):
See Also:
pilbuffer.py
>>> import Image
>>> x = np.zeros((200, 200, 4), dtype=np.int8)

TODO: RGBA images consist of 32-bit integers whose bytes are [RR,GG,BB,AA].
Fill x with opaque red [255,0,0,255]
Mangle it to (200,200) 32-bit integer array so that PIL accepts it
>>> img = Image.frombuffer("RGBA", (200, 200), data)
>>> img.save(test.png)

Q:
Check what happens if x is now modified, and img saved again.

8.3.3 The old buffer protocol

import numpy as np
import Image
# Lets make a sample image, RGBA format

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x = np.zeros((200, 200, 4), dtype=np.int8)

x[:,:,0] = 254 # red
x[:,:,3] = 255 # opaque
data = x.view(np.int32) # Check that you understand why this is OK!
img = Image.frombuffer("RGBA", (200, 200), data)
img.save(test.png)
#
# Modify the original data, and save again.
#
# It turns out that PIL, which knows next to nothing about Numpy,
# happily shares the same data.
#
x[:,:,1] = 254
img.save(test2.png)

8.3.4 Array interface protocol

Multidimensional buffers

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Data type information present

Numpy-specific approach; slowly deprecated (but not going away)
Not integrated in Python otherwise
See Also:
Documentation: http://docs.scipy.org/doc/numpy/reference/arrays.interface.html
>>> x = np.array([[1, 2], [3, 4]])
>>> x.__array_interface__
{data: (171694552, False),
# memory address of data, is readonly?
descr: [(, <i4)],
# data type descriptor
typestr: <i4,
# same, in another form
strides: None,
# strides; or None if in C-order
shape: (2, 2),
version: 3,
}
>>> import Image
>>> img = Image.open(test.png)
>>> img.__array_interface__
{data: a very long string,
shape: (200, 200, 4),
typestr: |u1}
>>> x = np.asarray(img)
>>> x.shape
(200, 200, 4)
>>> x.dtype
dtype(uint8)

Note: A more C-friendly variant of the array interface is also defined.

8.3.5 The new buffer protocol: PEP 3118

Multidimensional buffers
Data type information present
C-level interface; extensions to tp_as_buffer
Integrated into Python (>= 2.6)
Replaces the old buffer interface in Python 3
Next releases of Numpy (>= 1.5) will also implement it fully
Demo in Python 3 / Numpy dev version:
Python 3.1.2 (r312:79147, Apr 15 2010, 12:35:07)
[GCC 4.4.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy as np
>>> np.__version__
2.0.0.dev8469+15dcfb

Memoryview object exposes some of the stuff Python-side

>>>
>>>
>>>
l
>>>
4
>>>

x = np.array([[1, 2], [3, 4]])

y = memoryview(x)
y.format
y.itemsize
y.ndim

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2
>>> y.readonly
False
>>> y.shape
(2, 2)
>>> y.strides
(8, 4)

Roundtrips work
>>> z = np.asarray(y)
>>> z
array([[1, 2],
[3, 4]])
>>> x[0,0] = 9
>>> z
array([[9, 2],
[3, 4]])

Interoperability with the built-in Python array module

>>> import array
>>> x = array.array(h, b1212)
>>> y = np.asarray(x)
>>> y
array([12849, 12849], dtype=int16)
>>> y.base
<memory at 0xa225acc>

# 2 of int16, but no Numpy!

8.3.6 PEP 3118 details

Suppose: you have a new Python extension type MyObject (defined in C)
... and want it to interoperable with a (2, 2) array of int32
See Also:
myobject.c, myobject_test.py, setup_myobject.py
static PyBufferProcs myobject_as_buffer = {
(getbufferproc)myobject_getbuffer,
(releasebufferproc)myobject_releasebuffer,
};
/* .. and stick this to the type object */
static int
myobject_getbuffer(PyObject *obj, Py_buffer *view, int flags)
{
PyMyObjectObject *self = (PyMyObjectObject*)obj;
/* Called when something requests that a MyObject-type object
provides a buffer interface */
view->buf = self->buffer;
view->readonly = 0;
view->format = "i";
view->shape = malloc(sizeof(Py_ssize_t) * 2);
view->strides = malloc(sizeof(Py_ssize_t) * 2);;
view->suboffsets = NULL;
TODO: Just fill in view->len, view->itemsize, view->strides[0] and 1,
view->shape[0] and 1, and view->ndim.

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/* Note: if correct interpretation *requires* strides or shape,

you need to check flags for what was requested, and raise
appropriate errors.
The same if the buffer is not readable.
*/
view->obj = (PyObject*)self;
Py_INCREF(self);
return 0;
}
static void
myobject_releasebuffer(PyMemoryViewObject *self, Py_buffer *view)
{
if (view->shape) {
free(view->shape);
view->shape = NULL;
}
if (view->strides) {
free(view->strides);
view->strides = NULL;
}
}
/*
* Sample implementation of a custom data type that exposes an array
* interface. (And does nothing else :)
*
* Requires Python >= 3.1
*/
/*
* Mini-exercises:
*
* - make the array strided
* - change the data type
*
*/
#define PY_SSIZE_T_CLEAN
#include <Python.h>
#include "structmember.h"

typedef struct {
PyObject_HEAD
int buffer[4];
} PyMyObjectObject;

static int
myobject_getbuffer(PyObject *obj, Py_buffer *view, int flags)
{
PyMyObjectObject *self = (PyMyObjectObject*)obj;
/* Called when something requests that a MyObject-type object
provides a buffer interface */
view->buf = self->buffer;
view->readonly = 0;

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view->format = "i";
view->len = 4;
view->itemsize = sizeof(int);
view->ndim = 2;
view->shape = malloc(sizeof(Py_ssize_t) * 2);
view->shape[0] = 2;
view->shape[1] = 2;
view->strides = malloc(sizeof(Py_ssize_t) * 2);;
view->strides[0] = 2*sizeof(int);
view->strides[1] = sizeof(int);
view->suboffsets = NULL;
/* Note: if correct interpretation *requires* strides or shape,
you need to check flags for what was requested, and raise
appropriate errors.
The same if the buffer is not readable.
*/
view->obj = (PyObject*)self;
Py_INCREF(self);
return 0;
}
static void
myobject_releasebuffer(PyMemoryViewObject *self, Py_buffer *view)
{
if (view->shape) {
free(view->shape);
view->shape = NULL;
}
if (view->strides) {
free(view->strides);
view->strides = NULL;
}
}

static PyBufferProcs myobject_as_buffer = {

(getbufferproc)myobject_getbuffer,
(releasebufferproc)myobject_releasebuffer,
};
/*
* Standard stuff follows
*/
PyTypeObject PyMyObject_Type;
static PyObject *
myobject_new(PyTypeObject *subtype, PyObject *args, PyObject *kwds)
{
PyMyObjectObject *self;
static char *kwlist[] = {NULL};
if (!PyArg_ParseTupleAndKeywords(args, kwds, "", kwlist)) {
return NULL;
}
self = (PyMyObjectObject *)
PyObject_New(PyMyObjectObject, &PyMyObject_Type);
self->buffer[0] = 1;
self->buffer[1] = 2;
self->buffer[2] = 3;

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self->buffer[3] = 4;
return (PyObject*)self;
}

PyTypeObject PyMyObject_Type = {
PyVarObject_HEAD_INIT(NULL, 0)
"MyObject",
sizeof(PyMyObjectObject),
0,
/* methods */
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
&myobject_as_buffer,
Py_TPFLAGS_DEFAULT,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
myobject_new,
0,
0,
0,
0,
0,
0,
0,
0,
0,
};

/* tp_itemsize */
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*
/*

tp_dealloc */
tp_print */
tp_getattr */
tp_setattr */
tp_reserved */
tp_repr */
tp_as_number */
tp_as_sequence */
tp_as_mapping */
tp_hash */
tp_call */
tp_str */
tp_getattro */
tp_setattro */
tp_as_buffer */
tp_flags */
tp_doc */
tp_traverse */
tp_clear */
tp_richcompare */
tp_weaklistoffset */
tp_iter */
tp_iternext */
tp_methods */
tp_members */
tp_getset */
tp_base */
tp_dict */
tp_descr_get */
tp_descr_set */
tp_dictoffset */
tp_init */
tp_alloc */
tp_new */
tp_free */
tp_is_gc */
tp_bases */
tp_mro */
tp_cache */
tp_subclasses */
tp_weaklist */
tp_del */
tp_version_tag */

struct PyModuleDef moduledef = {

PyModuleDef_HEAD_INIT,
"myobject",
NULL,
-1,
NULL,
NULL,

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NULL,
NULL,
NULL
};
PyObject *PyInit_myobject(void) {
PyObject *m, *d;
if (PyType_Ready(&PyMyObject_Type) < 0) {
return NULL;
}
m = PyModule_Create(&moduledef);
d = PyModule_GetDict(m);
Py_INCREF(&PyMyObject_Type);
PyDict_SetItemString(d, "MyObject", (PyObject *)&PyMyObject_Type);
return m;
}

8.4 Siblings: chararray, maskedarray, matrix

chararray vectorized string operations
>>> x = np.array([a, bbb, ccc]).view(np.chararray)
>>> x.lstrip( )
chararray([a, bbb, ccc],
dtype=|S5)
>>> x.upper()
chararray([A, BBB, CCC],
dtype=|S5)

Note: .view() has a second meaning: it can make an ndarray an instance of a specialized ndarray subclass

MaskedArray dealing with (propagation of) missing data

For floats one could use NaNs, but masks work for all types
>>> x = np.ma.array([1, 2, 3, 4], mask=[0, 1, 0, 1])
>>> x
masked_array(data = [1 -- 3 --],
mask = [False True False True],
fill_value = 999999)
>>> y = np.ma.array([1, 2, 3, 4], mask=[0, 1, 1, 1])
>>> x + y
masked_array(data = [2 -- -- --],
mask = [False True True True],
fill_value = 999999)

Masking versions of common functions

>>> np.ma.sqrt([1, -1, 2, -2])
masked_array(data = [1.0 -- 1.41421356237 --],
mask = [False True False True],
fill_value = 1e+20)

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Note: Theres more to them!

recarray purely convenience

>>> arr = np.array([(a, 1), (b, 2)], dtype=[(x, S1), (y, int)])
>>> arr2 = arr.view(np.recarray)
>>> arr2.x
chararray([a, b],
dtype=|S1)
>>> arr2.y
array([1, 2])

matrix convenience?
always 2-D
* is the matrix product, not the elementwise one
>>> np.matrix([[1, 0], [0, 1]]) * np.matrix([[1, 2], [3, 4]])
matrix([[1, 2],
[3, 4]])

8.5 Summary
Anatomy of the ndarray: data, dtype, strides.
Universal functions: elementwise operations, how to make new ones
Ndarray subclasses
Various buffer interfaces for integration with other tools
Recent additions: PEP 3118, generalized ufuncs

8.6 Contributing to Numpy/Scipy

Get this tutorial: http://www.euroscipy.org/talk/882

8.6.1 Why
Theres a bug?
I dont understand what this is supposed to do?
I have this fancy code. Would you like to have it?
Id like to help! What can I do?

8.6.2 Reporting bugs

Bug tracker (prefer this)
http://projects.scipy.org/numpy
http://projects.scipy.org/scipy
Click the Register link to get an account
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Mailing lists ( scipy.org/Mailing_Lists )

If youre unsure
No replies in a week or so? Just file a bug ticket.

Good bug report

Title: numpy.random.permutations fails for non-integer arguments
Im trying to generate random permutations, using numpy.random.permutations
When calling numpy.random.permutation with non-integer arguments
it fails with a cryptic error message:
>>> np.random.permutation(12)
array([10, 9, 4, 7, 3, 8, 0, 6, 5, 1, 11, 2])
>>> np.random.permutation(long(12))
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "mtrand.pyx", line 3311, in mtrand.RandomState.permutation
File "mtrand.pyx", line 3254, in mtrand.RandomState.shuffle
TypeError: len() of unsized object
This also happens with long arguments, and so
np.random.permutation(X.shape[0]) where X is an array fails on 64
bit windows (where shape is a tuple of longs).
It would be great if it could cast to integer or at least raise a
proper error for non-integer types.
Im using Numpy 1.4.1, built from the official tarball, on Windows
64 with Visual studio 2008, on Python.org 64-bit Python.

0. What are you trying to do?

1. Small code snippet reproducing the bug (if possible)
What actually happens
What youd expect
2. Platform (Windows / Linux / OSX, 32/64 bits, x86/PPC, ...)
3. Version of Numpy/Scipy
>>> print numpy.__version__

Check that the following is what you expect

>>> print numpy.__file__

In case you have old/broken Numpy installations lying around.

If unsure, try to remove existing Numpy installations, and reinstall...

8.6.3 Contributing to documentation

1. Documentation editor
http://docs.scipy.org/numpy
Registration
Register an account
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Subscribe to scipy-dev mailing list (subscribers-only)

Problem with mailing lists: you get mail
* But: you can turn mail delivery off
* change your subscription options, at the bottom of
http://mail.scipy.org/mailman/listinfo/scipy-dev
Send a mail @ scipy-dev mailing list; ask for activation:
To: [email protected]
Hi,
Id like to edit Numpy/Scipy docstrings. My account is XXXXX
Cheers,
N. N.

Check the style guide:

http://docs.scipy.org/numpy/
Dont be intimidated; to fix a small thing, just fix it
Edit
2. Edit sources and send patches (as for bugs)
3. Complain on the mailing list

8.6.4 Contributing features

0. Ask on mailing list, if unsure where it should go
1. Write a patch, add an enhancement ticket on the bug tracket
2. OR, create a Git branch implementing the feature + add enhancement ticket.
Especially for big/invasive additions
http://projects.scipy.org/numpy/wiki/GitMirror
http://www.spheredev.org/wiki/Git_for_the_lazy
# Clone numpy repository
git clone --origin svn http://projects.scipy.org/git/numpy.git numpy
cd numpy
# Create a feature branch
git checkout -b name-of-my-feature-branch

svn/trunk

<edit stuff>
git commit -a

Create account on http://github.com (or anywhere)

Create a new repository @ Github
Push your work to github
git remote add github git@github:YOURUSERNAME/YOURREPOSITORYNAME.git
git push github name-of-my-feature-branch

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8.6.5 How to help, in general

Bug fixes always welcome!
What irks you most
Browse the tracker
Documentation work
API docs: improvements to docstrings
* Know some Scipy module well?
User guide
* Needs to be done eventually.
* Want to think? Come up with a Table of Contents
http://scipy.org/Developer_Zone/UG_Toc
Ask on communication channels:
numpy-discussion list
scipy-dev list

8.6. Contributing to Numpy/Scipy

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CHAPTER 9

Debugging code

author Gal Varoquaux

This tutorial explores tool to understand better your code base: debugging, to find and fix bugs.
It is not specific to the scientific Python community, but the strategies that we will employ are tailored to its needs.
Prerequisites

Numpy
IPython
nosetests (http://readthedocs.org/docs/nose/en/latest/)
line_profiler (http://packages.python.org/line_profiler/)
pyflakes (http://pypi.python.org/pypi/pyflakes)
gdb for the C-debugging part.

Chapters contents
Avoiding bugs (page 198)
Coding best practices to avoid getting in trouble (page 198)
pyflakes: fast static analysis (page 199)
* Running pyflakes on the current edited file (page 199)
* A type-as-go spell-checker like integration (page 200)
Debugging workflow (page 200)
Using the Python debugger (page 201)
Invoking the debugger (page 201)
* Postmortem (page 201)
* Step-by-step execution (page 203)
* Other ways of starting a debugger (page 204)
Debugger commands and interaction (page 205)
Debugging segmentation faults using gdb (page 205)

9.1 Avoiding bugs

9.1.1 Coding best practices to avoid getting in trouble

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Brian Kernighan
Everyone knows that debugging is twice as hard as writing a program in the first place. So if youre as
clever as you can be when you write it, how will you ever debug it?
We all write buggy code. Accept it. Deal with it.
Write your code with testing and debugging in mind.
Keep It Simple, Stupid (KISS).
What is the simplest thing that could possibly work?
Dont Repeat Yourself (DRY).
Every piece of knowledge must have a single, unambiguous, authoritative representation within a
system.
Constants, algorithms, etc...
Try to limit interdependencies of your code. (Loose Coupling)
Give your variables, functions and modules meaningful names (not mathematics names)

9.1.2 pyflakes: fast static analysis

They are several static analysis tools in Python; to name a few: pylint, pychecker, and pyflakes. Here we focus on
pyflakes, which is the simplest tool.
Fast, simple
Detects syntax errors, missing imports, typos on names.
Integrating pyflakes in your editor is highly recommended, it does yield productivity gains.
Running pyflakes on the current edited file
You can bind a key to run pyflakes in the current buffer.
In kate Menu: settings -> configure kate
In plugins enable external tools
In external Tools, add pyflakes:
kdialog --title "pyflakes %filename" --msgbox "$(pyflakes %filename)"

In TextMate
Menu: TextMate -> Preferences -> Advanced -> Shell variables, add a shell variable:
TM_PYCHECKER=/Library/Frameworks/Python.framework/Versions/Current/bin/pyflakes

Then Ctrl-Shift-V is binded to a pyflakes report

In vim In your .vimrc (binds F5 to pyflakes):
autocmd
autocmd
autocmd
autocmd

FileType
FileType
FileType
FileType

python let &mp = echo "*** running % ***" ; pyflakes %

tex,mp,rst,python imap <Esc>[15~ <C-O>:make!^M
tex,mp,rst,python map <Esc>[15~ :make!^M
tex,mp,rst,python set autowrite

In emacs In your .emacs (binds F5 to pyflakes):

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(defun pyflakes-thisfile () (interactive)

(compile (format "pyflakes %s" (buffer-file-name)))
)
(define-minor-mode pyflakes-mode
"Toggle pyflakes mode.
With no argument, this command toggles the mode.
Non-null prefix argument turns on the mode.
Null prefix argument turns off the mode."
;; The initial value.
nil
;; The indicator for the mode line.
" Pyflakes"
;; The minor mode bindings.
( ([f5] . pyflakes-thisfile) )
)
(add-hook python-mode-hook (lambda () (pyflakes-mode t)))

A type-as-go spell-checker like integration

In vim Use the pyflakes.vim plugin:

1. download the zip file from http://www.vim.org/scripts/script.php?script_id=2441
2. extract the files in ~/.vim/ftplugin/python
3. make sure your vimrc has filetype plugin indent on
In
emacs
Use
the
flymake
mode
with
pyflakes,
documented
http://www.plope.com/Members/chrism/flymake-mode : add the following to your .emacs file:

on

(when (load "flymake" t)

(defun flymake-pyflakes-init ()
(let* ((temp-file (flymake-init-create-temp-buffer-copy
flymake-create-temp-inplace))
(local-file (file-relative-name
temp-file
(file-name-directory buffer-file-name))))
(list "pyflakes" (list local-file))))
(add-to-list flymake-allowed-file-name-masks
("\\.py\\" flymake-pyflakes-init)))
(add-hook find-file-hook flymake-find-file-hook)

9.2 Debugging workflow

I you do have a non trivial bug, this is when debugging strategies kick in. There is no silver bullet. Yet, strategies
help:
For debugging a given problem, the favorable situation is when the problem is isolated in a
small number of lines of code, outside framework or application code, with short modify-runfail cycles
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Python Scientific lecture notes, Release 2011

1. Make it fail reliably. Find a test case that makes the code fail every time.
2. Divide and Conquer. Once you have a failing test case, isolate the failing code.
Which module.
Which function.
Which line of code.
=> isolate a small reproducible failure: a test case
3. Change one thing at a time and re-run the failing test case.
4. Use the debugger to understand what is going wrong.
5. Take notes and be patient. It may take a while.
Note: Once you have gone through this process: isolated a tight piece of code reproducing the bug and fix the
bug using this piece of code, add the corresponding code to your test suite.

9.3 Using the Python debugger

The python debugger, pdb: http://docs.python.org/library/pdb.html, allows you to inspect your code interactively.
Specifically it allows you to:
View the source code.
Walk up and down the call stack.
Inspect values of variables.
Modify values of variables.
Set breakpoints.
print
Yes, print statements do work as a debugging tool. However to inspect runtime, it is often more efficient
to use the debugger.

9.3.1 Invoking the debugger

Ways to launch the debugger:
1. Postmortem, launch debugger after module errors.
2. Launch the module with the debugger.
3. Call the debugger inside the module
Postmortem
Situation: Youre working in ipython and you get a traceback.
Here we debug the file index_error.py. When running it, an IndexError is raised. Type %debug and drop
into the debugger.
In [1]: %run index_error.py
--------------------------------------------------------------------------IndexError
Traceback (most recent call last)
/home/varoquau/dev/scipy-lecture-notes/advanced/debugging_optimizing/index_error.py in <module>()
6

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7 if __name__ == __main__:
----> 8
index_error()
9

/home/varoquau/dev/scipy-lecture-notes/advanced/debugging_optimizing/index_error.py in index_error
3 def index_error():
4
lst = list(foobar)
----> 5
print lst[len(lst)]
6
7 if __name__ == __main__:
IndexError: list index out of range

In [2]: %debug
> /home/varoquau/dev/scipy-lecture-notes/advanced/debugging_optimizing/index_error.py(5)index_erro
4
lst = list(foobar)
----> 5
print lst[len(lst)]
6
ipdb> list
1 """Small snippet to raise an IndexError."""
2
3 def index_error():
4
lst = list(foobar)
----> 5
print lst[len(lst)]
6
7 if __name__ == __main__:
8
index_error()
9
ipdb> len(lst)
6
ipdb> print lst[len(lst)-1]
r
ipdb> quit
In [3]:

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Post-mortem debugging without IPython

In some situations you cannot use IPython, for instance to debug a script that wants to be called from the
command line. In this case, you can call the script with python -m pdb script.py:

$ python -m pdb index_error.py

> /home/varoquau/dev/scipy-lecture-notes/advanced/debugging_optimizing/index_error.py(1)<module>(
-> """Small snippet to raise an IndexError."""
(Pdb) continue
Traceback (most recent call last):
File "/usr/lib/python2.6/pdb.py", line 1296, in main
pdb._runscript(mainpyfile)
File "/usr/lib/python2.6/pdb.py", line 1215, in _runscript
self.run(statement)
File "/usr/lib/python2.6/bdb.py", line 372, in run
exec cmd in globals, locals
File "<string>", line 1, in <module>
File "index_error.py", line 8, in <module>
index_error()
File "index_error.py", line 5, in index_error
print lst[len(lst)]
IndexError: list index out of range
Uncaught exception. Entering post mortem debugging
Running cont or step will restart the program
> /home/varoquau/dev/scipy-lecture-notes/advanced/debugging_optimizing/index_error.py(5)index_err
-> print lst[len(lst)]
(Pdb)

Step-by-step execution
Situation: You believe a bug exists in a module but are not sure where.
For instance we are trying to debug wiener_filtering.py. Indeed the code runs, but the filtering does not
work well.
Run the script with the debugger:

In [1]: %run -d wiener_filtering.py

*** Blank or comment
*** Blank or comment
*** Blank or comment
Breakpoint 1 at /home/varoquau/dev/scipy-lecture-notes/advanced/debugging_optimizing/wiener
NOTE: Enter c at the ipdb> prompt to start your script.
> <string>(1)<module>()

Enter the wiener_filtering.py file and set a break point at line 34:

ipdb> n
> /home/varoquau/dev/scipy-lecture-notes/advanced/debugging_optimizing/wiener_filtering.py(
3
1---> 4 import numpy as np
5 import scipy as sp

ipdb> b 34
Breakpoint 2 at /home/varoquau/dev/scipy-lecture-notes/advanced/debugging_optimizing/wiener

Continue execution to next breakpoint with c(ont(inue)):

ipdb> c
> /home/varoquau/dev/scipy-lecture-notes/advanced/debugging_optimizing/wiener_filtering.py(
33
"""
2--> 34
noisy_img = noisy_img
35
denoised_img = local_mean(noisy_img, size=size)

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Step into code with n(ext) and s(tep): next jumps to the next statement in the current execution
context, while step will go across execution contexts, i.e. enable exploring inside function calls:

ipdb> s
> /home/varoquau/dev/scipy-lecture-notes/advanced/debugging_optimizing/wiener_filtering.py(
2
34
noisy_img = noisy_img
---> 35
denoised_img = local_mean(noisy_img, size=size)
36
l_var = local_var(noisy_img, size=size)

ipdb> n
> /home/varoquau/dev/scipy-lecture-notes/advanced/debugging_optimizing/wiener_filtering.py(
35
denoised_img = local_mean(noisy_img, size=size)
---> 36
l_var = local_var(noisy_img, size=size)
37
for i in range(3):

Step a few lines and explore the local variables:

ipdb> n
> /home/varoquau/dev/scipy-lecture-notes/advanced/debugging_optimizing/wiener_filtering.py(
36
l_var = local_var(noisy_img, size=size)
---> 37
for i in range(3):
38
res = noisy_img - denoised_img
ipdb> print l_var
[[5868 5379 5316 ..., 5071 4799 5149]
[5013 363 437 ..., 346 262 4355]
[5379 410 344 ..., 392 604 3377]
...,
[ 435 362 308 ..., 275 198 1632]
[ 548 392 290 ..., 248 263 1653]
[ 466 789 736 ..., 1835 1725 1940]]
ipdb> print l_var.min()
0

Oh dear, nothing but integers, and 0 variation. Here is our bug, we are doing integer arithmetic.
Raising exception on numerical errors
When we run the wiener_filtering.py file, the following warnings are raised:
In [2]: %run wiener_filtering.py
Warning: divide by zero encountered in divide
Warning: divide by zero encountered in divide
Warning: divide by zero encountered in divide

We can turn these warnings in exception, which enables us to do post-mortem debugging on them, and find
our problem more quickly:
In [3]: np.seterr(all=raise)
Out[3]: {divide: print, invalid: print, over: print, under: ignore}

Other ways of starting a debugger

Raising an exception as a poor man break point
If you find it tedious to note the line number to set a break point, you can simply raise an exception at the
point that you want to inspect and use ipythons %debug. Note that in this case you cannot step or continue
the execution.
Debugging test failures using nosetests
You can run nosetests pdb to drop in post-mortem debugging on exceptions, and nosetests pdb-failure to
inspect test failures using the debugger.

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In addition, you can use the IPython interface for the debugger in nose by installing the nose plugin ipdbplugin. You can than pass ipdb and ipdb-failure options to nosetests.
Calling the debugger explicitly
Insert the following line where you want to drop in the debugger:
import pdb; pdb.set_trace()

Warning: When running nosetests, the output is captured, and thus it seems that the debugger does not work.
Simply run the nosetests with the -s flag.

Graphical debuggers
For stepping through code and inspecting variables, you might find it more convenient to use a graphical
debugger such as winpdb.
Alternatively, pudb is a good semi-graphical debugger with a text user interface in the console.

9.3.2 Debugger commands and interaction

l(list)
u(p)
d(own)
n(ext)
s(tep)
bt
a
!command

Lists the code at the current position

Walk up the call stack
Walk down the call stack
Execute the next line (does not go down in new functions)
Execute the next statement (goes down in new functions)
Print the call stack
Print the local variables
Exectute the given Python command (by opposition to pdb commands

Warning: Debugger commands are not Python code

You cannot name the variables the way you want. For instance, if in you cannot override the variables in the
current frame with the same name: use different names then your local variable when typing code in the
debugger.

9.4 Debugging segmentation faults using gdb

If you have a segmentation fault, you cannot debug it with pdb, as it crashes the Python interpreter before it can
drop in the debugger. Similarly, if you have a bug in C code embedded in Python, pdb is useless. For this we turn
to the gnu debugger, gdb, available on Linux.
Before we start with gdb, let us add a few Python-specific tools to it. For this we add a few macros to our ~/.gbdinit.
The optimal choice of macro depends on your Python version and your gdb version. I have added a simplified
version in gdbinit, but feel free to read DebuggingWithGdb.
To debug with gdb the Python script segfault.py, we can run the script in gdb as follows:
$ gdb python
...
(gdb) run segfault.py
Starting program: /usr/bin/python segfault.py
[Thread debugging using libthread_db enabled]
Program received signal SIGSEGV, Segmentation fault.
_strided_byte_copy (dst=0x8537478 "\360\343G", outstrides=4, src=
0x86c0690 <Address 0x86c0690 out of bounds>, instrides=32, N=3,

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elsize=4)
at numpy/core/src/multiarray/ctors.c:365
365
_FAST_MOVE(Int32);
(gdb)

We get a segfault, and gdb captures it for post-mortem debugging in the C level stack (not the Python call stack).
We can debug the C call stack using gdbs commands:
(gdb) up
#1 0x004af4f5 in _copy_from_same_shape (dest=<value optimized out>,
src=<value optimized out>, myfunc=0x496780 <_strided_byte_copy>,
swap=0)
at numpy/core/src/multiarray/ctors.c:748
748
myfunc(dit->dataptr, dest->strides[maxaxis],

As you can see, right now, we are in the C code of numpy. We would like to know what is the Python code that
triggers this segfault, so we go up the stack until we hit the Python execution loop:

(gdb) up
#8 0x080ddd23 in call_function (f=
Frame 0x85371ec, for file /home/varoquau/usr/lib/python2.6/site-packages/numpy/core/arrayprint
at ../Python/ceval.c:3750
3750
../Python/ceval.c: No such file or directory.
in ../Python/ceval.c

(gdb) up
#9 PyEval_EvalFrameEx (f=
Frame 0x85371ec, for file /home/varoquau/usr/lib/python2.6/site-packages/numpy/core/arrayprint
at ../Python/ceval.c:2412
2412
in ../Python/ceval.c
(gdb)

Once we are in the Python execution loop, we can use our special Python helper function. For instance we can
find the corresponding Python code:
(gdb) pyframe
/home/varoquau/usr/lib/python2.6/site-packages/numpy/core/arrayprint.py (158): _leading_trailing
(gdb)

This is numpy code, we need to go up until we find code that we have written:

(gdb) up
...
(gdb) up
#34 0x080dc97a in PyEval_EvalFrameEx (f=
Frame 0x82f064c, for file segfault.py, line 11, in print_big_array (small_array=<numpy.ndarray
1630
../Python/ceval.c: No such file or directory.
in ../Python/ceval.c
(gdb) pyframe
segfault.py (12): print_big_array

The corresponding code is:

1
2
3
4

def print_big_array(small_array):
big_array = make_big_array(small_array)
print big_array[-10:]
return big_array

Thus the segfault happens when printing big_array[-10:]. The reason is simply that big_array has been allocated
with its end outside the program memory.
Note: For a list of Python-specific commands defined in the gdbinit, read the source of this file.

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Wrap up exercise
The following script is well documented and hopefully legible. It seeks to answer a problem of actual interest
for numerical computing, but it does not work... Can you debug it?
Python source code: to_debug.py

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207

CHAPTER 10

Optimizing code

author Gal Varoquaux

Donald Knuth
Premature optimization is the root of all evil
This chapter deals with strategies to make Python code go faster.
Prerequisites
line_profiler (http://packages.python.org/line_profiler/)

Chapters contents
Optimization workflow (page 208)
Profiling Python code (page 209)
Timeit (page 209)
Profiler (page 209)
Line-profiler (page 210)
Making code go faster (page 211)
Algorithmic optimization (page 211)
* Example of the SVD (page 211)
Writing faster numerical code (page 212)

10.1 Optimization workflow

1. Make it work: write the code in a simple legible ways.
2. Make it work reliably: write automated test cases, make really sure that your algorithm is right and that if
you break it, the tests will capture the breakage.
3. Optimize the code by profiling simple use-cases to find the bottlenecks and speeding up these bottleneck,
finding a better algorithm or implementation. Keep in mind that a trade off should be found between
profiling on a realistic example and the simplicity and speed of execution of the code. For efficient work, it
is best to work with profiling runs lasting around 10s.

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10.2 Profiling Python code

No optimization without measuring!
Measure: profiling, timing
Youll have surprises: the fastest code is not always what you think

10.2.1 Timeit
In IPython, use timeit (http://docs.python.org/library/timeit.html) to time elementary operations:
In [1]: import numpy as np
In [2]: a = np.arange(1000)
In [3]: %timeit a ** 2
100000 loops, best of 3: 5.73 us per loop
In [4]: %timeit a ** 2.1
1000 loops, best of 3: 154 us per loop
In [5]: %timeit a * a
100000 loops, best of 3: 5.56 us per loop

Use this to guide your choice between strategies.

Note: For long running calls, using %time instead of %timeit; it is less precise but faster

10.2.2 Profiler
Useful when you have a large program to profile, for example the following file:
import numpy as np
from scipy import linalg
from ica import fastica
def test():
data = np.random.random((5000, 100))
u, s, v = linalg.svd(data)
pca = np.dot(u[:10, :], data)
results = fastica(pca.T, whiten=False)
test()

In IPython we can time the script:

In [1]: %run -t demo.py
IPython CPU timings (estimated):
User :
14.3929 s.
System:
0.256016 s.

and profile it:

In [2]: %run -p demo.py
916 function calls in 14.551 CPU seconds
Ordered by: internal time

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ncalls tottime
1
14.457
1
0.054
1
0.017
54
0.011
2
0.005
6
0.001
6
0.001
14
0.001
19
0.001
1
0.001
1
0.001
107
0.000
7
0.000
7
0.000
172
0.000
1
0.000
29
0.000
35
0.000
35
0.000
21
0.000
41
0.000
28
0.000
1
0.000
...

percall
14.457
0.054
0.017
0.000
0.002
0.000
0.000
0.000
0.000
0.001
0.001
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000

cumtime
14.479
0.054
0.021
0.011
0.005
0.001
0.001
0.001
0.001
0.008
14.551
0.001
0.004
0.002
0.000
14.551
0.000
0.000
0.001
0.001
0.000
0.000
0.008

percall
14.479
0.054
0.021
0.000
0.002
0.000
0.000
0.000
0.000
0.008
14.551
0.000
0.001
0.000
0.000
14.551
0.000
0.000
0.000
0.000
0.000
0.000
0.008

filename:lineno(function)
decomp.py:849(svd)
{method random_sample of mtrand.RandomState objects
function_base.py:645(asarray_chkfinite)
{numpy.core._dotblas.dot}
{method any of numpy.ndarray objects}
ica.py:195(gprime)
ica.py:192(g)
{numpy.linalg.lapack_lite.dsyevd}
twodim_base.py:204(diag)
ica.py:69(_ica_par)
{execfile}
defmatrix.py:239(__array_finalize__)
ica.py:58(_sym_decorrelation)
linalg.py:841(eigh)
{isinstance}
demo.py:1(<module>)
numeric.py:180(asarray)
defmatrix.py:193(__new__)
defmatrix.py:43(asmatrix)
defmatrix.py:287(__mul__)
{numpy.core.multiarray.zeros}
{method transpose of numpy.ndarray objects}
ica.py:97(fastica)

Clearly the svd (in decomp.py) is what takes most of our time, a.k.a. the bottleneck. We have to find a way to
make this step go faster, or to avoid this step (algorithmic optimization). Spending time on the rest of the code is
useless.

10.2.3 Line-profiler
The profiler is great: it tells us which function takes most of the time, but not where it is called.
For this, we use the line_profiler: in the source file, we decorate a few functions that we want to inspect with
@profile (no need to import it):
@profile
def test():
data = np.random.random((5000, 100))
u, s, v = linalg.svd(data)
pca = np.dot(u[:10, :], data)
results = fastica(pca.T, whiten=False)

Then we run the script using the kernprof.py program, with switches - and -v:
~ $ kernprof.py -l -v demo.py
Wrote profile results to demo.py.lprof
Timer unit: 1e-06 s
File: demo.py
Function: test at line 5
Total time: 14.2793 s
Line #
Hits
Time Per Hit
% Time Line Contents
==============================================================
5
@profile
6
def test():
7
1
19015 19015.0
0.1
data = np.random.random((5000, 100))
8
1
14242163 14242163.0
99.7
u, s, v = linalg.svd(data)

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9
10

1
1

10282
7799

10282.0
7799.0

0.1
0.1

pca = np.dot(u[:10, :], data)

results = fastica(pca.T, whiten=False)

The SVD is taking all the time. We need to optimise this line.

10.3 Making code go faster

Once we have identified the bottlenecks, we need to make the corresponding code go faster.

10.3.1 Algorithmic optimization

The first thing to look for is algorithmic optimization: are there ways to compute less, or better?
For a high-level view of the problem, a good understanding of the maths behind the algorithm helps. However, it
is not uncommon to find simple changes, like moving computation or memory allocation outside a for loop,
that bring in big gains.
Example of the SVD
In both examples above, the SVD - Singular Value Decomposition - is what takes most of the time. Indeed, the
computational cost of this algorithm is roughly n3 in the size of the input matrix.
However, in both of these example, we are not using all the output of the SVD, but only the first few rows of its
first return argument. If we use the svd implementation of scipy, we can ask for an incomplete version of the
SVD. Note that implementations of linear algebra in scipy are richer then those in numpy and should be preferred.
In [3]: %timeit np.linalg.svd(data)
1 loops, best of 3: 14.5 s per loop
In [4]: from scipy import linalg
In [5]: %timeit linalg.svd(data)
1 loops, best of 3: 14.2 s per loop
In [6]: %timeit linalg.svd(data, full_matrices=False)
1 loops, best of 3: 295 ms per loop
In [7]: %timeit np.linalg.svd(data, full_matrices=False)
1 loops, best of 3: 293 ms per loop

Real incomplete SVDs, e.g. computing only the first 10 eigenvectors, can be computed with arpack, available in
scipy.sparse.linalg.eigsh.
Computational linear algebra
For certain algorithms, many of the bottlenecks will be linear algebra computations. In this case, using the
right function to solve the right problem is key. For instance, an eigenvalue problem with a symmetric matrix
is easier to solve than with a general matrix. Also, most often, you can avoid inverting a matrix and use a
less costly (and more numerically stable) operation.
Know your computational linear algebra. When in doubt, explore scipy.linalg, and use %timeit to
try out different alternatives on your data.

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10.4 Writing faster numerical code

A complete discussion on advanced use of numpy is found in chapter Advanced Numpy (page 164), or in the
article The NumPy array: a structure for efficient numerical computation by van der Walt et al. Here we discuss
only some commonly encountered tricks to make code faster.
Vectorizing for loops
Find tricks to avoid for loops using numpy arrays. For this, masks and indices arrays can be useful.
Broadcasting
Use broadcasting (page 174) to do operations on arrays as small as possible before combining them.
In place operations
In [1]: a = np.zeros(1e7)
In [2]: %timeit global a ; a = 0*a
10 loops, best of 3: 111 ms per loop
In [3]: %timeit global a ; a *= 0
10 loops, best of 3: 48.4 ms per loop

note: we need global a in the timeit so that it work, as it is assigning to a, and thus considers it as a local
variable.
Be easy on the memory: use views, and not copies
Copying big arrays is as costly as making simple numerical operations on them:
In [1]: a = np.zeros(1e7)
In [2]: %timeit a.copy()
10 loops, best of 3: 124 ms per loop
In [3]: %timeit a + 1
10 loops, best of 3: 112 ms per loop

Beware of cache effects

Memory access is cheaper when it is grouped: accessing a big array in a continuous way is much faster than
random access. This implies amongst other things that smaller strides are faster (see CPU cache effects
(page 175)):
In [1]: c = np.zeros((1e4, 1e4), order=C)
In [2]: %timeit c.sum(axis=0)
1 loops, best of 3: 3.89 s per loop
In [3]: %timeit c.sum(axis=1)
1 loops, best of 3: 188 ms per loop
In [4]: c.strides
Out[4]: (80000, 8)

This is the reason why Fortran ordering or C ordering may make a big difference on operations. Using
numexpr can be useful to automatically optimize code for such effects.
Use compiled code
The last resort, once you are sure that all the high-level optimizations have been explored, is to transfer the
hot spots, i.e. the few lines or functions in which most of the time is spent, to compiled code. For compiled
code, the preferred option is to use Cython: it is easy to transform exiting Python code in compiled code,
and with a good use of the numpy support yields efficient code on numpy arrays, for instance by unrolling
loops.

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Warning: For all the above: profile and time your choices. Dont base your optimization on theoretical
considerations.

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CHAPTER 11

Sparse Matrices in SciPy

author Robert Cimrman

11.1 Introduction
(dense) matrix is:
mathematical object
data structure for storing a 2D array of values
important features:
memory allocated once for all items
usually a contiguous chunk, think NumPy ndarray
fast access to individual items (*)

11.1.1 Why Sparse Matrices?

the memory, that grows like n**2
small example (double precision matrix):
>>>
>>>
>>>
>>>
>>>
>>>
>>>

import numpy as np
import matplotlib.pyplot as plt
x = np.linspace(0, 1e6, 10)
plt.plot(x, 8.0 * (x**2) / 1e6, lw=5)
plt.xlabel(size n)
plt.ylabel(memory [MB])
plt.show()

11.1.2 Sparse Matrices vs. Sparse Matrix Storage Schemes

sparse matrix is a matrix, which is almost empty
storing all the zeros is wasteful -> store only nonzero items
think compression
pros: huge memory savings
cons: depends on actual storage scheme, (*) usually does not hold

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11.1.3 Typical Applications

solution of partial differential equations (PDEs)
the finite element method
mechanical engineering, electrotechnics, physics, ...
graph theory
nonzero at (i, j) means that node i is connected to node j
...

11.1.4 Prerequisites
recent versions of
numpy
scipy
matplotlib (optional)
ipython (the enhancements come handy)

11.1.5 Sparsity Structure Visualization

spy() from matplotlib
example plots:

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11.2 Storage Schemes

seven sparse matrix types in scipy.sparse:
1. csc_matrix: Compressed Sparse Column format
2. csr_matrix: Compressed Sparse Row format
3. bsr_matrix: Block Sparse Row format
4. lil_matrix: List of Lists format
5. dok_matrix: Dictionary of Keys format
6. coo_matrix: COOrdinate format (aka IJV, triplet format)
7. dia_matrix: DIAgonal format
each suitable for some tasks
many employ sparsetools C++ module by Nathan Bell
assume the following is imported:
>>> import numpy as np
>>> import scipy.sparse as sps
>>> import matplotlib.pyplot as plt

warning for NumPy users:

the multiplication with * is the matrix multiplication (dot product)
not part of NumPy!
* passing a sparse matrix object to NumPy functions expecting ndarray/matrix does not work

11.2.1 Common Methods

all scipy.sparse classes are subclasses of spmatrix
default implementation of arithmetic operations
* always converts to CSR
* subclasses override for efficiency
shape, data type set/get
nonzero indices
format conversion, interaction with NumPy (toarray(), todense())

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...
attributes:
mtx.A - same as mtx.toarray()
mtx.T - transpose (same as mtx.transpose())
mtx.H - Hermitian (conjugate) transpose
mtx.real - real part of complex matrix
mtx.imag - imaginary part of complex matrix
mtx.size - the number of nonzeros (same as self.getnnz())
mtx.shape - the number of rows and columns (tuple)
data usually stored in NumPy arrays

11.2.2 Sparse Matrix Classes

Diagonal Format (DIA)
very simple scheme
diagonals in dense NumPy array of shape (n_diag, length)
fixed length -> waste space a bit when far from main diagonal
subclass of _data_matrix (sparse matrix classes with data attribute)
offset for each diagonal
0 is the main diagonal
negative offset = below
positive offset = above
fast matrix * vector (sparsetools)
fast and easy item-wise operations
manipulate data array directly (fast NumPy machinery)
constructor accepts:
dense matrix (array)
sparse matrix
shape tuple (create empty matrix)
(data, offsets) tuple
no slicing, no individual item access
use:
rather specialized
solving PDEs by finite differences
with an iterative solver

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Examples
create some DIA matrices:
>>> data = np.array([[1, 2, 3, 4]]).repeat(3, axis=0)
>>> data
array([[1, 2, 3, 4],
[1, 2, 3, 4],
[1, 2, 3, 4]])
>>> offsets = np.array([0, -1, 2])
>>> mtx = sps.dia_matrix((data, offsets), shape=(4, 4))
>>> mtx
<4x4 sparse matrix of type <type numpy.int32>
with 9 stored elements (3 diagonals) in DIAgonal format>
>>> mtx.todense()
matrix([[1, 0, 3, 0],
[1, 2, 0, 4],
[0, 2, 3, 0],
[0, 0, 3, 4]])
>>> data = np.arange(12).reshape((3, 4)) + 1
>>> data
array([[ 1, 2, 3, 4],
[ 5, 6, 7, 8],
[ 9, 10, 11, 12]])
>>> mtx = sps.dia_matrix((data, offsets), shape=(4, 4))
>>> mtx.data
array([[ 1, 2, 3, 4],
[ 5, 6, 7, 8],
[ 9, 10, 11, 12]])
>>> mtx.offsets
array([ 0, -1, 2])
>>> print mtx
(0, 0)
1
(1, 1)
2
(2, 2)
3
(3, 3)
4
(1, 0)
5
(2, 1)
6
(3, 2)
7
(0, 2)
11
(1, 3)
12
>>> mtx.todense()
matrix([[ 1, 0, 11, 0],
[ 5, 2, 0, 12],
[ 0, 6, 3, 0],
[ 0, 0, 7, 4]])

explanation with a scheme:

offset: row
2:
1:
0:
-1:
-2:
-3:

9
--10-----1 . 11 .
5 2 . 12
. 6 3 .
. . 7 4
---------8

matrix-vector multiplication

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>>> vec = np.ones((4,))

>>> vec
array([ 1., 1., 1., 1.])
>>> mtx * vec
array([ 12., 19.,
9., 11.])
>>> mtx.toarray() * vec
array([[ 1.,
0., 11.,
0.],
[ 5.,
2.,
0., 12.],
[ 0.,
6.,
3.,
0.],
[ 0.,
0.,
7.,
4.]])

List of Lists Format (LIL)

row-based linked list
each row is a Python list (sorted) of column indices of non-zero elements
rows stored in a NumPy array (dtype=np.object)
non-zero values data stored analogously
efficient for constructing sparse matrices incrementally
constructor accepts:
dense matrix (array)
sparse matrix
shape tuple (create empty matrix)
flexible slicing, changing sparsity structure is efficient
slow arithmetics, slow column slicing due to being row-based
use:
when sparsity pattern is not known apriori or changes
example: reading a sparse matrix from a text file

Examples
create an empty LIL matrix:
>>> mtx = sps.lil_matrix((4, 5))

prepare random data:

>>> from
>>> data
>>> data
array([[
[

numpy.random import rand

= np.round(rand(2, 3))
0.,
0.,

0.,
0.,

1.],
1.]])

assign the data using fancy indexing:

>>> mtx[:2, [1, 2, 3]] = data
>>> mtx
<4x5 sparse matrix of type <type numpy.float64>
with 2 stored elements in LInked List format>
>>> print mtx
(0, 3)
1.0
(1, 3)
1.0
>>> mtx.todense()

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matrix([[ 0., 0.,

[ 0., 0.,
[ 0., 0.,
[ 0., 0.,
>>> mtx.toarray()
array([[ 0., 0.,
[ 0., 0.,
[ 0., 0.,
[ 0., 0.,

0.,
0.,
0.,
0.,
0.,
0.,
0.,
0.,

1.,
1.,
0.,
0.,
1.,
1.,
0.,
0.,

0.],
0.],
0.],
0.]])
0.],
0.],
0.],
0.]])

more slicing and indexing:

>>> mtx = sps.lil_matrix([[0, 1, 2, 0], [3, 0, 1, 0], [1, 0, 0, 1]])
>>> mtx.todense()
matrix([[0, 1, 2, 0],
[3, 0, 1, 0],
[1, 0, 0, 1]])
>>> print mtx
(0, 1)
1
(0, 2)
2
(1, 0)
3
(1, 2)
1
(2, 0)
1
(2, 3)
1
>>> mtx[:2, :]
<2x4 sparse matrix of type <type numpy.int32>
with 4 stored elements in LInked List format>
>>> mtx[:2, :].todense()
matrix([[0, 1, 2, 0],
[3, 0, 1, 0]])
>>> mtx[1:2, [0,2]].todense()
matrix([[3, 1]])
>>> mtx.todense()
matrix([[0, 1, 2, 0],
[3, 0, 1, 0],
[1, 0, 0, 1]])

Dictionary of Keys Format (DOK)

subclass of Python dict
keys are (row, column) index tuples (no duplicate entries allowed)
values are corresponding non-zero values
efficient for constructing sparse matrices incrementally
constructor accepts:
dense matrix (array)
sparse matrix
shape tuple (create empty matrix)
efficient O(1) access to individual elements
flexible slicing, changing sparsity structure is efficient
can be efficiently converted to a coo_matrix once constructed
slow arithmetics (for loops with dict.iteritems())
use:
when sparsity pattern is not known apriori or changes

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Examples
create a DOK matrix element by element:
>>> mtx = sps.dok_matrix((5, 5), dtype=np.float64)
>>> mtx
<5x5 sparse matrix of type <type numpy.float64>
with 0 stored elements in Dictionary Of Keys format>
>>> for ir in range(5):
>>>
for ic in range(5):
>>>
mtx[ir, ic] = 1.0 * (ir != ic)
>>> mtx
<5x5 sparse matrix of type <type numpy.float64>
with 25 stored elements in Dictionary Of Keys format>
>>> mtx.todense()
matrix([[ 0., 1., 1., 1., 1.],
[ 1., 0., 1., 1., 1.],
[ 1., 1., 0., 1., 1.],
[ 1., 1., 1., 0., 1.],
[ 1., 1., 1., 1., 0.]])

something is wrong, lets start over:

>>> mtx = sps.dok_matrix((5, 5), dtype=np.float64)
>>> for ir in range(5):
>>>
for ic in range(5):
>>>
if (ir != ic): mtx[ir, ic] = 1.0
>>> mtx
<5x5 sparse matrix of type <type numpy.float64>
with 20 stored elements in Dictionary Of Keys format>

slicing and indexing:

>>> mtx[1, 1]
0.0
>>> mtx[1, 1:3]
<1x2 sparse matrix of type <type numpy.float64>
with 1 stored elements in Dictionary Of Keys format>
>>> mtx[1, 1:3].todense()
matrix([[ 0., 1.]])
>>> mtx[[2,1], 1:3].todense()
-----------------------------------------------------------Traceback (most recent call last):
<snip>
NotImplementedError: fancy indexing supported over one axis only

Coordinate Format (COO)

also known as the ijv or triplet format
three NumPy arrays: row, col, data
data[i] is value at (row[i], col[i]) position
permits duplicate entries
subclass of _data_matrix (sparse matrix classes with data attribute)
fast format for constructing sparse matrices
constructor accepts:
dense matrix (array)
sparse matrix

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shape tuple (create empty matrix)

(data, ij) tuple
very fast conversion to and from CSR/CSC formats
fast matrix * vector (sparsetools)
fast and easy item-wise operations
manipulate data array directly (fast NumPy machinery)
no slicing, no arithmetics (directly)
use:
facilitates fast conversion among sparse formats
when converting to other format (usually CSR or CSC), duplicate entries are summed together
* facilitates efficient construction of finite element matrices

Examples
create empty COO matrix:
>>> mtx = sps.coo_matrix((3, 4), dtype=np.int8)
>>> mtx.todense()
matrix([[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0]], dtype=int8)

create using (data, ij) tuple:

>>> row = np.array([0, 3, 1, 0])
>>> col = np.array([0, 3, 1, 2])
>>> data = np.array([4, 5, 7, 9])
>>> mtx = sps.coo_matrix((data, (row, col)), shape=(4, 4))
>>> mtx
<4x4 sparse matrix of type <type numpy.int32>
with 4 stored elements in COOrdinate format>
>>> mtx.todense()
matrix([[4, 0, 9, 0],
[0, 7, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 5]])

duplicates entries are summed together:

>>> row = np.array([0, 0, 1, 3, 1, 0, 0])
>>> col = np.array([0, 2, 1, 3, 1, 0, 0])
>>> data = np.array([1, 1, 1, 1, 1, 1, 1])
>>> mtx = sps.coo_matrix((data, (row, col)), shape=(4, 4))
>>> mtx.todense()
matrix([[3, 0, 1, 0],
[0, 2, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 1]])

no slicing...:
>>> mtx[2, 3]
-----------------------------------------------------------Traceback (most recent call last):
File "<ipython console>", line 1, in <module>
TypeError: coo_matrix object is unsubscriptable

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Compressed Sparse Row Format (CSR)

row oriented
three NumPy arrays: indices, indptr, data
* indices is array of column indices
* data is array of corresponding nonzero values
* indptr points to row starts in indices and data
* length is n_row + 1, last item = number of values = length of both indices and data
* nonzero values of the i-th row are data[indptr[i]:indptr[i+1]] with column
indices indices[indptr[i]:indptr[i+1]]
* item (i, j) can be accessed as data[indptr[i]+k], where k is position of j in
indices[indptr[i]:indptr[i+1]]
subclass of _cs_matrix (common CSR/CSC functionality)
* subclass of _data_matrix (sparse matrix classes with data attribute)
fast matrix vector products and other arithmetics (sparsetools)
constructor accepts:
dense matrix (array)
sparse matrix
shape tuple (create empty matrix)
(data, ij) tuple
(data, indices, indptr) tuple
efficient row slicing, row-oriented operations
slow column slicing, expensive changes to the sparsity structure
use:
actual computations (most linear solvers support this format)

Examples
create empty CSR matrix:
>>> mtx = sps.csr_matrix((3, 4), dtype=np.int8)
>>> mtx.todense()
matrix([[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0]], dtype=int8)

create using (data, ij) tuple:

>>> row = np.array([0, 0, 1, 2, 2, 2])
>>> col = np.array([0, 2, 2, 0, 1, 2])
>>> data = np.array([1, 2, 3, 4, 5, 6])
>>> mtx = sps.csr_matrix((data, (row, col)), shape=(3, 3))
>>> mtx
<3x3 sparse matrix of type <type numpy.int32>
with 6 stored elements in Compressed Sparse Row format>
>>> mtx.todense()
matrix([[1, 0, 2],
[0, 0, 3],
[4, 5, 6]])

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>>> mtx.data
array([1, 2, 3, 4, 5, 6])
>>> mtx.indices
array([0, 2, 2, 0, 1, 2])
>>> mtx.indptr
array([0, 2, 3, 6])

create using (data, indices, indptr) tuple:

>>> data = np.array([1, 2, 3, 4, 5, 6])
>>> indices = np.array([0, 2, 2, 0, 1, 2])
>>> indptr = np.array([0, 2, 3, 6])
>>> mtx = sps.csr_matrix((data, indices, indptr), shape=(3, 3))
>>> mtx.todense()
matrix([[1, 0, 2],
[0, 0, 3],
[4, 5, 6]])

Compressed Sparse Column Format (CSC)

column oriented
three NumPy arrays: indices, indptr, data
* indices is array of row indices
* data is array of corresponding nonzero values
* indptr points to column starts in indices and data
* length is n_col + 1, last item = number of values = length of both indices and data
* nonzero values of the i-th column are data[indptr[i]:indptr[i+1]] with row
indices indices[indptr[i]:indptr[i+1]]
* item (i, j) can be accessed as data[indptr[j]+k], where k is position of i in
indices[indptr[j]:indptr[j+1]]
subclass of _cs_matrix (common CSR/CSC functionality)
* subclass of _data_matrix (sparse matrix classes with data attribute)
fast matrix vector products and other arithmetics (sparsetools)
constructor accepts:
dense matrix (array)
sparse matrix
shape tuple (create empty matrix)
(data, ij) tuple
(data, indices, indptr) tuple
efficient column slicing, column-oriented operations
slow row slicing, expensive changes to the sparsity structure
use:
actual computations (most linear solvers support this format)

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Examples
create empty CSC matrix:
>>> mtx = sps.csc_matrix((3, 4), dtype=np.int8)
>>> mtx.todense()
matrix([[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0]], dtype=int8)

create using (data, ij) tuple:

>>> row = np.array([0, 0, 1, 2, 2, 2])
>>> col = np.array([0, 2, 2, 0, 1, 2])
>>> data = np.array([1, 2, 3, 4, 5, 6])
>>> mtx = sps.csc_matrix((data, (row, col)), shape=(3, 3))
>>> mtx
<3x3 sparse matrix of type <type numpy.int32>
with 6 stored elements in Compressed Sparse Column format>
>>> mtx.todense()
matrix([[1, 0, 2],
[0, 0, 3],
[4, 5, 6]])
>>> mtx.data
array([1, 4, 5, 2, 3, 6])
>>> mtx.indices
array([0, 2, 2, 0, 1, 2])
>>> mtx.indptr
array([0, 2, 3, 6])

create using (data, indices, indptr) tuple:

>>> data = np.array([1, 4, 5, 2, 3, 6])
>>> indices = np.array([0, 2, 2, 0, 1, 2])
>>> indptr = np.array([0, 2, 3, 6])
>>> mtx = sps.csc_matrix((data, indices, indptr), shape=(3, 3))
>>> mtx.todense()
matrix([[1, 0, 2],
[0, 0, 3],
[4, 5, 6]])

Block Compressed Row Format (BSR)

basically a CSR with dense sub-matrices of fixed shape instead of scalar items
block size (R, C) must evenly divide the shape of the matrix (M, N)
three NumPy arrays: indices, indptr, data
* indices is array of column indices for each block
* data is array of corresponding nonzero values of shape (nnz, R, C)
* ...
subclass of _cs_matrix (common CSR/CSC functionality)
* subclass of _data_matrix (sparse matrix classes with data attribute)
fast matrix vector products and other arithmetics (sparsetools)
constructor accepts:
dense matrix (array)
sparse matrix

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shape tuple (create empty matrix)

(data, ij) tuple
(data, indices, indptr) tuple
many arithmetic operations considerably more efficient than CSR for sparse matrices with dense submatrices
use:
like CSR
vector-valued finite element discretizations

Examples
create empty BSR matrix with (1, 1) block size (like CSR...):
>>> mtx = sps.bsr_matrix((3, 4), dtype=np.int8)
>>> mtx
<3x4 sparse matrix of type <type numpy.int8>
with 0 stored elements (blocksize = 1x1) in Block Sparse Row format>
>>> mtx.todense()
matrix([[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0]], dtype=int8)

create empty BSR matrix with (3, 2) block size:

>>> mtx = sps.bsr_matrix((3, 4), blocksize=(3, 2), dtype=np.int8)
>>> mtx
<3x4 sparse matrix of type <type numpy.int8>
with 0 stored elements (blocksize = 3x2) in Block Sparse Row format>
>>> mtx.todense()
matrix([[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0]], dtype=int8)

a bug?
create using (data, ij) tuple with (1, 1) block size (like CSR...):
>>> row = np.array([0, 0, 1, 2, 2, 2])
>>> col = np.array([0, 2, 2, 0, 1, 2])
>>> data = np.array([1, 2, 3, 4, 5, 6])
>>> mtx = sps.bsr_matrix((data, (row, col)), shape=(3, 3))
>>> mtx
<3x3 sparse matrix of type <type numpy.int32>
with 6 stored elements (blocksize = 1x1) in Block Sparse Row format>
>>> mtx.todense()
matrix([[1, 0, 2],
[0, 0, 3],
[4, 5, 6]])
>>> mtx.data
array([[[1]],
[[2]],
[[3]],
[[4]],
[[5]],

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[[6]]])
>>> mtx.indices
array([0, 2, 2, 0, 1, 2])
>>> mtx.indptr
array([0, 2, 3, 6])

create using (data, indices, indptr) tuple with (2, 2) block size:
>>> indptr = np.array([0, 2, 3, 6])
>>> indices = np.array([0, 2, 2, 0, 1, 2])
>>> data = np.array([1, 2, 3, 4, 5, 6]).repeat(4).reshape(6, 2, 2)
>>> mtx = sps.bsr_matrix((data, indices, indptr), shape=(6, 6))
>>> mtx.todense()
matrix([[1, 1, 0, 0, 2, 2],
[1, 1, 0, 0, 2, 2],
[0, 0, 0, 0, 3, 3],
[0, 0, 0, 0, 3, 3],
[4, 4, 5, 5, 6, 6],
[4, 4, 5, 5, 6, 6]])
>>> data
array([[[1, 1],
[1, 1]],
[[2, 2],
[2, 2]],
[[3, 3],
[3, 3]],
[[4, 4],
[4, 4]],
[[5, 5],
[5, 5]],
[[6, 6],
[6, 6]]])

11.2.3 Summary
Table 11.1: Summary of storage schemes.
format
DIA

matrix *
vector
sparsetools

get
item
.

fancy
get
.

set
item
.

fancy
set
.

LIL

via CSR

yes

yes

yes

yes

DOK

python

yes

yes

yes

COO

sparsetools

one axis
only
.

CSR

sparsetools

yes

yes

slow

CSC

sparsetools

yes

yes

BSR

sparsetools

11.2. Storage Schemes

solvers

note
has data array, specialized

iterative
iterative
iterative
iterative
any

slow

any

specialized

arithmetics via CSR,

incremental construction
O(1) item access, incremental
construction
has data array, facilitates fast
conversion
has data array, fast row-wise
ops
has data array, fast column-wise
ops
has data array, specialized

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11.3 Linear System Solvers

sparse matrix/eigenvalue problem solvers live in scipy.sparse.linalg
the submodules:
dsolve: direct factorization methods for solving linear systems
isolve: iterative methods for solving linear systems
eigen: sparse eigenvalue problem solvers
all solvers are accessible from:
>>> import scipy.sparse.linalg as spla
>>> spla.__all__
[LinearOperator, Tester, arpack, aslinearoperator, bicg,
bicgstab, cg, cgs, csc_matrix, csr_matrix, dsolve,
eigen, eigen_symmetric, factorized, gmres, interface,
isolve, iterative, lgmres, linsolve, lobpcg, lsqr,
minres, np, qmr, speigs, spilu, splu, spsolve, svd,
test, umfpack, use_solver, utils, warnings]

11.3.1 Sparse Direct Solvers

default solver: SuperLU 4.0
included in SciPy
real and complex systems
both single and double precision
optional: umfpack
real and complex systems
double precision only
recommended for performance
wrappers now live in scikits.umfpack
check-out the new scikits.suitesparse by Nathaniel Smith
Examples
import the whole module, and see its docstring:
>>> import scipy.sparse.linalg.dsolve as dsl
>>> help(dsl)

both superlu and umfpack can be used (if the latter is installed) as follows:
prepare a linear system:
>>> import numpy as np
>>> import scipy.sparse as sps
>>> mtx = sps.spdiags([[1, 2, 3, 4, 5], [6, 5, 8, 9, 10]], [0, 1], 5, 5)
>>> mtx.todense()
matrix([[ 1, 5, 0, 0, 0],
[ 0, 2, 8, 0, 0],
[ 0, 0, 3, 9, 0],
[ 0, 0, 0, 4, 10],
[ 0, 0, 0, 0, 5]])
>>> rhs = np.array([1, 2, 3, 4, 5])

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solve as single precision real:

>>>
>>>
>>>
>>>

mtx1 = mtx.astype(np.float32)
x = dsl.spsolve(mtx1, rhs, use_umfpack=False)
print x
print "Error: ", mtx1 * x - b

solve as double precision real:

>>>
>>>
>>>
>>>

mtx2 = mtx.astype(np.float64)
x = dsl.spsolve(mtx2, rhs, use_umfpack=True)
print x
print "Error: ", mtx2 * x - b

solve as single precision complex:

>>>
>>>
>>>
>>>

mtx1 = mtx.astype(np.complex64)
x = dsl.spsolve(mtx1, rhs, use_umfpack=False)
print x
print "Error: ", mtx1 * x - b

solve as double precision complex:

>>>
>>>
>>>
>>>

mtx2 = mtx.astype(np.complex128)
x = dsl.spsolve(mtx2, rhs, use_umfpack=True)
print x
print "Error: ", mtx2 * x - b

"""
Construct a 1000x1000 lil_matrix and add some values to it, convert it
to CSR format and solve A x = b for x:and solve a linear system with a
direct solver.
"""
import numpy as np
import scipy.sparse as sps
from matplotlib import pyplot as plt
from scipy.sparse.linalg.dsolve import linsolve
rand = np.random.rand
mtx = sps.lil_matrix((1000, 1000), dtype=np.float64)
mtx[0, :100] = rand(100)
mtx[1, 100:200] = mtx[0, :100]
mtx.setdiag(rand(1000))
plt.clf()
plt.spy(mtx, marker=., markersize=2)
plt.show()
mtx = mtx.tocsr()
rhs = rand(1000)
x = linsolve.spsolve(mtx, rhs)
print rezidual:, np.linalg.norm(mtx * x - rhs)

examples/direct_solve.py

11.3.2 Iterative Solvers

the isolve module contains the following solvers:
bicg (BIConjugate Gradient)

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bicgstab (BIConjugate Gradient STABilized)

cg (Conjugate Gradient) - symmetric positive definite matrices only
cgs (Conjugate Gradient Squared)
gmres (Generalized Minimal RESidual)
minres (MINimum RESidual)
qmr (Quasi-Minimal Residual)
Common Parameters
mandatory:
A [{sparse matrix, dense matrix, LinearOperator}] The N-by-N matrix of the linear system.
b [{array, matrix}] Right hand side of the linear system. Has shape (N,) or (N,1).
optional:
x0 [{array, matrix}] Starting guess for the solution.
tol [float] Relative tolerance to achieve before terminating.
maxiter [integer] Maximum number of iterations. Iteration will stop after maxiter steps even if the specified
tolerance has not been achieved.
M [{sparse matrix, dense matrix, LinearOperator}] Preconditioner for A. The preconditioner should approximate the inverse of A. Effective preconditioning dramatically improves the rate of convergence,
which implies that fewer iterations are needed to reach a given error tolerance.
callback [function] User-supplied function to call after each iteration. It is called as callback(xk), where
xk is the current solution vector.
LinearOperator Class
from scipy.sparse.linalg.interface import LinearOperator

common interface for performing matrix vector products

useful abstraction that enables using dense and sparse matrices within the solvers, as well as matrix-free
solutions
has shape and matvec() (+ some optional parameters)
example:
>>> import numpy as np
>>> from scipy.sparse.linalg import LinearOperator
>>> def mv(v):
...
return np.array([2*v[0], 3*v[1]])
...
>>> A = LinearOperator((2, 2), matvec=mv)
>>> A
<2x2 LinearOperator with unspecified dtype>
>>> A.matvec(np.ones(2))
array([ 2., 3.])
>>> A * np.ones(2)
array([ 2., 3.])

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A Few Notes on Preconditioning

problem specific
often hard to develop
if not sure, try ILU
available in dsolve as spilu()

11.3.3 Eigenvalue Problem Solvers

The eigen module
arpack * a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems
lobpcg (Locally Optimal Block Preconditioned Conjugate Gradient Method) * works very well in combination with PyAMG * example by Nathan Bell:
"""
Compute eigenvectors and eigenvalues using a preconditioned eigensolver
In this example Smoothed Aggregation (SA) is used to precondition
the LOBPCG eigensolver on a two-dimensional Poisson problem with
Dirichlet boundary conditions.
"""
import scipy
from scipy.sparse.linalg import lobpcg
from pyamg import smoothed_aggregation_solver
from pyamg.gallery import poisson
N = 100
K = 9
A = poisson((N,N), format=csr)
# create the AMG hierarchy
ml = smoothed_aggregation_solver(A)
# initial approximation to the K eigenvectors
X = scipy.rand(A.shape[0], K)
# preconditioner based on ml
M = ml.aspreconditioner()
# compute eigenvalues and eigenvectors with LOBPCG
W,V = lobpcg(A, X, M=M, tol=1e-8, largest=False)

#plot the eigenvectors

import pylab
pylab.figure(figsize=(9,9))
for i in range(K):
pylab.subplot(3, 3, i+1)
pylab.title(Eigenvector %d % i)
pylab.pcolor(V[:,i].reshape(N,N))
pylab.axis(equal)
pylab.axis(off)
pylab.show()

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examples/pyamg_with_lobpcg.py
example by Nils Wagner:
examples/lobpcg_sakurai.py
output:
$ python examples/lobpcg_sakurai.py
Results by LOBPCG for n=2500
[ 0.06250083

0.06250028

0.06250007]

Exact eigenvalues
[ 0.06250005

0.0625002

0.06250044]

Elapsed time 7.01

11.4 Other Interesting Packages

PyAMG
algebraic multigrid solvers
http://code.google.com/p/pyamg
Pysparse
own sparse matrix classes
matrix and eigenvalue problem solvers

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http://pysparse.sourceforge.net/

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CHAPTER 12

Image manipulation and processing

using Numpy and Scipy

authors Emmanuelle Gouillart, Gal Varoquaux

Image = 2-D numerical array
(or 3-D: CT, MRI, 2D + time; 4-D, ...)
Here, image == Numpy array np.array
Tools used in this tutorial:
numpy: basic array manipulation
scipy: scipy.ndimage submodule dedicated to image processing (n-dimensional images). See
http://docs.scipy.org/doc/scipy/reference/tutorial/ndimage.html
a few examples use specialized toolkits working with np.array:
Scikit Image
scikit-learn
Common tasks in image processing:
Input/Output, displaying images
Basic manipulations: cropping, flipping, rotating, ...
Image filtering: denoising, sharpening
Image segmentation: labeling pixels corresponding to different objects
Classification
...
More powerful and complete modules:
OpenCV (Python bindings)
CellProfiler
ITK with Python bindings
many more...

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Chapters contents
Opening and writing to image files (page 235)
Displaying images (page 236)
Basic manipulations (page 238)
Statistical information (page 239)
Geometrical transformations (page 240)
Image filtering (page 240)
Blurring/smoothing (page 241)
Sharpening (page 241)
Denoising (page 242)
Mathematical morphology (page 245)
Feature extraction (page 249)
Edge detection (page 249)
Segmentation (page 251)
Measuring objects properties (page 255)

12.1 Opening and writing to image files

Writing an array to a file
>>>
>>>
>>>
>>>

import scipy
l = scipy.lena()
from scipy import misc
misc.imsave(lena.png, l) # uses the Image module (PIL)

Creating a numpy array from an image file

>>> lena = misc.imread(lena.png)
>>> type(lena)
<type numpy.ndarray>
>>> lena.shape, lena.dtype
((512, 512), dtype(uint8))

dtype is uint8 for 8-bit images (0-255)

Opening raw files (camera, 3-D images)
>>> l.tofile(lena.raw) # Create raw file
>>> lena_from_raw = np.fromfile(lena.raw, dtype=np.int64)
>>> lena_from_raw.shape

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(262144,)
>>> lena_from_raw.shape = (512, 512)
>>> import os
>>> os.remove(lena.raw)

Need to know the shape and dtype of the image (how to separate data bytes).
For large data, use np.memmap for memory mapping:
>>> lena_memmap = np.memmap(lena.raw, dtype=np.int64, shape=(512, 512))

(data are read from the file, and not loaded into memory)
Working on a list of image files
>>> from glob import glob
>>> filelist = glob(pattern*.png)
>>> filelist.sort()

12.2 Displaying images

Use matplotlib and imshow to display an image inside a matplotlib figure:
>>> l = scipy.lena()
>>> import matplotlib.pyplot as plt
>>> plt.imshow(l, cmap=plt.cm.gray)
<matplotlib.image.AxesImage object at 0x3c7f710>

Increase contrast by setting min and max values:

>>> plt.imshow(l, cmap=plt.cm.gray, vmin=30, vmax=200)
<matplotlib.image.AxesImage object at 0x33ef750>
>>> # Remove axes and ticks
>>> plt.axis(off)
(-0.5, 511.5, 511.5, -0.5)

Draw contour lines:

>>> plt.contour(l, [60, 211])
<matplotlib.contour.ContourSet instance at 0x33f8c20>
import numpy as np
import scipy
import matplotlib.pyplot as plt
l = scipy.lena()
plt.figure(figsize=(10, 3.6))
plt.subplot(131)
plt.imshow(l, cmap=plt.cm.gray)
plt.subplot(132)
plt.imshow(l, cmap=plt.cm.gray, vmin=30, vmax=200)
plt.axis(off)
plt.subplot(133)
plt.imshow(l, cmap=plt.cm.gray)
plt.contour(l, [60, 211])
plt.axis(off)
plt.subplots_adjust(wspace=0, hspace=0., top=0.99, bottom=0.01, left=0.05, right=0.99)
plt.show()

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0
100
200
300
400
500
0

100

200

300

400

500

For fine inspection of intensity variations, use interpolation=nearest:

>>> plt.imshow(l[200:220, 200:220], cmap=plt.cm.gray)
>>> plt.imshow(l[200:220, 200:220], cmap=plt.cm.gray, interpolation=nearest)
import numpy as np
import scipy
import matplotlib.pyplot as plt
l = scipy.lena()
plt.figure(figsize=(8, 4))
plt.subplot(121)
plt.imshow(l[200:220, 200:220], cmap=plt.cm.gray)
plt.axis(off)
plt.subplot(122)
plt.imshow(l[200:220, 200:220], cmap=plt.cm.gray, interpolation=nearest)
plt.axis(off)
plt.subplots_adjust(wspace=0.02, hspace=0.02, top=1, bottom=0, left=0, right=1)
plt.show()

Other packages sometimes use graphical toolkits for visualization (GTK, Qt):

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>>> import scikits.image.io as im_io

>>> im_io.use_plugin(gtk, imshow)
>>> im_io.imshow(l)

3-D visualization: Mayavi

See 3D plotting with Mayavi (page 264) and Volumetric data (page 267).
Image plane widgets
Isosurfaces
...

12.3 Basic manipulations

Images are arrays: use the whole numpy machinery.

>>> lena = scipy.lena()

>>> lena[0, 40]
166
>>> # Slicing
>>> lena[10:13, 20:23]
array([[158, 156, 157],
[157, 155, 155],
[157, 157, 158]])
>>> lena[100:120] = 255
>>>

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>>>
>>>
>>>
>>>
>>>
>>>
>>>

lx, ly = lena.shape
X, Y = np.ogrid[0:lx, 0:ly]
mask = (X - lx/2)**2 + (Y - ly/2)**2 > lx*ly/4
# Masks
lena[mask] = 0
# Fancy indexing
lena[range(400), range(400)] = 255

import numpy as np
import scipy
import matplotlib.pyplot as plt
lena = scipy.lena()
lena[10:13, 20:23]
lena[100:120] = 255
lx, ly = lena.shape
X, Y = np.ogrid[0:lx, 0:ly]
mask = (X - lx/2)**2 + (Y - ly/2)**2 > lx*ly/4
lena[mask] = 0
lena[range(400), range(400)] = 255
plt.figure(figsize=(3,3))
plt.axes([0, 0, 1, 1])
plt.imshow(lena, cmap=plt.cm.gray)
plt.axis(off)

12.3.1 Statistical information

>>> lena = scipy.lena()
>>> lena.mean()
124.04678344726562
>>> lena.max(), lena.min()
(245, 25)

np.histogram

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12.3.2 Geometrical transformations

>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>

lena = scipy.lena()
lx, ly = lena.shape
# Copping
crop_lena = lena[lx/4:-lx/4, ly/4:-ly/4]
# up <-> down flip
flip_ud_lena = np.flipud(lena)
# rotation
rotate_lena = ndimage.rotate(lena, 45)
rotate_lena_noreshape = ndimage.rotate(lena, 45, reshape=False)

import numpy as np
import scipy
from scipy import ndimage
import matplotlib.pyplot as plt
lena = scipy.lena()
lx, ly = lena.shape
# Copping
crop_lena = lena[lx/4:-lx/4, ly/4:-ly/4]
# up <-> down flip
flip_ud_lena = np.flipud(lena)
# rotation
rotate_lena = ndimage.rotate(lena, 45)
rotate_lena_noreshape = ndimage.rotate(lena, 45, reshape=False)
plt.figure(figsize=(12.5, 2.5))

plt.subplot(151)
plt.imshow(lena, cmap=plt.cm.gray)
plt.axis(off)
plt.subplot(152)
plt.imshow(crop_lena, cmap=plt.cm.gray)
plt.axis(off)
plt.subplot(153)
plt.imshow(flip_ud_lena, cmap=plt.cm.gray)
plt.axis(off)
plt.subplot(154)
plt.imshow(rotate_lena, cmap=plt.cm.gray)
plt.axis(off)
plt.subplot(155)
plt.imshow(rotate_lena_noreshape, cmap=plt.cm.gray)
plt.axis(off)
plt.subplots_adjust(wspace=0.02, hspace=0.3, top=1, bottom=0.1, left=0, right=1)

12.4 Image filtering

Local filters: replace the value of pixels by a function of the values of neighboring pixels.
Neighbourhood: square (choose size), disk, or more complicated structuring element.
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12.4.1 Blurring/smoothing
Gaussian filter from scipy.ndimage:
>>> lena = scipy.lena()
>>> blurred_lena = ndimage.gaussian_filter(lena, sigma=3)
>>> very_blurred = ndimage.gaussian_filter(lena, sigma=5)

Uniform filter
>>> local_mean = ndimage.uniform_filter(lena, size=11)
import numpy as np
import scipy
from scipy import ndimage
import matplotlib.pyplot as plt
lena = scipy.lena()
blurred_lena = ndimage.gaussian_filter(lena, sigma=3)
very_blurred = ndimage.gaussian_filter(lena, sigma=5)
local_mean = ndimage.uniform_filter(lena, size=11)
plt.figure(figsize=(9, 3))
plt.subplot(131)
plt.imshow(blurred_lena, cmap=plt.cm.gray)
plt.axis(off)
plt.subplot(132)
plt.imshow(very_blurred, cmap=plt.cm.gray)
plt.axis(off)
plt.subplot(133)
plt.imshow(local_mean, cmap=plt.cm.gray)
plt.axis(off)
plt.subplots_adjust(wspace=0, hspace=0., top=0.99, bottom=0.01, left=0.01, right=0.99)

12.4.2 Sharpening
Sharpen a blurred image:

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>>> lena = scipy.lena()

>>> blurred_l = ndimage.gaussian_filter(lena, 3)

increase the weight of edges by adding an approximation of the Laplacian:

>>> filter_blurred_l = ndimage.gaussian_filter(blurred_l, 1)
>>> alpha = 30
>>> sharpened = blurred_l + alpha * (blurred_l - filter_blurred_l)
import numpy as np
import scipy
from scipy import ndimage
import matplotlib.pyplot as plt
l = scipy.lena()
blurred_l = ndimage.gaussian_filter(l, 3)
filter_blurred_l = ndimage.gaussian_filter(blurred_l, 1)
alpha = 30
sharpened = blurred_l + alpha * (blurred_l - filter_blurred_l)
plt.figure(figsize=(12, 4))
plt.subplot(131)
plt.imshow(l, cmap=plt.cm.gray)
plt.axis(off)
plt.subplot(132)
plt.imshow(blurred_l, cmap=plt.cm.gray)
plt.axis(off)
plt.subplot(133)
plt.imshow(sharpened, cmap=plt.cm.gray)
plt.axis(off)

12.4.3 Denoising
Noisy lena:
>>> l = scipy.lena()
>>> l = l[230:310, 210:350]
>>> noisy = l + 0.4*l.std()*np.random.random(l.shape)

A Gaussian filter smoothes the noise out... and the edges as well:
>>> gauss_denoised = ndimage.gaussian_filter(noisy, 2)

Most local linear isotropic filters blur the image (ndimage.uniform_filter)

A median filter preserves better the edges:
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>>> med_denoised = ndimage.median_filter(noisy, 3)

import numpy as np
import scipy
from scipy import ndimage
import matplotlib.pyplot as plt
l = scipy.lena()
l = l[230:290, 220:320]
noisy = l + 0.4*l.std()*np.random.random(l.shape)
gauss_denoised = ndimage.gaussian_filter(noisy, 2)
med_denoised = ndimage.median_filter(noisy, 3)

plt.figure(figsize=(12,2.8))
plt.subplot(131)
plt.imshow(noisy, cmap=plt.cm.gray, vmin=40, vmax=220)
plt.axis(off)
plt.title(noisy, fontsize=20)
plt.subplot(132)
plt.imshow(gauss_denoised, cmap=plt.cm.gray, vmin=40, vmax=220)
plt.axis(off)
plt.title(Gaussian filter, fontsize=20)
plt.subplot(133)
plt.imshow(med_denoised, cmap=plt.cm.gray, vmin=40, vmax=220)
plt.axis(off)
plt.title(Median filter, fontsize=20)
plt.subplots_adjust(wspace=0.02, hspace=0.02, top=0.9, bottom=0, left=0, right=1)

noisy

Gaussian filter

Median filter

Median filter: better result for straight boundaries (low curvature):

>>>
>>>
>>>
>>>
>>>

im = np.zeros((20, 20))
im[5:-5, 5:-5] = 1
im = ndimage.distance_transform_bf(im)
im_noise = im + 0.2*np.random.randn(*im.shape)
im_med = ndimage.median_filter(im_noise, 3)

import numpy as np
import scipy
from scipy import ndimage
import matplotlib.pyplot as plt
im = np.zeros((20, 20))
im[5:-5, 5:-5] = 1
im = ndimage.distance_transform_bf(im)
im_noise = im + 0.2*np.random.randn(*im.shape)
im_med = ndimage.median_filter(im_noise, 3)

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plt.figure(figsize=(16, 5))
plt.subplot(141)
plt.imshow(im, interpolation=nearest)
plt.axis(off)
plt.title(Original image, fontsize=20)
plt.subplot(142)
plt.imshow(im_noise, interpolation=nearest, vmin=0, vmax=5)
plt.axis(off)
plt.title(Noisy image, fontsize=20)
plt.subplot(143)
plt.imshow(im_med, interpolation=nearest, vmin=0, vmax=5)
plt.axis(off)
plt.title(Median filter, fontsize=20)
plt.subplot(144)
plt.imshow(np.abs(im - im_med), cmap=plt.cm.hot, interpolation=nearest)
plt.axis(off)
plt.title(Error, fontsize=20)

plt.subplots_adjust(wspace=0.02, hspace=0.02, top=0.9, bottom=0, left=0, right=1)

Original image

Noisy image

Median filter

Error

Other rank filter: ndimage.maximum_filter, ndimage.percentile_filter

Other local non-lienear filters: Wiener (scipy.signal.wiener), etc.
Non-local filters
Total-variation (TV) denoising. Find a new image so that the total-variation of the image (integral of the norm
L1 of the gradient) is minimized, while being close to the measured image:
>>>
>>>
>>>
>>>
>>>

# from scikits.image.filter import tv_denoise

from tv_denoise import tv_denoise
tv_denoised = tv_denoise(noisy, weight=10)
# More denoising (to the expense of fidelity to data)
tv_denoised = tv_denoise(noisy, weight=50)

The total variation filter tv_denoise is available in the scikits.image, (doc: http://scikitsimage.org/docs/dev/api/scikits.image.filter.html#tv-denoise), but for convenience weve shipped it as a
standalone module with this tutorial.
import numpy as np
import scipy
from scipy import ndimage
import matplotlib.pyplot as plt
# from scikits.image.filter import tv_denoise
from tv_denoise import tv_denoise
l = scipy.lena()
l = l[230:290, 220:320]

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noisy = l + 0.4*l.std()*np.random.random(l.shape)
tv_denoised = tv_denoise(noisy, weight=10)

plt.figure(figsize=(12,2.8))
plt.subplot(131)
plt.imshow(noisy, cmap=plt.cm.gray, vmin=40, vmax=220)
plt.axis(off)
plt.title(noisy, fontsize=20)
plt.subplot(132)
plt.imshow(tv_denoised, cmap=plt.cm.gray, vmin=40, vmax=220)
plt.axis(off)
plt.title(TV denoising, fontsize=20)
tv_denoised = tv_denoise(noisy, weight=50)
plt.subplot(133)
plt.imshow(tv_denoised, cmap=plt.cm.gray, vmin=40, vmax=220)
plt.axis(off)
plt.title((more) TV denoising, fontsize=20)
plt.subplots_adjust(wspace=0.02, hspace=0.02, top=0.9, bottom=0, left=0, right=1)

noisy

TV denoising

(more) TV denoising

12.4.4 Mathematical morphology

See http://en.wikipedia.org/wiki/Mathematical_morphology
Probe an image with a simple shape (a structuring element), and modify this image according to how the shape
locally fits or misses the image.
Structuring element:
>>> el = ndimage.generate_binary_structure(2, 1)
>>> el
array([[False, True, False],
[ True, True, True],
[False, True, False]], dtype=bool)
>>> el.astype(np.int)
array([[0, 1, 0],
[1, 1, 1],
[0, 1, 0]])

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Erosion = minimum filter. Replace the value of a pixel by the minimal value covered by the structuring element.:
>>> a = np.zeros((7,7), dtype=np.int)
>>> a[1:6, 2:5] = 1
>>> a
array([[0, 0, 0, 0, 0, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0]])
>>> ndimage.binary_erosion(a).astype(a.dtype)
array([[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 1, 0, 0, 0],
[0, 0, 0, 1, 0, 0, 0],
[0, 0, 0, 1, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0]])
>>> #Erosion removes objects smaller than the structure
>>> ndimage.binary_erosion(a, structure=np.ones((5,5))).astype(a.dtype)
array([[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0]])

Dilation: maximum filter:

>>> a = np.zeros((5, 5))
>>> a[2, 2] = 1
>>> a
array([[ 0., 0., 0., 0.,

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[ 0., 0., 0., 0., 0.],

[ 0., 0., 1., 0., 0.],
[ 0., 0., 0., 0., 0.],
[ 0., 0., 0., 0., 0.]])
>>> ndimage.binary_dilation(a).astype(a.dtype)
array([[ 0., 0., 0., 0., 0.],
[ 0., 0., 1., 0., 0.],
[ 0., 1., 1., 1., 0.],
[ 0., 0., 1., 0., 0.],
[ 0., 0., 0., 0., 0.]])

Also works for grey-valued images:

>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
...

np.random.seed(2)
x, y = (63*np.random.random((2, 8))).astype(np.int)
im[x, y] = np.arange(8)
bigger_points = ndimage.grey_dilation(im, size=(5, 5), structure=np.ones((5, 5)))
square = np.zeros((16, 16))
square[4:-4, 4:-4] = 1
dist = ndimage.distance_transform_bf(square)
dilate_dist = ndimage.grey_dilation(dist, size=(3, 3), \
structure=np.ones((3, 3)))

import numpy as np
from scipy import ndimage
import matplotlib.pyplot as plt
im = np.zeros((64, 64))
np.random.seed(2)
x, y = (63*np.random.random((2, 8))).astype(np.int)
im[x, y] = np.arange(8)
bigger_points = ndimage.grey_dilation(im, size=(5, 5), structure=np.ones((5, 5)))
square = np.zeros((16, 16))
square[4:-4, 4:-4] = 1
dist = ndimage.distance_transform_bf(square)
dilate_dist = ndimage.grey_dilation(dist, size=(3, 3), \
structure=np.ones((3, 3)))
plt.figure(figsize=(12.5, 3))
plt.subplot(141)
plt.imshow(im, interpolation=nearest, cmap=plt.cm.spectral)
plt.axis(off)
plt.subplot(142)
plt.imshow(bigger_points, interpolation=nearest, cmap=plt.cm.spectral)
plt.axis(off)
plt.subplot(143)
plt.imshow(dist, interpolation=nearest, cmap=plt.cm.spectral)
plt.axis(off)
plt.subplot(144)
plt.imshow(dilate_dist, interpolation=nearest, cmap=plt.cm.spectral)
plt.axis(off)
plt.subplots_adjust(wspace=0, hspace=0.02, top=0.99, bottom=0.01, left=0.01, right=0.99)

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Opening: erosion + dilation:

>>> a = np.zeros((5,5), dtype=np.int)
>>> a[1:4, 1:4] = 1; a[4, 4] = 1
>>> a
array([[0, 0, 0, 0, 0],
[0, 1, 1, 1, 0],
[0, 1, 1, 1, 0],
[0, 1, 1, 1, 0],
[0, 0, 0, 0, 1]])
>>> # Opening removes small objects
>>> ndimage.binary_opening(a, structure=np.ones((3,3))).astype(np.int)
array([[0, 0, 0, 0, 0],
[0, 1, 1, 1, 0],
[0, 1, 1, 1, 0],
[0, 1, 1, 1, 0],
[0, 0, 0, 0, 0]])
>>> # Opening can also smooth corners
>>> ndimage.binary_opening(a).astype(np.int)
array([[0, 0, 0, 0, 0],
[0, 0, 1, 0, 0],
[0, 1, 1, 1, 0],
[0, 0, 1, 0, 0],
[0, 0, 0, 0, 0]])

Application: remove noise:

>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>

square = np.zeros((32, 32))

square[10:-10, 10:-10] = 1
np.random.seed(2)
x, y = (32*np.random.random((2, 20))).astype(np.int)
square[x, y] = 1
open_square = ndimage.binary_opening(square)
eroded_square = ndimage.binary_erosion(square)
reconstruction = ndimage.binary_propagation(eroded_square, mask=square)

import numpy as np
from scipy import ndimage
import matplotlib.pyplot as plt
square = np.zeros((32, 32))
square[10:-10, 10:-10] = 1
np.random.seed(2)
x, y = (32*np.random.random((2, 20))).astype(np.int)
square[x, y] = 1
open_square = ndimage.binary_opening(square)
eroded_square = ndimage.binary_erosion(square)
reconstruction = ndimage.binary_propagation(eroded_square, mask=square)

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plt.figure(figsize=(9.5, 3))
plt.subplot(131)
plt.imshow(square, cmap=plt.cm.gray, interpolation=nearest)
plt.axis(off)
plt.subplot(132)
plt.imshow(open_square, cmap=plt.cm.gray, interpolation=nearest)
plt.axis(off)
plt.subplot(133)
plt.imshow(reconstruction, cmap=plt.cm.gray, interpolation=nearest)
plt.axis(off)
plt.subplots_adjust(wspace=0, hspace=0.02, top=0.99, bottom=0.01, left=0.01, right=0.99)

Closing: dilation + erosion

Many other mathematical morphology operations: hit and miss transform, tophat, etc.

12.5 Feature extraction

12.5.1 Edge detection
Synthetic data:
>>>
>>>
>>>
>>>
>>>

im = np.zeros((256, 256))
im[64:-64, 64:-64] = 1
im = ndimage.rotate(im, 15, mode=constant)
im = ndimage.gaussian_filter(im, 8)

Use a gradient operator (Sobel) to find high intensity variations:

>>> sx = ndimage.sobel(im, axis=0, mode=constant)
>>> sy = ndimage.sobel(im, axis=1, mode=constant)
>>> sob = np.hypot(sx, sy)
import numpy as np
from scipy import ndimage
import matplotlib.pyplot as plt
im = np.zeros((256, 256))
im[64:-64, 64:-64] = 1
im = ndimage.rotate(im, 15, mode=constant)
im = ndimage.gaussian_filter(im, 8)
sx = ndimage.sobel(im, axis=0, mode=constant)
sy = ndimage.sobel(im, axis=1, mode=constant)
sob = np.hypot(sx, sy)

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plt.figure(figsize=(16, 5))
plt.subplot(141)
plt.imshow(im, cmap=plt.cm.gray)
plt.axis(off)
plt.title(square, fontsize=20)
plt.subplot(142)
plt.imshow(sx)
plt.axis(off)
plt.title(Sobel (x direction), fontsize=20)
plt.subplot(143)
plt.imshow(sob)
plt.axis(off)
plt.title(Sobel filter, fontsize=20)
im += 0.07*np.random.random(im.shape)
sx = ndimage.sobel(im, axis=0, mode=constant)
sy = ndimage.sobel(im, axis=1, mode=constant)
sob = np.hypot(sx, sy)
plt.subplot(144)
plt.imshow(sob)
plt.axis(off)
plt.title(Sobel for noisy image, fontsize=20)

plt.subplots_adjust(wspace=0.02, hspace=0.02, top=1, bottom=0, left=0, right=0.9)

square

Sobel (x direction)

Sobel filter

Sobel for noisy image

Canny filter
The Canny filter is available in the scikits.image (doc), but for convenience weve shipped it as a
standalone module with this tutorial.
>>>
>>>
>>>
>>>
>>>

#from scikits.image.filter import canny

#or use module shipped with tutorial
im += 0.1*np.random.random(im.shape)
edges = canny(im, 1, 0.4, 0.2) # not enough smoothing
edges = canny(im, 3, 0.3, 0.2) # better parameters

import numpy as np
from scipy import ndimage
import matplotlib.pyplot as plt
#from scikits.image.filter import canny
from image_source_canny import canny
im = np.zeros((256, 256))
im[64:-64, 64:-64] = 1
im = ndimage.rotate(im, 15, mode=constant)

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im = ndimage.gaussian_filter(im, 8)
im += 0.1*np.random.random(im.shape)
edges = canny(im, 1, 0.4, 0.2)
plt.figure(figsize=(12, 4))
plt.subplot(131)
plt.imshow(im, cmap=plt.cm.gray)
plt.axis(off)
plt.subplot(132)
plt.imshow(edges, cmap=plt.cm.gray)
plt.axis(off)

edges = canny(im, 3, 0.3, 0.2)

plt.subplot(133)
plt.imshow(edges, cmap=plt.cm.gray)
plt.axis(off)
plt.subplots_adjust(wspace=0.02, hspace=0.02, top=1, bottom=0, left=0, right=1)

Several parameters need to be adjusted... risk of overfitting

12.5.2 Segmentation
Histogram-based segmentation (no spatial information)
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>

n = 10
l = 256
im = np.zeros((l, l))
np.random.seed(1)
points = l*np.random.random((2, n**2))
im[(points[0]).astype(np.int), (points[1]).astype(np.int)] = 1
im = ndimage.gaussian_filter(im, sigma=l/(4.*n))
#
mask = (im > im.mean()).astype(np.float)
#
mask += 0.1 * im
#
img = mask + 0.2*np.random.randn(*mask.shape)
#
hist, bin_edges = np.histogram(img, bins=60)
bin_centers = 0.5*(bin_edges[:-1] + bin_edges[1:])
#
binary_img = img > 0.5

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import numpy as np
from scipy import ndimage
import matplotlib.pyplot as plt
np.random.seed(1)
n = 10
l = 256
im = np.zeros((l, l))
points = l*np.random.random((2, n**2))
im[(points[0]).astype(np.int), (points[1]).astype(np.int)] = 1
im = ndimage.gaussian_filter(im, sigma=l/(4.*n))
mask = (im > im.mean()).astype(np.float)
mask += 0.1 * im
img = mask + 0.2*np.random.randn(*mask.shape)
hist, bin_edges = np.histogram(img, bins=60)
bin_centers = 0.5*(bin_edges[:-1] + bin_edges[1:])
binary_img = img > 0.5
plt.figure(figsize=(11,4))
plt.subplot(131)
plt.imshow(img)
plt.axis(off)
plt.subplot(132)
plt.plot(bin_centers, hist, lw=2)
plt.axvline(0.5, color=r, ls=--, lw=2)
plt.text(0.57, 0.8, histogram, fontsize=20, transform = plt.gca().transAxes)
plt.yticks([])
plt.subplot(133)
plt.imshow(binary_img, cmap=plt.cm.gray, interpolation=nearest)
plt.axis(off)
plt.subplots_adjust(wspace=0.02, hspace=0.3, top=1, bottom=0.1, left=0, right=1)

histogram

1.0

0.5 0.0

0.5

1.0

1.5

2.0

Automatic thresholding: use Gaussian mixture model:

>>>
>>>
>>>
>>>
>>>
>>>
>>>

mask = (im > im.mean()).astype(np.float)

mask += 0.1 * im
img = mask + 0.3*np.random.randn(*mask.shape)
from scikits.learn.mixture import GMM

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>>> classif = GMM(n_components=2, cvtype=full)

>>> classif.fit(img.reshape((img.size, 1)))
GMM(cvtype=full, n_components=2)
>>>
>>> classif.means
array([[ 0.9353155 ],
[-0.02966039]])
>>> np.sqrt(classif.covars).ravel()
array([ 0.35074631, 0.28225327])
>>> classif.weights
array([ 0.40989799, 0.59010201])
>>> threshold = np.mean(classif.means)
>>> binary_img = img > threshold

Use mathematical morphology to clean up the result:

>>>
>>>
>>>
>>>

# Remove small white regions

open_img = ndimage.binary_opening(binary_img)
# Remove small black hole
close_img = ndimage.binary_closing(open_img)

import numpy as np
from scipy import ndimage
import matplotlib.pyplot as plt
from scikits.learn.mixture import GMM
np.random.seed(1)
n = 10
l = 256
im = np.zeros((l, l))
points = l*np.random.random((2, n**2))
im[(points[0]).astype(np.int), (points[1]).astype(np.int)] = 1
im = ndimage.gaussian_filter(im, sigma=l/(4.*n))
mask = (im > im.mean()).astype(np.float)

img = mask + 0.3*np.random.randn(*mask.shape)

binary_img = img > 0.5
# Remove small white regions
open_img = ndimage.binary_opening(binary_img)
# Remove small black hole
close_img = ndimage.binary_closing(open_img)
plt.figure(figsize=(12, 3))
l = 128

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plt.subplot(141)
plt.imshow(binary_img[:l, :l], cmap=plt.cm.gray)
plt.axis(off)
plt.subplot(142)
plt.imshow(open_img[:l, :l], cmap=plt.cm.gray)
plt.axis(off)
plt.subplot(143)
plt.imshow(close_img[:l, :l], cmap=plt.cm.gray)
plt.axis(off)
plt.subplot(144)
plt.imshow(mask[:l, :l], cmap=plt.cm.gray)
plt.contour(close_img[:l, :l], [0.5], linewidths=2, colors=r)
plt.axis(off)
plt.subplots_adjust(wspace=0.02, hspace=0.3, top=1, bottom=0.1, left=0, right=1)
# Better than opening and closing: use reconstruction
eroded_img = ndimage.binary_erosion(binary_img)
reconstruct_img = ndimage.binary_propagation(eroded_img, mask=binary_img)
tmp = np.logical_not(reconstruct_img)
eroded_tmp = ndimage.binary_erosion(tmp)
reconstruct_final = np.logical_not(ndimage.binary_propagation(eroded_tmp, mask=tmp))
"""
plt.subplot(141)
plt.imshow(binary_img[:l, :l], cmap=plt.cm.gray)
plt.axis(off)
plt.subplot(142)
plt.imshow(eroded_img[:l, :l], cmap=plt.cm.gray)
plt.axis(off)
plt.subplot(143)
plt.imshow(reconstruct_img[:l, :l], cmap=plt.cm.gray)
plt.axis(off)
plt.subplot(144)
plt.imshow(mask[:l, :l], cmap=plt.cm.gray)
plt.contour(reconstruct_final[:l, :l], [0.5], lw=4)
plt.axis(off)
"""

Exercise
Check that reconstruction operations (erosion + propagation) produce a better result than opening/closing:
>>> eroded_img = ndimage.binary_erosion(binary_img)
>>> reconstruct_img = ndimage.binary_propagation(eroded_img,
>>> mask=binary_img)
>>> tmp = np.logical_not(reconstruct_img)
>>> eroded_tmp = ndimage.binary_erosion(tmp)
>>> reconstruct_final =
>>> np.logical_not(ndimage.binary_propagation(eroded_tmp, mask=tmp))
>>> np.abs(mask - close_img).mean()
0.014678955078125
>>> np.abs(mask - reconstruct_final).mean()
0.0042572021484375

Exercise
Check how a first denoising step (median filter, total variation) modifies the histogram, and check that the
resulting histogram-based segmentation is more accurate.

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Graph-based segmentation: use spatial information.

>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>

from scikits.learn.feature_extraction import image

from scikits.learn.cluster import spectral_clustering
l = 100
x, y = np.indices((l, l))
center1
center2
center3
center4

=
=
=
=

(28,
(40,
(67,
(24,

24)
50)
58)
70)

radius1, radius2, radius3, radius4 = 16, 14, 15, 14

circle1
circle2
circle3
circle4

=
=
=
=

(x
(x
(x
(x

center1[0])**2
center2[0])**2
center3[0])**2
center4[0])**2

+
+
+
+

(y
(y
(y
(y

center1[1])**2
center2[1])**2
center3[1])**2
center4[1])**2

<
<
<
<

radius1**2
radius2**2
radius3**2
radius4**2

# 4 circles
img = circle1 + circle2 + circle3 + circle4
mask = img.astype(bool)
img = img.astype(float)
img += 1 + 0.2*np.random.randn(*img.shape)
# Convert the image into a graph with the value of the gradient on
the
# edges.
graph = image.img_to_graph(img, mask=mask)
# Take a decreasing function of the gradient: we take it weakly
# dependant from the gradient the segmentation is close to a voronoi
graph.data = np.exp(-graph.data/graph.data.std())
labels = spectral_clustering(graph, k=4, mode=arpack)
label_im = -np.ones(mask.shape)
label_im[mask] = labels

12.6 Measuring objects properties

ndimage.measurements
Synthetic data:

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>>>
>>>
>>>
>>>
>>>
>>>
>>>

n = 10
l = 256
im = np.zeros((l, l))
points = l*np.random.random((2, n**2))
im[(points[0]).astype(np.int), (points[1]).astype(np.int)] = 1
im = ndimage.gaussian_filter(im, sigma=l/(4.*n))
mask = im > im.mean()

Analysis of connected components

Label connected components: ndimage.label:
>>> label_im, nb_labels = ndimage.label(mask)
>>> nb_labels # how many regions?
23
>>> plt.imshow(label_im)
<matplotlib.image.AxesImage object at 0x6624d50>
import numpy as np
from scipy import ndimage
import matplotlib.pyplot as plt
np.random.seed(1)
n = 10
l = 256
im = np.zeros((l, l))
points = l*np.random.random((2, n**2))
im[(points[0]).astype(np.int), (points[1]).astype(np.int)] = 1
im = ndimage.gaussian_filter(im, sigma=l/(4.*n))
mask = im > im.mean()
label_im, nb_labels = ndimage.label(mask)
plt.figure(figsize=(9,3))
plt.subplot(131)
plt.imshow(im)
plt.axis(off)
plt.subplot(132)
plt.imshow(mask, cmap=plt.cm.gray)
plt.axis(off)
plt.subplot(133)
plt.imshow(label_im, cmap=plt.cm.spectral)
plt.axis(off)
plt.subplots_adjust(wspace=0.02, hspace=0.02, top=1, bottom=0, left=0, right=1)

Compute size, mean_value, etc. of each region:

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>>> sizes = ndimage.sum(mask, label_im, range(nb_labels + 1))

>>> mean_vals = ndimage.sum(im, label_im, range(1, nb_labels + 1))

Clean up small connect components:

>>> mask_size = sizes < 1000
>>> remove_pixel = mask_size[label_im]
>>> remove_pixel.shape
(256, 256)
>>> label_im[remove_pixel] = 0
>>> plt.imshow(label_im)

Now reassign labels with np.searchsorted:

>>> labels = np.unique(label_im)
>>> label_im = np.searchsorted(labels, label_im)
import numpy as np
from scipy import ndimage
import matplotlib.pyplot as plt
np.random.seed(1)
n = 10
l = 256
im = np.zeros((l, l))
points = l*np.random.random((2, n**2))
im[(points[0]).astype(np.int), (points[1]).astype(np.int)] = 1
im = ndimage.gaussian_filter(im, sigma=l/(4.*n))
mask = im > im.mean()
label_im, nb_labels = ndimage.label(mask)
sizes = ndimage.sum(mask, label_im, range(nb_labels + 1))
mask_size = sizes < 1000
remove_pixel = mask_size[label_im]
label_im[remove_pixel] = 0
labels = np.unique(label_im)
label_clean = np.searchsorted(labels, label_im)

plt.figure(figsize=(6 ,3))
plt.subplot(121)
plt.imshow(label_im, cmap=plt.cm.spectral)
plt.axis(off)
plt.subplot(122)
plt.imshow(label_clean, vmax=nb_labels, cmap=plt.cm.spectral)
plt.axis(off)
plt.subplots_adjust(wspace=0.01, hspace=0.01, top=1, bottom=0, left=0, right=1)

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Find region of interest enclosing object:

>>> slice_x, slice_y = ndimage.find_objects(label_im==4)[0]
>>> roi = im[slice_x, slice_y]
>>> plt.imshow(roi)
import numpy as np
from scipy import ndimage
import matplotlib.pyplot as plt
np.random.seed(1)
n = 10
l = 256
im = np.zeros((l, l))
points = l*np.random.random((2, n**2))
im[(points[0]).astype(np.int), (points[1]).astype(np.int)] = 1
im = ndimage.gaussian_filter(im, sigma=l/(4.*n))
mask = im > im.mean()
label_im, nb_labels = ndimage.label(mask)
sizes = ndimage.sum(mask, label_im, range(nb_labels + 1))
mask_size = sizes < 1000
remove_pixel = mask_size[label_im]
label_im[remove_pixel] = 0
labels = np.unique(label_im)
label_im = np.searchsorted(labels, label_im)
slice_x, slice_y = ndimage.find_objects(label_im==4)[0]
roi = im[slice_x, slice_y]
plt.figure(figsize=(4, 2))
plt.axes([0, 0, 1, 1])
plt.imshow(roi)
plt.axis(off)

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Other spatial measures: ndimage.center_of_mass, ndimage.maximum_position, etc.

Can be used outside the limited scope of segmentation applications.
Example: block mean:
>>>
>>>
>>>
>>>
>>>
>>>
>>>

l = scipy.lena()
sx, sy = l.shape
X, Y = np.ogrid[0:sx, 0:sy]
regions = sy/6 * (X/4) + Y/6 # note that we use broadcasting
block_mean = ndimage.mean(l, labels=regions, index=np.arange(1,
regions.max() +1))
block_mean.shape = (sx/4, sy/6)

import numpy as np
import scipy
from scipy import ndimage
import matplotlib.pyplot as plt
l = scipy.lena()
sx, sy = l.shape
X, Y = np.ogrid[0:sx, 0:sy]
regions = sy/6 * (X/4) + Y/6
block_mean = ndimage.mean(l, labels=regions, index=np.arange(1, regions.max() +1))
block_mean.shape = (sx/4, sy/6)
plt.figure(figsize=(5,5))
plt.imshow(block_mean, cmap=plt.cm.gray)
plt.axis(off)

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When regions are regular blocks, it is more efficient to use stride tricks (Example: fake dimensions with strides
(page 173)).
Non-regularly-spaced blocks: radial mean:
>>> rbin = (20* r/r.max()).astype(np.int)
>>> radial_mean = ndimage.mean(l, labels=rbin, index=np.arange(1, rbin.max() +1))
import numpy as np
import scipy
from scipy import ndimage
import matplotlib.pyplot as plt
l = scipy.lena()
sx, sy = l.shape
X, Y = np.ogrid[0:sx, 0:sy]

r = np.hypot(X - sx/2, Y - sy/2)

rbin = (20* r/r.max()).astype(np.int)
radial_mean = ndimage.mean(l, labels=rbin, index=np.arange(1, rbin.max() +1))
plt.figure(figsize=(5,5))
plt.axes([0, 0, 1, 1])
plt.imshow(rbin, cmap=plt.cm.spectral)
plt.axis(off)

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Other measures
Correlation function, Fourier/wavelet spectrum, etc.
One example with mathematical morphology: granulometry (http://en.wikipedia.org/wiki/Granulometry_%28morphology%29)
>>>
...
...
...
...
...
...
>>>
>>>
...
...
...
...
...
...
...
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>

def disk_structure(n):
struct = np.zeros((2 * n + 1, 2 * n + 1))
x, y = np.indices((2 * n + 1, 2 * n + 1))
mask = (x - n)**2 + (y - n)**2 <= n**2
struct[mask] = 1
return struct.astype(np.bool)

def granulometry(data, sizes=None):

s = max(data.shape)
if sizes == None:
sizes = range(1, s/2, 2)
granulo = [ndimage.binary_opening(data, \
structure=disk_structure(n)).sum() for n in sizes]
return granulo

np.random.seed(1)
n = 10
l = 256
im = np.zeros((l, l))
points = l*np.random.random((2, n**2))
im[(points[0]).astype(np.int), (points[1]).astype(np.int)] = 1
im = ndimage.gaussian_filter(im, sigma=l/(4.*n))

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>>> mask = im > im.mean()

>>>
>>> granulo = granulometry(mask, sizes=np.arange(2, 19, 4))
import numpy as np
from scipy import ndimage
import matplotlib.pyplot as plt
def disk_structure(n):
struct = np.zeros((2 * n + 1, 2 * n + 1))
x, y = np.indices((2 * n + 1, 2 * n + 1))
mask = (x - n)**2 + (y - n)**2 <= n**2
struct[mask] = 1
return struct.astype(np.bool)

def granulometry(data, sizes=None):

s = max(data.shape)
if sizes == None:
sizes = range(1, s/2, 2)
granulo = [ndimage.binary_opening(data, \
structure=disk_structure(n)).sum() for n in sizes]
return granulo

np.random.seed(1)
n = 10
l = 256
im = np.zeros((l, l))
points = l*np.random.random((2, n**2))
im[(points[0]).astype(np.int), (points[1]).astype(np.int)] = 1
im = ndimage.gaussian_filter(im, sigma=l/(4.*n))
mask = im > im.mean()
granulo = granulometry(mask, sizes=np.arange(2, 19, 4))
plt.figure(figsize=(6, 2.2))
plt.subplot(121)
plt.imshow(mask, cmap=plt.cm.gray)
opened = ndimage.binary_opening(mask, structure=disk_structure(10))
opened_more = ndimage.binary_opening(mask, structure=disk_structure(14))
plt.contour(opened, [0.5], colors=b, linewidths=2)
plt.contour(opened_more, [0.5], colors=r, linewidths=2)
plt.axis(off)
plt.subplot(122)
plt.plot(np.arange(2, 19, 4), granulo, ok, ms=8)

plt.subplots_adjust(wspace=0.02, hspace=0.15, top=0.95, bottom=0.15, left=0, right=0.95)

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25000
20000
15000
10000
5000
02 4 6 8 10 12 14 16 18

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CHAPTER 13

3D plotting with Mayavi

author Gal Varoquaux

13.1 A simple example

Warning: Start ipython -wthread
import numpy as np
x, y = np.mgrid[-10:10:100j, -10:10:100j]
r = np.sqrt(x**2 + y**2)
z = np.sin(r)/r
from enthought.mayavi import mlab
mlab.surf(z, warp_scale=auto)
mlab.outline()
mlab.axes()

np.mgrid[-10:10:100j, -10:10:100j] creates an x,y grid, going from -10 to 10, with 100 steps in each directions.

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13.2 3D plotting functions

13.2.1 Points
In [1]: import numpy as np
In [2]: from enthought.mayavi import mlab
In [3]: x, y, z, value = np.random.random((4, 40))
In [4]: mlab.points3d(x, y, z, value)
Out[4]: <enthought.mayavi.modules.glyph.Glyph object at 0xc3c795c>

13.2.2 Lines
In [5]: mlab.clf()
In [6]: t = np.linspace(0, 20, 200)
In [7]: mlab.plot3d(np.sin(t), np.cos(t), 0.1*t, t)
Out[7]: <enthought.mayavi.modules.surface.Surface object at 0xcc3e1dc>

13.2.3 Elevation surface

In [8]: mlab.clf()

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In [9]: x, y = np.mgrid[-10:10:100j, -10:10:100j]

In [10]: r = np.sqrt(x**2 + y**2)
In [11]: z = np.sin(r)/r
In [12]: mlab.surf(z, warp_scale=auto)
Out[12]: <enthought.mayavi.modules.surface.Surface object at 0xcdb98fc>

13.2.4 Arbitrary regular mesh

In [13]: mlab.clf()
In [14]: phi, theta = np.mgrid[0:np.pi:11j, 0:2*np.pi:11j]
In [15]: x = np.sin(phi) * np.cos(theta)
In [16]: y = np.sin(phi) * np.sin(theta)
In [17]: z = np.cos(phi)
In [18]: mlab.mesh(x, y, z)
In [19]: mlab.mesh(x, y, z, representation=wireframe, color=(0, 0, 0))
Out[19]: <enthought.mayavi.modules.surface.Surface object at 0xce1017c>

Note: A surface is defined by points connected to form triangles or polygones. In mlab.func and mlab.mesh, the
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connectivity is implicity given by the layout of the arrays. See also mlab.triangular_mesh.
Our data is often more than points and values: it needs some connectivity information

13.2.5 Volumetric data

In [20]: mlab.clf()
In [21]: x, y, z = np.mgrid[-5:5:64j, -5:5:64j, -5:5:64j]
In [22]: values = x*x*0.5 + y*y + z*z*2.0
In [23]: mlab.contour3d(values)
Out[24]: <enthought.mayavi.modules.iso_surface.IsoSurface object at 0xcfe392c>

This function works with a regular orthogonal grid:

In [25]: s = mlab.pipeline.scalar_field(values)
In [26]: ipw_x = mlab.pipeline.image_plane_widget(s, plane_orientation=x_axes)

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In [27]: ipw_y = mlab.pipeline.image_plane_widget(s,

plane_orientation=y_axes)

Interactive image plane widgets: drag to change the visualized plane.

13.3 Figures and decorations

13.3.1 Figure management
Here is a list of functions useful to control the current figure
Get the current figure:
Clear the current figure:
Set the current figure:
Save figure to image file:
Change the view:

mlab.gcf()
mlab.clf()
mlab.figure(1, bgcolor=(1, 1, 1), fgcolor=(0.5, 0.5, 0.5)
mlab.savefig(foo.png, size=(300, 300))
mlab.view(azimuth=45, elevation=54, distance=1.)

13.3.2 Changing plot properties

In general, many properties of the various objects on the figure can be changed. If these visualization are created
via mlab functions, the easiest way to change them is to use the keyword arguments of these functions, as described
in the docstrings.

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Example docstring: mlab.mesh

Plots a surface using grid-spaced data supplied as 2D arrays.
Function signatures:
mesh(x, y, z, ...)

x, y, z are 2D arrays, all of the same shape, giving the positions of the vertices of the surface. The connectivity
between these points is implied by the connectivity on the arrays.
For simple structures (such as orthogonal grids) prefer the surf function, as it will create more efficient data
structures.
Keyword arguments:
color the color of the vtk object. Overides the colormap, if any, when specified.
This is specified as a triplet of float ranging from 0 to 1, eg (1, 1, 1) for white.
colormap type of colormap to use.
extent [xmin, xmax, ymin, ymax, zmin, zmax] Default is the x, y, z arrays extents.
Use this to change the extent of the object created.
figure Figure to populate.
line_width The with of the lines, if any used. Must be a float. Default: 2.0
mask boolean mask array to suppress some data points.
mask_points If supplied, only one out of mask_points data point is displayed.
This option is usefull to reduce the number of points displayed on large datasets
Must be an integer or None.
mode the mode of the glyphs. Must be 2darrow or 2dcircle or 2dcross or
2ddash or 2ddiamond or 2dhooked_arrow or 2dsquare or 2dthick_arrow
or 2dthick_cross or 2dtriangle or 2dvertex or arrow or cone or cube or
cylinder or point or sphere. Default: sphere
name the name of the vtk object created.
representation the representation type used for the surface. Must be surface or
wireframe or points or mesh or fancymesh. Default: surface
resolution The resolution of the glyph created. For spheres, for instance, this is the
number of divisions along theta and phi. Must be an integer. Default: 8
scalars optional scalar data.
scale_factor scale factor of the glyphs used to represent the vertices, in fancy_mesh
mode. Must be a float. Default: 0.05
scale_mode the scaling mode for the glyphs (vector, scalar, or none).
transparent make the opacity of the actor depend on the scalar.
tube_radius radius of the tubes used to represent the lines, in mesh mode. If None,
simple lines are used.
tube_sides number of sides of the tubes used to represent the lines. Must be an
integer. Default: 6
vmax vmax is used to scale the colormap If None, the max of the data will be used
vmin vmin is used to scale the colormap If None, the min of the data will be used
Example:
In [1]: import numpy as np
In [2]: r, theta = np.mgrid[0:10, -np.pi:np.pi:10j]
In [3]: x = r*np.cos(theta)
In [4]: y = r*np.sin(theta)
In [5]: z = np.sin(r)/r
In [6]: from enthought.mayavi import mlab
In [7]: mlab.mesh(x, y, z, colormap=gist_earth, extent=[0, 1, 0, 1, 0, 1])
Out[7]: <enthought.mayavi.modules.surface.Surface object at 0xde6f08c>

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In [8]: mlab.mesh(x, y, z, extent=[0, 1, 0, 1, 0, 1],

...: representation=wireframe, line_width=1, color=(0.5, 0.5, 0.5))
Out[8]: <enthought.mayavi.modules.surface.Surface object at 0xdd6a71c>

13.3.3 Decorations
Different items can be added to the figure to carry extra information, such as a colorbar or a title.
In [9]: mlab.colorbar(Out[7], orientation=vertical)
Out[9]: <tvtk_classes.scalar_bar_actor.ScalarBarActor object at 0xd897f8c>
In [10]: mlab.title(polar mesh)
Out[10]: <enthought.mayavi.modules.text.Text object at 0xd8ed38c>
In [11]: mlab.outline(Out[7])
Out[11]: <enthought.mayavi.modules.outline.Outline object at 0xdd21b6c>
In [12]: mlab.axes(Out[7])
Out[12]: <enthought.mayavi.modules.axes.Axes object at 0xd2e4bcc>

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Warning: extent: If we specified extents for a plotting object, mlab.outline and mlab.axes dont get them
by default.

13.4 Interaction
The quicket way to create beautiful visualization with Mayavi is probably to interactivly tweak the various settings.
Click on the Mayavi button in the scene, and you can control properties of objects with dialogs.

To find out what code can be used to program these changes, click on the red button as you modify those properties,
and it will generate the corresponding lines of code.

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271

CHAPTER 14

Sympy : Symbolic Mathematics in

Python

author Fabian Pedregosa

Objectives
1.
2.
3.
4.
5.

Evaluate expressions with arbitrary precision.

Perform algebraic manipulations on symbolic expressions.
Perform basic calculus tasks (limits, differentiation and integration) with symbolic expressions.
Solve polynomial and transcendental equations.
Solve some differential equations.

What is SymPy? SymPy is a Python library for symbolic mathematics. It aims become a full featured computer
algebra system that can compete directly with commercial alternatives (Mathematica, Maple) while keeping the
code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python
and does not require any external libraries.
Sympy documentation and packages for installation can be found on http://sympy.org/

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Chapters contents
First Steps with SymPy (page 273)
Using SymPy as a calculator (page 273)
Exercises (page 274)
Symbols (page 274)
Algebraic manipulations (page 274)
Expand (page 274)
Simplify (page 274)
Exercises (page 275)
Calculus (page 275)
Limits (page 275)
Differentiation (page 275)
Series expansion (page 276)
Exercises (page 276)
Integration (page 276)
Exercises (page 276)
Equation solving (page 276)
Exercises (page 277)
Linear Algebra (page 277)
Matrices (page 277)
Differential Equations (page 278)
Exercises (page 278)

14.1 First Steps with SymPy

14.1.1 Using SymPy as a calculator
SymPy defines three numerical types: Real, Rational and Integer.
The Rational class represents a rational number as a pair of two Integers: the numerator and the denominator, so
Rational(1,2) represents 1/2, Rational(5,2) 5/2 and so on:
>>> from sympy import *
>>> a = Rational(1,2)
>>> a
1/2
>>> a*2
1

SymPy uses mpmath in the background, which makes it possible to perform computations using arbitraryprecision arithmetic. That way, some special constants, like e, pi, oo (Infinity), are treated as symbols and can be
evaluated with arbitrary precision:
>>> pi**2
pi**2
>>> pi.evalf()
3.14159265358979
>>> (pi+exp(1)).evalf()
5.85987448204884

as you see, evalf evaluates the expression to a floating-point number.

There is also a class representing mathematical infinity, called oo:

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>>> oo > 99999

True
>>> oo + 1
oo

14.1.2 Exercises
1. Calculate

2 with 100 decimals.

2. Calculate 1/2 + 1/3 in rational arithmetic.

14.1.3 Symbols
In contrast to other Computer Algebra Systems, in SymPy you have to declare symbolic variables explicitly:
>>> from sympy import *
>>> x = Symbol(x)
>>> y = Symbol(y)

Then you can manipulate them:

>>> x+y+x-y
2*x
>>> (x+y)**2
(x + y)**2

Symbols can now be manipulated using some of python operators: +, -, *, ** (arithmetic), &, |, ~ , >>, <<
(boolean).

14.2 Algebraic manipulations

SymPy is capable of performing powerful algebraic manipulations. Well take a look into some of the most
frequently used: expand and simplify.

14.2.1 Expand
Use this to expand an algebraic expression. It will try to denest powers and multiplications:
In [23]: expand((x+y)**3)
Out[23]: 3*x*y**2 + 3*y*x**2 + x**3 + y**3

Further options can be given in form on keywords:

In [28]: expand(x+y, complex=True)
Out[28]: I*im(x) + I*im(y) + re(x) + re(y)
In [30]: expand(cos(x+y), trig=True)
Out[30]: cos(x)*cos(y) - sin(x)*sin(y)

14.2.2 Simplify
Use simplify if you would like to transform an expression into a simpler form:
In [19]: simplify((x+x*y)/x)
Out[19]: 1 + y

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Simplification is a somewhat vague term, and more precises alternatives to simplify exists: powsimp (simplification of exponents), trigsimp (for trigonometric expressions) , logcombine, radsimp, together.

14.2.3 Exercises
1. Calculate the expanded form of (x + y)6 .
2. Simplify the trigonometric expression sin(x) / cos(x)

14.3 Calculus
14.3.1 Limits
Limits are easy to use in SymPy, they follow the syntax limit(function, variable, point), so to compute the limit of
f(x) as x -> 0, you would issue limit(f, x, 0):
>>> limit(sin(x)/x, x, 0)
1

you can also calculate the limit at infinity:

>>> limit(x, x, oo)
oo
>>> limit(1/x, x, oo)
0
>>> limit(x**x, x, 0)
1

14.3.2 Differentiation
You can differentiate any SymPy expression using diff(func, var). Examples:
>>> diff(sin(x), x)
cos(x)
>>> diff(sin(2*x), x)
2*cos(2*x)
>>> diff(tan(x), x)
1 + tan(x)**2

You can check, that it is correct by:

>>> limit((tan(x+y)-tan(x))/y, y, 0)
1 + tan(x)**2

Higher derivatives can be calculated using the diff(func, var, n) method:

>>> diff(sin(2*x), x, 1)
2*cos(2*x)
>>> diff(sin(2*x), x, 2)
-4*sin(2*x)
>>> diff(sin(2*x), x, 3)
-8*cos(2*x)

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14.3.3 Series expansion

SymPy also knows how to compute the Taylor series of an expression at a point. Use series(expr, var):
>>>
1 >>>
1 +

series(cos(x), x)
x**2/2 + x**4/24 + O(x**6)
series(1/cos(x), x)
x**2/2 + 5*x**4/24 + O(x**6)

14.3.4 Exercises
1. Calculate lim x > 0, sin(x)/x
2. Calulate the derivative of log(x) for x.

14.3.5 Integration
SymPy has support for indefinite and definite integration of transcendental elementary and special functions via
integrate() facility, which uses powerful extended Risch-Norman algorithm and some heuristics and pattern
matching. You can integrate elementary functions:
>>> integrate(6*x**5, x)
x**6
>>> integrate(sin(x), x)
-cos(x)
>>> integrate(log(x), x)
-x + x*log(x)
>>> integrate(2*x + sinh(x), x)
cosh(x) + x**2

Also special functions are handled easily:

>>> integrate(exp(-x**2)*erf(x), x)
pi**(1/2)*erf(x)**2/4

It is possible to compute definite integral:

>>> integrate(x**3, (x, -1, 1))
0
>>> integrate(sin(x), (x, 0, pi/2))
1
>>> integrate(cos(x), (x, -pi/2, pi/2))
2

Also improper integrals are supported as well:

>>> integrate(exp(-x), (x, 0, oo))
1
>>> integrate(exp(-x**2), (x, -oo, oo))
pi**(1/2)

14.3.6 Exercises

14.4 Equation solving

SymPy is able to solve algebraic equations, in one and several variables:
In [7]: solve(x**4 - 1, x)
Out[7]: [I, 1, -1, -I]

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As you can see it takes as first argument an expression that is supposed to be equaled to 0. It is able to solve a large
part of polynomial equations, and is also capable of solving multiple equations with respect to multiple variables
giving a tuple as second argument:
In [8]: solve([x + 5*y - 2, -3*x + 6*y - 15], [x, y])
Out[8]: {y: 1, x: -3}

It also has (limited) support for trascendental equations:

In [9]: solve(exp(x) + 1, x)
Out[9]: [pi*I]

Another alternative in the case of polynomial equations is factor. factor returns the polynomial factorized
into irreducible terms, and is capable of computing the factorization over various domains:
In [10]: f = x**4 - 3*x**2 + 1
In [11]: factor(f)
Out[11]: (1 + x - x**2)*(1 - x - x**2)
In [12]: factor(f, modulus=5)
Out[12]: (2 + x)**2*(2 - x)**2

SymPy is also able to solve boolean equations, that is, to decide if a certain boolean expression is satisfiable or
not. For this, we use the function satisfiable:
In [13]: satisfiable(x & y)
Out[13]: {x: True, y: True}

This tells us that (x & y) is True whenever x and y are both True. If an expression cannot be true, i.e. no values of
its arguments can make the expression True, it will return False:
In [14]: satisfiable(x & ~x)
Out[14]: False

14.4.1 Exercises
1. Solve the system of equations x + y = 2, 2 x + y = 0
2. Are there boolean values x, y that make (~x | y) & (~y | x) true?

14.5 Linear Algebra

14.5.1 Matrices
Matrices are created as instances from the Matrix class:
>>>
>>>
[1,
[0,

from sympy import Matrix

Matrix([[1,0], [0,1]])
0]
1]

unlike a NumPy array, you can also put Symbols in it:

>>>
>>>
>>>
>>>
[1,
[y,

x = Symbol(x)
y = Symbol(y)
A = Matrix([[1,x], [y,1]])
A
x]
1]

>>> A**2

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[1 + x*y,
2*x]
[
2*y, 1 + x*y]

14.5.2 Differential Equations

SymPy is capable of solving (some) Ordinary Differential Equations. sympy.ode.dsolve works like this:
In [4]: f(x).diff(x, x) + f(x)
Out[4]:
2
d
-----(f(x)) + f(x)
dx dx
In [5]: dsolve(f(x).diff(x, x) + f(x), f(x))
Out[5]: C1*sin(x) + C2*cos(x)

Keyword arguments can be given to this function in order to help if find the best possible resolution system. For
example, if you know that it is a separable equations, you can use keyword hint=separable to force dsolve to
resolve it as a separable equation.
In [6]: dsolve(sin(x)*cos(f(x)) + cos(x)*sin(f(x))*f(x).diff(x), f(x), hint=separable) Out[6]: -log(1 sin(f(x))**2)/2 == C1 + log(1 - sin(x)**2)/2

14.5.3 Exercises
1. Solve the Bernoulli differential equation x*f(x).diff(x) + f(x) - f(x)**2
Warning: TODO: correct this equation and convert to math directive!
2. Solve the same equation using hint=Bernoulli. What do you observe ?

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CHAPTER 15

scikit-learn: machine learning in

Python

author Fabian Pedregosa

Machine learning is a rapidly-growing field with several machine learning frameworks available for Python:

Prerequisites

Numpy, Scipy
IPython
matplotlib
scikit-learn (http://scikit-learn.sourceforge.net)

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Chapters contents
Loading an example dataset (page 280)
Learning and Predicting (page 281)
Supervised learning (page 281)
k-Nearest neighbors classifier (page 281)
Support vector machines (SVMs) for classification (page 282)
Clustering: grouping observations together (page 283)
K-means clustering (page 283)
Dimension Reduction with Principal Component Analysis (page 284)
Putting it all together : face recognition with Support Vector Machines (page 285)

15.1 Loading an example dataset

First we will load some data to play with. The data we will use is a very simple flower database known as the Iris
dataset.
We have 150 observations of the iris flower specifying some of its characteristics: sepal length, sepal width, petal
length and petal width together with its subtype: Iris Setosa, Iris Versicolour, Iris Virginica.
To load the dataset into a Python object:
>>> from scikits.learn import datasets
>>> iris = datasets.load_iris()

This data is stored in the .data member, which is a (n_samples, n_features) array.
>>> iris.data.shape
(150, 4)

It is made of 150 observations of irises, each described by the 4 features mentioned earlier.
The information about the class of each observation is stored in the target attribute of the dataset. This is an integer
1D array of length n_samples:
>>> iris.target.shape
(150,)
>>> import numpy as np
>>> np.unique(iris.target)
[0, 1, 2]

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An example of reshaping data: the digits dataset

The digits dataset is made of 1797 images, where each one is a 8x8 pixel image representing a hand-written
digits
>>> digits = datasets.load_digits()
>>> digits.images.shape
(1797, 8, 8)
>>> import pylab as pl
>>> pl.imshow(digits.images[0], cmap=pl.cm.gray_r)
<matplotlib.image.AxesImage object at ...>

To use this dataset with the scikit, we transform each 8x8 image in a feature vector of length 64
>>> data = digits.images.reshape((digits.images.shape[0], -1))

15.1.1 Learning and Predicting

Now that weve got some data, we would like to learn from the data and predict on new one. In scikit-learn,
we learn from existing data by creating an estimator and calling its fit(X, Y) method.
>>> from scikits.learn import svm
>>> clf = svm.LinearSVC()
>>> clf.fit(iris.data, iris.target) # learn form the data

Once we have learned from the data, we can access the parameters of the model:
>>> clf.coef_
...

And it can be used to predict the most likely outcome on unseen data:
>>> clf.predict([[ 5.0,
array([0], dtype=int32)

3.6,

1.3,

0.25]])

15.2 Supervised learning

15.2.1 k-Nearest neighbors classifier
The simplest possible classifier is the nearest neighbor: given a new observation, take the label of the closest
learned observation.

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KNN (k nearest neighbors) classification example:

>>> # Create and fit a nearest-neighbor classifier
>>> from scikits.learn import neighbors
>>> knn = neighbors.NeighborsClassifier()
>>> knn.fit(iris.data, iris.target)
NeighborsClassifier(n_neighbors=5, leaf_size=20, algorithm=auto)
>>> knn.predict([[0.1, 0.2, 0.3, 0.4]])
array([0])

Training set and testing set

When experimenting with learning algorithm, it is important not to test the prediction of an estimator on the
data used to fit the estimator.

15.2.2 Support vector machines (SVMs) for classification

Linear Support Vector Machines
SVMs try to build a plane maximizing the margin between the two classes. It selects a subset of the input, called
the support vectors, which are the observations closest to the separating plane.

>>> from scikits.learn import svm

>>> svc = svm.SVC(kernel=linear)
>>> svc.fit(iris.data, iris.target)

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SVC(kernel=linear, C=1.0, probability=False, degree=3, coef0=0.0, tol=0.001,

shrinking=True, gamma=0.0)

There are several support vector machine implementations in scikit-learn. The most used ones are svm.SVC,
svm.NuSVC and svm.LinearSVC.
Excercise
Try classifying the digits dataset with svm.SVC. Leave out the last 10% and test prediction performance on
these observations.

Using kernels
Classes are not always separable by a hyper-plane, thus it would be desirable to a build decision function that is
not linear but that may be for instance polynomial or exponential:
Linear kernel

Polynomial kernel

RBF kernel (Radial Basis Function)

>>> svc = svm.SVC(kernel=linear)

>>> svc = svm.SVC(kernel=poly,
>>> svc = svm.SVC(kernel=rbf)
...
degree=3)
>>> # gamma: inverse of size of
>>> # degree: polynomial degree
>>> # radial kernel

Exercise
Which of the kernels noted above has a better prediction performance on the digits dataset ?

15.3 Clustering: grouping observations together

Given the iris dataset, if we knew that there were 3 types of Iris, but did not have access to their labels: we could
try a clustering task: split the observations into groups called clusters.

15.3.1 K-means clustering

The simplest clustering algorithm is the k-means.
>>> from scikits.learn import cluster, datasets
>>> iris = datasets.load_iris()
>>> k_means = cluster.KMeans(k=3)
>>> k_means.fit(iris.data)
KMeans(verbose=0, k=3, max_iter=300, init=k-means++,...
>>> print k_means.labels_[::10]
[1 1 1 1 1 0 0 0 0 0 2 2 2 2 2]
>>> print iris.target[::10]
[0 0 0 0 0 1 1 1 1 1 2 2 2 2 2]

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Ground truth

K-means (3 clusters)

K-means (8 clusters)

Application to Image Compression

Clustering can be seen as a way of choosing a small number of observations from the information. For
instance, this can be used to posterize an image (conversion of a continuous gradation of tone to several
regions of fewer tones):
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>

import scipy as sp
lena = sp.lena()
X = lena.reshape((-1, 1)) # We need an (n_sample, n_feature) array
k_means = cluster.KMeans(k=5)
k_means.fit(X)
values = k_means.cluster_centers_.squeeze()
labels = k_means.labels_
lena_compressed = np.choose(labels, values)
lena_compressed.shape = lena.shape

Raw image

K-means quantization

15.3.2 Dimension Reduction with Principal Component Analysis

The cloud of points spanned by the observations above is very flat in one direction, so that one feature can almost
be exactly computed using the 2 other. PCA finds the directions in which the data is not flat
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When used to transform data, PCA can reduce the dimensionality of the data by projecting on a principal subspace.
Warning: Depending on your version of scikit-learn PCA will be in module decomposition or pca.
>>> from scikits.learn import decomposition
>>> pca = decomposition.PCA(n_components=2)
>>> pca.fit(iris.data)
PCA(copy=True, n_components=2, whiten=False)
>>> X = pca.transform(iris.data)

Now we can visualize the (transformed) iris dataset!

>>> import pylab as pl
>>> pl.scatter(X[:, 0], X[:, 1], c=iris.target)
>>> pl.show()

PCA is not just useful for visualization of high dimensional datasets. It can also be used as a preprocessing step
to help speed up supervised methods that are not computationally efficient with high dimensions.

15.4 Putting it all together : face recognition with Support Vector

Machines
An example showcasing face recognition using Principal Component Analysis for dimension reduction and Support Vector Machines for classification.

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"""
Stripped-down version of the face recognition example by Olivier Grisel
http://scikit-learn.sourceforge.net/dev/auto_examples/applications/face_recognition.html
## original shape of images: 50, 37
"""
import numpy as np
from scikits.learn import cross_val, datasets, decomposition, svm
# ..
# .. load data ..
lfw_people = datasets.fetch_lfw_people(min_faces_per_person=70, resize=0.4)
faces = np.reshape(lfw_people.data, (lfw_people.target.shape[0], -1))
train, test = iter(cross_val.StratifiedKFold(lfw_people.target, k=4)).next()
X_train, X_test = faces[train], faces[test]
y_train, y_test = lfw_people.target[train], lfw_people.target[test]
# ..
# .. dimension reduction ..
pca = decomposition.RandomizedPCA(n_components=150, whiten=True)
pca.fit(X_train)
X_train_pca = pca.transform(X_train)
X_test_pca = pca.transform(X_test)
# ..
# .. classification ..
clf = svm.SVC(C=5., gamma=0.001)
clf.fit(X_train_pca, y_train)
# ..
# .. predict on new images ..
for i in range(1, 10):
print lfw_people.target_names[clf.predict(X_test_pca[i])[0]]
_ = pl.imshow(X_test[i].reshape(50, 37), cmap=pl.cm.gray)
_ = raw_input()

Full code: faces.py

PythonScientific.pdf
PythonScientific-simple.pdf
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286

Bibliography

[Mallet09] Mallet, C. and Bretar, F. Full-Waveform Topographic Lidar:

State-of-the-Art. ISPRS Journal of Photogrammetry and Remote Sensing 64(1), pp.1-16, January 2009
http://dx.doi.org/10.1016/j.isprsjprs.2008.09.007

287

Index

D
diff, 275, 278
differentiation, 275
dsolve, 278

E
equations
algebraic, 276
differential, 278

I
integration, 276

M
Matrix, 277

P
Python Enhancement Proposals
PEP 255, 151
PEP 3118, 186
PEP 3129, 161
PEP 318, 153, 161
PEP 342, 151
PEP 343, 161
PEP 380, 153
PEP 8, 156

S
solve, 276

288