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Python Data
Visualization Cookbook

Over 60 recipes that will enable you to learn how to

create attractive visualizations using Python's most
popular libraries

Igor Milovanović

BIRMINGHAM - MUMBAI

www.it-ebooks.info
Python Data Visualization Cookbook

Copyright © 2013 Packt Publishing

All rights reserved. No part of this book may be reproduced, stored in a retrieval system, or
transmitted in any form or by any means, without the prior written permission of the publisher,
except in the case of brief quotations embedded in critical articles or reviews.

Every effort has been made in the preparation of this book to ensure the accuracy of the
information presented. However, the information contained in this book is sold without
warranty, either express or implied. Neither the author, nor Packt Publishing, and its dealers
and distributors will be held liable for any damages caused or alleged to be caused directly or
indirectly by this book.

Packt Publishing has endeavored to provide trademark information about all of the companies
and products mentioned in this book by the appropriate use of capitals. However, Packt
Publishing cannot guarantee the accuracy of this information.

First published: November 2013

Production Reference: 1191113

Published by Packt Publishing Ltd.

Livery Place
35 Livery Street
Birmingham B3 2PB, UK.

ISBN 978-1-78216-336-7

www.packtpub.com

Cover Image by Gorkee Bhardwaj ([email protected])

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 Credits

Author Project Coordinator

Igor Milovanović Rahul Dixit

Reviewers Proofreaders
Tarek Amr Amy Johnson
Simeone Franklin Lindsey Thomas
Jayesh K. Gupta
Indexer
Kostiantyn Kucher
Mariammal Chettiyar
Kenneth Emeka Odoh
Graphics
Acquisition Editor Abhinash Sahu
James Jones
Production Coordinator
Lead Technical Editor Shantanu Zagade
Ankita Shashi
Cover Work
Technical Editors Shantanu Zagade
Pratik More
Amit Ramadas
Ritika Singh

Copy Editors
Brandt D'Mello
Janbal Dharmaraj
Deepa Nambiar
Kirti Pai
Laxmi Subramanian

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 About the Author

Igor Milovanović is an experienced developer with a strong background in Linux

system and software engineering. He has skills in building scalable data-driven
distributed software-rich systems.

He is an Evangelist for high-quality systems design who holds strong interests in software
architecture and development methodologies. He is always persistent on advocating
methodologies that promote high-quality software, such as test-driven development,
one-step builds, and continuous integration.

He also possesses solid knowledge of product development. Having field experience and
official training, he is capable of transferring knowledge and communication flow from
business to developers and vice versa.

I am most grateful to my fiance for letting me spend endless hours on the

work instead with her and for being an avid listener to my endless book
monologues. I want to also thank my brother for always being my strongest
supporter. I am thankful to my parents for letting me develop myself in
various ways and become the person I am today.
I could not write this book without enormous energy from open source
community that developed Python, matplotlib, and all libraries that we
have used in this book. I owe the most to the people behind all these
projects. Thank you.

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 About the Reviewers

Tarek Amr achieved his postgraduate degree in Data Mining and Information Retrieval from
the University of East Anglia. He has about 10 years' experience in Software Development.
He has been volunteering in Global Voices Online (GVO) since 2007, and currently he is the
local ambassador of the Open Knowledge Foundation (OKFN) in Egypt. Words such as Open
Data, Government 2.0, Data Visualisation, Data Journalism, Machine Learning, and Natural
Language Processing are like music to his ears.

Tarek's Twitter handle is @gr33ndata and his homepage is

http://tarekamr.appspot.com/.

Jayesh K. Gupta is the Lead Developer of Matlab Toolbox for Biclustering Analysis (MTBA).
He is currently an undergraduate student and researcher at IIT Kanpur. His interests lie in the
field of pattern recognition. His interests also lie in basic sciences, recognizing them as the
means of analyzing patterns in nature. Coming to IIT, he realized how this analysis is being
augmented by Machine Learning algorithms with various diverse applications. He believes
that augmenting human thought with machine intelligence is one of the best ways to advance
human knowledge. He is a long time technophile and a free-software Evangelist. He usually
goes by the handle, rejuvyesh online. He is also an avid reader and his books can be checked
out at Goodreads. Checkout his projects at Bitbucket and GitHub. For all links visit http://
home.iitk.ac.in/~jayeshkg/. He can be contacted at [email protected].

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Kostiantyn Kucher was born in Odessa, Ukraine. He received his Master's degree in
Computer Science from Odessa National Polytechnic University in 2012. He used Python
as well as Matplotlib and PIL for Machine Learning and Image Recognition purposes.

Currently, Kostiantyn is a PhD student in Computer Science specializing in Information

Visualization. He conducts his research under the supervision of Prof. Dr. Andreas Kerren
with the ISOVIS group at the Computer Science Department of Linnaeus University
(Växjö, Sweden).

Kenneth Emeka Odoh performs research on state of the art Data Visualization
techniques. His research interest includes exploratory search where the users are
guided to their search results using visual clues.

Kenneth is proficient in Python programming. He has presented a Python conference

talk at Pycon, Finland in 2012 where he spoke about Data Visualization in Django to
a packed audience.

He currently works as a Graduate Researcher at the University of Regina, Canada.

He is a polyglot with experience in developing applications in C, C++, Python, and
Java programming languages.

When Kenneth is not writing source codes, you can find him singing at the Campion College
chant choir.

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www.it-ebooks.info
 Table of Contents
Preface 1
Chapter 1: Preparing Your Working Environment 5
Introduction 5
Installing matplotlib, NumPy, and SciPy 6
Installing virtualenv and virtualenvwrapper 8
Installing matplotlib on Mac OS X 10
Installing matplotlib on Windows 11
Installing Python Imaging Library (PIL) for image processing 12
Installing a requests module 14
Customizing matplotlib's parameters in code 14
Customizing matplotlib's parameters per project 16
Chapter 2: Knowing Your Data 19
Introduction 19
Importing data from CSV 20
Importing data from Microsoft Excel files 22
Importing data from fixed-width datafiles 25
Importing data from tab-delimited files 27
Importing data from a JSON resource 28
Exporting data to JSON, CSV, and Excel 31
Importing data from a database 36
Cleaning up data from outliers 40
Reading files in chunks 46
Reading streaming data sources 48
Importing image data into NumPy arrays 50
Generating controlled random datasets 56
Smoothing the noise in real-world data 64

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Table of Contents
Chapter 3: Drawing Your First Plots and Customizing Them 71
Introduction 72
Defining plot types – bar, line, and stacked charts 72
Drawing a simple sine and cosine plot 78
Defining axis lengths and limits 81
Defining plot line styles, properties, and format strings 84
Setting ticks, labels, and grids 89
Adding a legend and annotations 92
Moving spines to the center 95
Making histograms 96
Making bar charts with error bars 99
Making pie charts count 101
Plotting with filled areas 103
Drawing scatter plots with colored markers 105
Chapter 4: More Plots and Customizations 109
Introduction 109
Setting the transparency and size of axis labels 110
Adding a shadow to the chart line 113
Adding a data table to the figure 116
Using subplots 118
Customizing grids 121
Creating contour plots 125
Filling an under-plot area 128
Drawing polar plots 131
Visualizing the filesystem tree using a polar bar 134
Chapter 5: Making 3D Visualizations 139
Introduction 139
Creating 3D bars 139
Creating 3D histograms 143
Animating in matplotlib 146
Animating with OpenGL 150

ii

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 Table of Contents

Chapter 6: Plotting Charts with Images and Maps 157

Introduction 157
Processing images with PIL 158
Plotting with images 164
Displaying an image with other plots in the figure 168
Plotting data on a map using Basemap 172
Plotting data on a map using Google Map API 177
Generating CAPTCHA images 183
Chapter 7: Using Right Plots to Understand Data 189
Introduction 189
Understanding logarithmic plots 190
Understanding spectrograms 193
Creating a stem plot 198
Drawing streamlines of vector flow 201
Using colormaps 205
Using scatter plots and histograms 210
Plotting the cross-correlation between two variables 217
Importance of autocorrelation 220
Chapter 8: More on matplotlib Gems 225
Introduction 225
Drawing barbs 225
Making a box and a whisker plot 229
Making Gantt charts 232
Making errorbars 237
Making use of text and font properties 240
Rendering text with LaTeX 246
Understanding the difference between pyplot and OO API 250
Index 257

iii

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Table of Contents

iv

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 Preface
The best data is the data that we can see and understand. As developers, we want to
create and build the most comprehensive and understandable visualizations. It is not always
simple; we need to find the data, read it, clean it, massage it, and then use the right tool to
visualize it. This book explains the process of how to read, clean, and visualize the data into
information with straight and simple (and not so simple) recipes.

How to read local data, remote data, CSV, JSON, and data from relational databases are all
explained in this book.

Some simple plots can be plotted with a simple one-liner in Python using matplotlib, but
doing more advanced charting requires knowledge of more than just Python. We need to
understand the information theory and human perception aesthetics to produce the most
appealing visualizations.

This book will explain some practices behind plotting with matplotlib in Python, statistics used,
and usage examples for different charting features we should use in an optimal way.

This book is written and the code is developed on Ubuntu 12.03 using Python 2.7,
IPython 0.13.2, virtualenv 1.9.1, matplotlib 1.2.1, NumPy 1.7.1, and SciPy 0.11.0.

What this book covers

Chapter 1, Preparing Your Working Environment, covers a set of installation recipes and
advices on how to install the required Python packages and libraries on your platform.

Chapter 2, Knowing Your Data, introduces you to common data formats and how to read and
write them, be it CSV, JSON, XSL, or relational databases.

Chapter 3, Drawing Your First Plots and Customizing Them, starts with drawing simple plots
and covers some of the customization.

Chapter 4, More Plots and Customizations, follows up from previous chapter and covers more
advanced charts and grid customization.

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Preface

Chapter 5, Making 3D Visualizations, covers three-dimensional data visualizations such as

3D bars, 3D histograms, and also matplotlib animations.

Chapter 6, Plotting Charts with Images and Maps, covers image processing, projecting data
onto maps, and creating CAPTCHA test images.

Chapter 7, Using Right Plots to Understand Data, covers explanations and recipes on some
more advanced plotting techniques such as spectrograms and correlations.

Chapter 8, More on matplotlib Gems, covers a set of charts such as Gantt charts, box plots,
and whisker plots, and also explains how to use LaTeX for rendering text in matplotlib.

What you need for this book

For this book, you will need Python 2.7.3 or a later version installed on your operating system.
This book was written using Ubuntu 12.03's Python default version (2.7.3).

Other software packages used in this book are IPython, which is an interactive Python
environment that is very powerful, and flexible. This can be installed using package
managers for Linux-based OSes or prepared installers for Windows and Mac OSes.

If you are new to Python installation and software installation in general, it is very much
recommended to use prepackaged scientific Python distributions such as Anaconda,
Enthought Python Distribution, or Python(X,Y).

Other required software mainly comprises of Python packages that are all installed using
the Python installation manager, pip, which itself is installed using Python's easy_install
setup tool.

Who this book is for

Python Data Visualization Cookbook is for developers who already know about Python
programming in general. If you have heard about data visualization but don't know where to
start, this book will guide you from the start and help you understand data, data formats,
data visualization, and how to use Python to visualize data.

You will need to know some general programming concepts, and any kind of programming
experience will be helpful. However, the code in this book is explained almost line by line. You
don't need math for this book; every concept that is introduced is thoroughly explained in plain
English, and references are available for further interest in the topic.

Conventions
In this book, you will find a number of styles of text that distinguish between different kinds of
information. Here are some examples of these styles, and an explanation of their meaning.

www.it-ebooks.info
 Another Random Document on
Scribd Without Any Related Topics
 "Compel them to come in."—ST. LUKE'S GOSPEL

You "made a virtue of necessity"

By divine sanction; you, the loth, the grey,
The random, gentle, unconvinced; O be
The crowned!—you may, you may.

You, the compelled, be feasted! You, the caught,

Be freemen of the gates that word unlocks!
Accept your victory from that unsought,
That heavenly paradox.

THE VOICE OF A BIRD

"He shall rise up at the voice of a bird."—ECCLESIASTES

Who then is "he"?

Dante, Keats, Shakespeare, Milton, Shelley; all
Rose in their greatness at the shrill decree,
The little rousing inarticulate call.

For they stood up

At the bird-voice, of lark, of nightingale,
Drank poems from that throat as from a cup.
Over the great world's notes did these prevail.

And not alone

The signal poets woke. In listening man,
Woman, and child a poet stirs unknown,
Throughout the Mays of birds since Mays began.

He rose, he heard—
Our father, our St. Peter, in his tears—
The crowing, twice, of the prophetic bird,
The saddest cock-crow of our human years.

THE QUESTION

IL POETA MI DISSE, "CHE PENSI?"

Virgil stayed Dante with a wayside word;

But long, and how, and loud and urgently
The poets of my passion have I heard
Summoning me.

It is their closest whisper and their call.

Their greatness to this lowliness hath spoken,
Their voices rest upon that interval,
Their sign, their token.

Man at his little prayer tells Heaven his thought,

To man entrusts his thought—"Friend, this is mine."
The immortal poets within my breast have sought,
Saying, "What is thine?"

THE LAWS OF VERSE

Dear laws, come to my breast!

Take all my frame, and make your close arms meet
Around me; and so ruled, so warmed, so pressed,
I breathe, aware; I feel my wild heart beat.
 Dear laws, be wings to me!
The feather merely floats. O be it heard
Through weight of life—the skylark's gravity—
That I am not a feather, but a bird.

"THE RETURN TO NATURE"

Histories of Modern Poetry

(I) PROMETHEUS

It was the south: mid-everything,

Mid-land, mid-summer, noon;
And deep within a limpid spring
The mirrored sun of June.

Splendour in freshness! Ah, who stole

This sun, this fire, from heaven?
He holds it shining in his soul,
Prometheus the forgiven.

(II) THETIS

In her bright title poets dare

What the wild eye of fancy sees—
Similitude—the clear, the fair
Light mystery of images.

Round the blue sea I love the best

The argent foam played, slender, fleet;
I saw—past Wordsworth and the rest—
Her natural, Greek, and silver feet.

TO SILENCE

"SPACE, THE BOUND OF A SOLID": SILENCE, THEN,

THE FORM OF A MELODY

Silence, for thine idleness I raise

My silence-bounded singing in thy praise,
But for thy moulding of my Mozart's tune,
Thy hold upon the bird that sings the moon,
Thy magisterial ways.

Man's lovely definite melody-shapes are thine,

Outlined, controlled, compressed, complete, divine.
Also thy fine intrusions do I trace,
Thy afterthoughts, thy wandering, thy grace,
Within the poet's line.

Thy secret is the song that is to be.

Music had never stature but for thee,
Sculptor! strong as the sculptor Space whose hand
Urged the Discobolus and bade him stand.
*****
Man, on his way to Silence, stops to hear and see.

THE ENGLISH METRES

The rooted liberty of flowers in breeze
Is theirs, by national luck impulsive, terse,
Tethered, uncaptured, rules obeyed "at ease,"
Time-strengthened laws of verse.

Or they are like our seasons that admit

Inflexion, not infraction: Autumn hoar,
Winter more tender than our thoughts of it,
But a year's steadfast four;

Redundant syllables of Summer rain,

And displaced accents of authentic Spring;
Spondaic clouds above a gusty plain
With dactyls on the wing.

Not Common Law, but Equity, is theirs—

Our metres; play and agile foot askance,
And distant, beckoning, blithely rhyming pairs,
Unknown to classic France;

Unknown to Italy. Ay, count, collate,

Latins! with eye foreseeing on the time,
And numbered fingers, and approaching fate
On the appropriate rhyme.

Nay, nobly our grave measures are decreed:

Heroic, Alexandrine with the stay,
Deliberate; or else like him whose speed
Did outrun Peter, urgent in the break of day.

"RIVERS UNKNOWN TO SONG"

James Thomson
Wide waters in the waste; or, out of reach,
Rough Alpine falls where late a glacier hung;
Or rivers groping for the alien beach,
Through continents, unsung.

Nay, not these nameless, these remote, alone;

But all the streams from all the watersheds—
Peneus, Danube, Nile—are the unknown.
Young in their ancient beds.

Man has no tale for them. O travellers swift

From secrets to oblivion! Waters wild
That pass in act to bend a flower, or lift
The bright limbs of a child!

For they are new, they are fresh; there's no surprise

Like theirs on earth. O strange for evermore!
This moment's Tiber with his shining eyes
Never saw Rome before.

Man has no word for their eternity—

Rhine, Avon, Arno, younglings, youth uncrowned:
Ignorant, innocent, instantaneous, free,
Unwelcomed, unrenowned.

TO THE MOTHER OF CHRIST

THE SON OF MAN

We too (one cried), we too,

We the unready, the perplexed, the cold,
Must shape the Eternal in our thoughts anew,
Cherish, possess, enfold.
 Thou sweetly, we in strife.
It is our passion to conceive Him thus
In mind, in sense, within our house of life;
That seed is locked in us.

We must affirm our Son

From the ambiguous Nature's difficult speech,
Gather in darkness that resplendent One,
Close as our grasp can reach.

Nor shall we ever rest

From this our task. An hour sufficed for thee,
Thou innocent! He lingers in the breast
Of our humanity.

A COMPARISON IN A SEASIDE FIELD

'Tis royal and authentic June

Over this poor soil blossoming;
Here lies, beneath an upright noon,
Thin nation for so wild a king.

Far off, the noble Summer rules,

Violent in the ardent rose,
His sun alight in mirroring pools,
Braggart on Alps of vanquished snows;

Away, aloft, true to his hour,

Announced, his colour, his fire, his jest.
But here, in negligible flower,
Summer is not proclaimed:—confessed.
A woman I marked; for her no state,
Small joy, no song. She had her boon,
Her only youth, true to its date,
Faintly perceptible, her June.

SURMISE

THE TRACK OF A HUMAN MOOD

Not wish, nor fear, nor quite expectancy

Is that vague spirit Surmise,
That wanderer, that wonderer, whom we see
Within each other's eyes;

And yet not often. For she flits away,

Fitful as infant thought,
Visitant at a venture, hope at play,
Unversed in facts, untaught.

In "the wide fields of possibility"

Surmise, conjecturing,
Makes little trials, incredulous, that flee
Abroad on random wing.

One day this inarticulate shall find speech,

This hoverer seize our breath.
Surmise shall close with man—with all, with each—
In her own sovereign hour, the moments of our death.
 TO ANTIQUITY

"... REVERENCE FOR OUR FATHERS, WITH THEIR

STORES OF EXPERIENCES"
An author whose name I did not note

O our young ancestor,

Our boy in Letters, how we trudge oppressed
With our "experiences," and you of yore
Flew light, and blessed!

Youngling, in your new town,

Tight, like a box of toys—the town that is
Our shattered, open ruin, with its crown
Of histories;

You with your morning words,

Fresh from the night, your yet un-sonneted moon,
Your passion undismayed, cool as a bird's
Ignorant tune;

O youngling! how is this?

Your poems are not wearied yet, not dead,
Must I bow low? or, With an envious kiss,
Put you to bed?

CHRISTMAS NIGHT
"IF I CANNOT SEE THEE PRESENT I WILL MOURN
THEE ABSENT, FOR THIS ALSO IS A PROOF OF LOVE"
Thomas à Kempis
We do not find Him on the difficult earth,
In surging human-kind,
In wayside death or accidental birth,
Or in the "march of mind."

Nature, her nests, her prey, the fed, the caught,

Hid Him so well, so well,
His steadfast secret there seems to our thought
Life's saddest miracle.

He's but conjectured in man's happiness,

Suspected in man's tears,
Or lurks beyond the long, discouraged guess,
Grown fainter through the years.

*****

But absent, absent now? Ah, what is this,

Near as in child-birth bed,
Laid on our sorrowful hearts, close to a kiss?
A homeless childish head.

THE OCTOBER REDBREAST

Autumn is weary, halt, and old;

Ah, but she owns the song of joy!
Her colours fade, her woods are cold.
Her singing-bird's a boy, a boy.

In lovely Spring the birds were bent

On nests, on use, on love, forsooth!
Grown-up were they. This boy's content,
For his is liberty, his is youth.
The musical stripling sings for play
Taking no thought, and virgin-glad.
For duty sang those mates in May.
This singing-bird's a lad, a lad.

TO "A CERTAIN RICH MAN"

"I HAVE FIVE BRETHREN.... FATHER, I BESEECH

THEE ... LEST THEY COME TO THIS PLACE"
St. Luke's Gospel

Thou wouldst not part thy spoil

Gained from the beggar's want, the weakling's toil,
Nor spare a jot of sumptuousness or state
For Lazarus at the gate.

And in the appalling night

Of expiation, as in day's delight,
Thou heldst thy niggard hand; it would not share
One hour of thy despair.

Those five—thy prayer for them!

O generous! who, condemned, wouldst not condemn,
Whose ultimate human greatness proved thee so
A miser of thy woe.

EVERLASTING FAREWELLS
 "EVERLASTING FAREWELLS! AND AGAIN, AND
YET AGAIN ... EVERLASTING FAREWELLS!"
De Quincey

"Farewells!" O what a word!

Denying this agony, denying the affrights,
Denying all De Quincey spoke or heard
In the infernal sadness of his nights.

How mend these strange "farewells"?

"Vale"? "Addio"? "Leb'wohl"? Not one but seems
A tranquil refutation; tolling bells
That yet behold the terror of his dreams.

THE POET TO THE BIRDS

You bid me hold my peace,

Or so I think, you birds; you'll not forgive
My kill-joy song that makes the wild song cease,
Silent or fugitive.

Yon thrush stopt in mid-phrase

At my mere footfall; and a longer note
Took wing and fled afield, and went its ways
Within the blackbird's throat.

Hereditary song,
Illyrian lark and Paduan nightingale,
Is yours, unchangeable the ages long;
Assyria heard your tale;

Therefore you do not die.

But single, local, lonely, mortal, new,
Unlike, and thus like all my race, am I,
Preluding my adieu.
My human song must be
My human thought. Be patient till 'tis done.
I shall not hold my little peace; for me
There is no peace but one.

AT NIGHT

To W. M.

Home, home from the horizon far and clear,

Hither the soft wings sweep;
Flocks of the memories of the day draw near
The dovecote doors of sleep.

Oh, which are they that come through sweetest light

Of all these homing birds?
Which with the straightest and the swiftest flight?
Your words to me, your words!

WARWICK BROS. & RUTTER LIMITED, TORONTO

PRINTERS & BOOKBINDERS

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