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[1]
Learning IPython for Interactive
Computing and Data
Visualization
Second Edition
Cyrille Rossant
BIRMINGHAM - MUMBAI
Learning IPython for Interactive Computing
and Data Visualization
Second Edition
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.
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of the information presented. However, the information contained in this book
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companies and products mentioned in this book by the appropriate use of capitals.
However, Packt Publishing cannot guarantee the accuracy of this information.
ISBN 978-1-78398-698-9
www.packtpub.com
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About the Author
In the open source area, he is a core developer for several interesting and popular
projects, such as IPython/Jupyter, Bokeh, and Nikola. He has also started his own
projects, being RISE, an extension to enable amazing live slides in the Jupyter
notebook, the most popular one. He has also written several tutorials about
the Scientific Python tools (available at Github) and presented several talks
at international conferences.
He has an ambition to simplify his work with open software and use and develop
new ones; sometimes obtaining good results, at other times, negative. You can reach
Nicola on his website at http://rainnic.altervista.org.
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[i]
Table of Contents
[ ii ]
Table of Contents
Manipulating data 69
Selecting data 69
Selecting columns 70
Selecting rows 70
Filtering with boolean indexing 72
Computing with numbers 73
Working with text 75
Working with dates and times 76
Handling missing data 77
Complex operations 78
Group-by 78
Joins 80
Summary 83
Chapter 3: Numerical Computing with NumPy 85
A primer to vector computing 85
Multidimensional arrays 86
The ndarray 86
Vector operations on ndarrays 87
How fast are vector computations in NumPy? 88
How an ndarray is stored in memory 89
Why operations on ndarrays are fast 91
Creating and loading arrays 91
Creating arrays 91
Loading arrays from files 93
Basic array manipulations 94
Computing with NumPy arrays 97
Selection and indexing 98
Boolean operations on arrays 99
Mathematical operations on arrays 100
A density map with NumPy 103
Other topics 107
Summary 108
Chapter 4: Interactive Plotting and Graphical Interfaces 109
Choosing a plotting backend 109
Inline plots 109
Exported figures 111
GUI toolkits 111
Dynamic inline plots 113
Web-based visualization 114
[ iii ]
Table of Contents
[ iv ]
Table of Contents
[v]
Preface
Data analysis skills are now essential in scientific research, engineering, finance,
economics, journalism, and many other domains. With its high accessibility and
vibrant ecosystem, Python is one of the most appreciated open source languages for
data science.
The first edition of Learning IPython for Interactive Computing and Data Visualization
was published in April 2013, several months before the release of IPython 1.0. This
new edition targets IPython 4.0, released in August 2015. In addition to reflecting the
novelties of this new version of IPython, the present book is also more accessible to
non-programmer beginners. The first chapter contains a brand new crash course on
Python programming, as well as detailed installation instructions.
Since the first edition of this book, IPython's popularity has grown significantly,
with an estimated user base of several millions of people and ongoing collaborations
with large companies like Microsoft, Google, IBM, and others. The project itself has
been subject to important changes, with a refactoring into a language-independent
interface called the Jupyter Notebook, and a set of backend kernels in various
languages. The Notebook is no longer reserved to Python; it can now also be used
with R, Julia, Ruby, Haskell, and many more languages (50 at the time of this
writing!).
[ vii ]
Preface
The Jupyter project has received significant funding in 2015 from the Leona M. and
Harry B. Helmsley Charitable Trust, the Gordon and Betty Moore Foundation, and
the Alfred P. Sloan Foundation, which will allow the developers to focus on the
growth and maturity of the project in the years to come.
Chapter 3, Numerical Computing with NumPy, details how to use NumPy for efficient
computing on multidimensional numerical arrays.
Chapter 6, Customizing IPython, shows how IPython and the Jupyter Notebook can be
extended for customized use-cases.
[ viii ]
Preface
Since our world is becoming more and more data-driven, knowing how to analyze
data effectively is an essential skill to learn. If you're used to spreadsheet programs
like Microsoft Excel, you will appreciate Python for its much larger range of analysis
and visualization possibilities. Knowing this general-purpose language will also let
you share your data and analysis with other programs and libraries.
Conventions
In this book, you will find a number of text styles that distinguish between different
kinds of information. Here are some examples of these styles and an explanation of
their meaning.
Code words in text, database table names, folder names, filenames, file extensions,
pathnames, dummy URLs, user input, and Twitter handles are shown as follows:
"Run it with a command like bash Anaconda3-2.3.0-Linux-x86_64.sh (if
necessary, replace the filename by the one you downloaded)."
[ ix ]
Preface
New terms and important words are shown in bold. Words that you see on the
screen, for example, in menus or dialog boxes, appear in the text like this: "To create
a new notebook, click on the New button, and select Notebook (Python 3)."
Reader feedback
Feedback from our readers is always welcome. Let us know what you think about
this book—what you liked or disliked. Reader feedback is important for us as it helps
us develop titles that you will really get the most out of.
If there is a topic that you have expertise in and you are interested in either writing
or contributing to a book, see our author guide at www.packtpub.com/authors.
You can also report any issues at https://github.com/ipython-books/minibook-
2nd-code/issues.
[x]
Preface
Customer support
Now that you are the proud owner of a Packt book, we have a number of things to
help you to get the most from your purchase.
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Although we have taken every care to ensure the accuracy of our content, mistakes
do happen. If you find a mistake in one of our books—maybe a mistake in the text or
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[ xi ]
Piracy
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Questions
If you have a problem with any aspect of this book, you can contact us at
[email protected], and we will do our best to address the problem.
Getting Started with IPython
In this chapter, we will cover the following topics:
In the past few years, Python has also emerged as one of the leading open
platforms for data science and high-performance numerical computing. This might
seem surprising as Python was not originally designed for scientific computing.
Python's interpreted nature makes it much slower than lower-level languages like
C or Fortran, which are more amenable to number crunching and the efficient
implementation of complex mathematical algorithms.
However, the performance of these low-level languages comes at a cost: they are
hard to use and they require advanced knowledge of how computers work. In the
late 1990s, several scientists began investigating the possibility of using Python for
numerical computing by interoperating it with mainstream C/Fortran scientific
libraries. This would bring together the ease-of-use of Python with the performance
of C/Fortran: the dream of any scientist!
[1]
Getting Started with IPython
Consequently, the past 15 years have seen the development of widely-used libraries
such as NumPy (providing a practical array data structure), SciPy (scientific
computing), matplotlib (graphical plotting), pandas (data analysis and statistics),
scikit-learn (machine learning), SymPy (symbolic computing), and Jupyter/IPython
(efficient interfaces for interactive computing). Python, along with this set of
libraries, is sometimes referred to as the SciPy stack or PyData platform.
Competing platforms
Python has several competitors. For example, MATLAB (by Mathworks)
is a commercial software focusing on numerical computing that is
widely-used in scientific research and engineering. SPSS (by IBM) is a
commercial software for statistical analysis. Python, however, is free and
open source, and that's one of its greatest strengths. Alternative open
source platforms include R (specialized in statistics) and Julia (a young
language for high-performance numerical computing).
This book provides a solid introduction to the whole platform by focusing on one
of its main components: Jupyter/IPython.
[2]
Chapter 1
Example of a notebook
It quickly became clear that this interface could be used with languages other than
Python such as R, Julia, Lua, Ruby, and many others. Further, the Notebook is not
restricted to scientific computing: it can be used for academic courses, software
documentation, or book writing thanks to conversion tools targeting Markdown,
HTML, PDF, ODT, and many other formats. Therefore, the IPython developers
decided in 2014 to acknowledge the general-purpose nature of the Notebook by
giving a new name to the project: Jupyter.
[3]
Getting Started with IPython
In August 2015, the IPython/Jupyter developers achieved the "Big Split" by splitting
the previous monolithic IPython codebase into a set of smaller projects, including
the language-independent Jupyter Notebook (see https://blog.jupyter.
org/2015/08/12/first-release-of-jupyter/). For example, the parallel
computing features of IPython are now implemented in a standalone Python
package named ipyparallel, the IPython widgets are implemented in ipywidgets,
and so on. This separation makes the code of the project more modular and facilitates
third-party contributions. IPython itself is now a much smaller project than before
since it only features the interactive Python terminal and the Python kernel for the
Jupyter Notebook.
This book gives you a solid introduction to Jupyter and the SciPy
platform. The IPython Interactive Computing and Visualization Cookbook
(http://ipython-books.github.io/cookbook/) is the sequel of
this introductory-level book. In 15 chapters and more than 500 pages,
it contains a hundred recipes covering a wide range of interactive
numerical computing techniques and data science topics. The IPython
Cookbook is an excellent addition to the present IPython minibook if
you're interested in delving into the platform in much greater detail.
[4]
Chapter 1
References
Here are a few references about IPython and the Notebook:
Anaconda comes with a package manager named conda, which lets you manage
your Python distribution and install new packages.
Miniconda
Miniconda (http://conda.pydata.org/miniconda.html) is
a light version of Anaconda that gives you the ability to only install
the packages you need.
[5]
Getting Started with IPython
Downloading Anaconda
The first step is to download Anaconda from Continuum Analytics' website
(http://continuum.io/downloads). This is actually not the easiest part since
several versions are available. Three properties define a particular version:
• The operating system (OS): Linux, Mac OS X, or Windows. This will depend
on the computer you want to install Python on.
• 32-bit or 64-bit: You want the 64-bit version, unless you're on an old or low-
end computer. The 64-bit version will allow you to manipulate large datasets.
• The version of Python: 2.7, or 3.4 (or later). In this book, we will use
Python 3.4. You can also use Python 3.5 (released in September 2015)
which introduces many features, including a new @ operator for matrix
multiplication. However, it is easy to temporarily switch to a Python 2.7
environment with Anaconda if necessary (see the next section).
Once you have found the right link for your OS and Python 3 64-bit, you can
download the package. You should then find it in your downloads directory
(depending on your OS and your browser's settings).
Installing Anaconda
The Anaconda installer comes in different flavors depending on your OS, as follows:
• Linux: The Linux installer is a bash .sh script. Run it with a command
like bash Anaconda3-2.3.0-Linux-x86_64.sh (if necessary, replace the
filename by the one you downloaded).
• Mac: The Mac graphical installer is a .pkg file that you can run with a
double-click.
• Windows: The Windows graphical installer is an .exe file that you can run
with a double-click.
[6]
Chapter 1
Then, follow the instructions to install Anaconda on your computer. Here are a few
remarks:
• You don't need administrator rights to install Anaconda. In most cases, you
can choose to install it in your personal user account.
• Choose to put Anaconda in your system path, so that Anaconda's Python is
the system default.
Anaconda comes with a graphical launcher that you can use to start
IPython, manage environments, and so on. You will find more details
at http://docs.continuum.io/anaconda-launcher/
You can skip this section if you already know how to do these things.
Opening a terminal
A terminal is a command-line application that lets you interact with your computer
by typing commands with the keyboard, instead of clicking on windows with the
mouse. While most computer users only know Graphical User Interfaces, developers
and scientists generally need to know how to use the command-line interface for
advanced usage. To use the command-line interface, follow the instructions that are
specific to your OS:
• On Windows, you can use Powershell. Press the Windows + R keys, type
powershell in the Run box, and press Enter. You will find more information
about Powershell at https://blog.udemy.com/powershell-tutorial/.
Alternatively, you can use the older Windows terminal by typing cmd in the
Run box.
• On OS X, you can open the Terminal application, for example by pressing
Cmd + Space, typing terminal, and pressing Enter.
• On Linux, you can open the Terminal from your application manager.
[8]
Chapter 1
If you have this problem, you may need to add the path to the Anaconda executables
to your system path. For example, this path will be ~/anaconda3/bin if you chose to
install Anaconda in ~/anaconda3. The bin directory contains Anaconda executables
including python.
If you have any problem installing and testing Anaconda, you can ask for help on
the mailing list (see the link in the References section under the Installing Python with
Anaconda section of this chapter).
Next, exit the Python prompt by typing exit() and pressing Enter.
Managing environments
Anaconda lets you create different isolated Python environments. For example, you
can have a Python 2 distribution for the rare cases where you need to temporarily
switch to Python 2.
[9]
Getting Started with IPython
This will create a new isolated environment named py2 based on the original
Anaconda distribution, but with Python 2.7. You could also use the command conda
env: type conda env -h to see the details.
You can now activate your py2 environment by typing the following command in a
terminal:
• Windows: activate py2 (note that you might have problems with
Powershell, see https://github.com/conda/conda/issues/626, or use the
old cmd terminal)
• Linux and Mac OS X: source activate py2
Now, you should see a (py2) prefix in front of your terminal prompt. Typing
python in your terminal with the py2 environment activated will open a Python 2
interpreter.
[ 10 ]
Exploring the Variety of Random
Documents with Different Content
go about from place to place; kanaka i ka ohi i ka ia, a me na
but just looked on as the men wahine.
and women helped themselves
to the fish.
One day while the two were in I kekahi la, ia laua e moe ana,
bed, an aunt of Kaalaea’s, hele mai la, kekahi makuahine o
together with several others, Kaalaea, a me kekahi poe e ae, a
came into the house where the hiki i kahi a laua nei e moe ana,
two were sleeping. These people e hele ana i ka lawaia papai. I
were on their way to catch mai la ka makuahine: “E
crabs. While in the house, the Kaalaea, e ala e hele kakou i ka
aunt said: “Wake up, Puniakaia, lawaia papai; o ke aha kau hana,
and let us go crabbing. What do o ka moe wale iho la no, a ala ae
you do, any way? Just sleep, and wae i ka piapia o na maka, popoi
when you get up clean your eyes i ka nalo a ai ae.” Ia ia e olelo
and catch flies and eat?” While ana, e nana mai ana no o
the aunt was speaking, Puniakaia maloko o ke kihei
Puniakaia was listening through kalukalu nahenahe, me ke ala
the soft mantle that covered mai no, a hoolohe; aka, o ka
them; the aunt did not know makuahine nana i olelo, aole ona
this, however, for she thought he manao e ala ana, ua manao no
was asleep. ia, e hiamoe ana o Puniakaia.
After living with his mother for a He mau la i hala o ka noho ana,
few days, Puniakaia decided to holo o Puniakaia i Kauai e
go to Kauai to make a visit; so makaikai ai, hele aku la ia a hiki i
he started out until he came to ka lae o Kaena ma Waianae, e
the Kaena point, at Waianae, noho ana keia poe e hoa i na
where he met some men who waa, a e holo i Kauai. Ninau aku
were lashing their canoe for a la o Puniakaia: “E holo ana ko
trip to Kauai. Puniakaia upon oukou waa i hea?” “I Kauai.”
coming up to these men, asked “Aole la hoi e pono owau kekahi
them: “Where are you going e holo pu me oukou?” “I ke aha
with this canoe?” “To Kauai.” hoi! O ka waa no paha ia.” O ke
“Can I go with you?” “And why kumu o keia ae ana e holo pu i
not? The canoe is yours.” 8 The Kauai, o ka nana mai o lakou la
reason why these people allowed a ike i ke kanaka maikai o
Puniakaia to go to Kauai with Puniakaia.
them was because he was such
a handsome looking man.
Some time after Puniakaia had Mahope o keia noho ana, iho aku
been living with this woman, he la o Puniakaia i kahakai me ka
went down one day to the beach wahine, aia hoi, e hoomakaukau
accompanied by the woman and ana kekahi mau kanaka e holo i
there saw two men preparing to ka lawaia. Ninau aku la o
go out fishing. Upon coming up Puniakaia: “He aha ka olua
to the fishermen, Puniakaia lawaia?” Hai mai laua ala: “He
asked them: “What kind of lawaia oio, elua no nae kauna ke
fishing are you two going out loaa mai, aohe mahuahua loa.” I
for?” The two replied: “Oio 10 aku o Puniakaia: “Ae, owau no
fishing; but the most we will ka mea e loaa ai ka ia, mai ka
ever catch will be about eight, moana a ka honua, mai lalo a
not very many.” Puniakaia said: luna o ke kai, o ka ia, ohi ke
“Yes, I will be the one who will kanaka a haalele, kopi a pilau, ai
get you all you want, from the ka puaa me ka ilio, a e
ocean to the land, from the hoomaunauna.” Olelo mai na
bottom of the sea to the top and kanaka: “Wahahee oe; noho
the people will not be able to wale ae nei no makou i nei wahi
carry away all the fish; they will aohe ia pela ke ku ana.” [161]
salt some and the pigs and dogs
will eat their full and a lot will be
wasted.” The two men then said:
“You are deceiving us. We have
lived here all our lives and have
never seen so much fish.” [160]
After the night was spent and A hala ae la ka po, hiki mai la ka
the dawn of the new day began wehe ana o ka pawa o ke ao, oili
to break, Puniakaia came out of ae la ia a waho o ka hale, nana
the house and looked toward the aku la ia i ke kai, ua hele a ehu i
sea, when he saw the surface as ka ia, mai luna, a lalo. Ia wa,
well as the lower portion of the holo ana o Uhumakaikai malalo
sea brown with fish. Shortly after ona, lalau iho la ia a hii ae la,
this Uhumakaikai passed below honi iho la, a kaukau iho: “U;
him; he then reached down, aole au i manao e haalele ia oe, i
took it up and hugged and hele mai au me kuu manao e
kissed it. Then he said: “Yes, I makaikai ia Oahu a puni, alaila,
did not intend to leave you hoi aku ia oe, eia ka au e hala
behind; I came with the idea of ana i Kauai nei, nolaila, mai ike
making a tour of sightseeing ole oe i ko’u puumake, e hiki ole
around Oahu, and then go back mai nei oe, make au.”
to you; but instead I came to
Kauai and came near not being
able to see you again. Had you
failed me I would have been
killed.”
[Contents]
Legend of Maniniholokuaua He Kaao no
Keliimalolo.
Because of this loss of his canoe, No keia lilo ana o ka waa, hoi
he immediately returned to Oahu mai la i Oahu a holo ma Kauai, e
and soon after set out for Kauai, imi ana i makaia, nana e kii ka
in search of some one who waa. Eia ke ano o ia huaolelo,
would be able to return him his makaia, he kanaka mama loa i
canoe. He wished to get a good ka holo. Holo aku la keia a pae
runner. On this trip to Kauai he ma Mana i Kauai, hapai aku la i
first landed at Mana; after he na waa a kau i uka, hele aku la e
landed he carried his canoe auau, wehe ae la i kahi malo a
ashore and went for a swim. kapae ma kapa, lele iho la auau i
Upon coming to the pool he loko o ka wai. Ku ana o
disrobed and jumped in. Just as Kamaakamikioi me
he got into the water, Kamaakauluohia, mai Niihau mai
Kamaakamikioi and laua, he mau keiki laua na
Kamaakauluohia arrived from Halulu. He mau kanaka mama
Niihau. They were the sons of laua ma ka hele ana, he umi
Halulu. These two men were puni o Kauai i ka la hookahi; no
noted for their fleetness and ko laua mama loa, ua hiki ia laua
could make ten circuits of Kauai ke holo mai ka aina a ke kai, mai
in one day. Being very swift they ka honua a i ka lewa, he oi ko
could run on land and sea and laua mama mamua o Keliimalolo
from the earth to the skies. They a me Maniniholokuaua. Lalau iho
were greater runners than either la laua i ka malo o Keliimalolo, a
Keliimalolo or Maniniholokuaua. holo aku la, alualu aku la o
As soon as they arrived at the Keliimalolo mahope, aohe launa
pool they picked up the malo of aku, holo aku la laua la a loko o
Keliimalolo and ran away with it. ke kai ku mai. Kahea aku o
Keliimalolo got out of the pool Keliimalolo: [167]“Hoi mai olua i
and started to chase the two to uka nei i mau aikane olua na’u.”
try and recover his malo; but he A hiki mai la laua, i aku o
could not catch up with them. Keliimalolo: “O olua ka ka mea e
The two ran out onto the sea, on ku ai kuu makaia.” Hai aku la oia
the surface, and when at some i kona holo ana i Molokai, a me
distance from the shore they ka lilo ana o ka waa ia
stood and looked at Keliimalolo. Maniniholokuaua.
Keliimalolo [166]then called out to
them, saying: “You two come A lohe laua la. Olelo mai o
ashore and let us be friends.” Kamaakamikioi a me
After the two had come ashore Kamaakauluohia: “Ae, e hoi oe i
Keliimalolo said to them: “You Oahu, a na po i o Kane hiki aku
two will be the means of maua; e kau ana auanei elua
restoring to me what I have opua la o maua ia.” Eia nae, i
lost.” He then related to them his aku laua ia Keliimalolo: “E
trip to Molokai and how his kaapuni kakou ia Kauai nei i
canoe was stolen by hookahi la.” Ae mai o Keliimalolo.
Maniniholokuaua. After the two
had listened to the narrative,
they said to Keliimalolo: “You
return to Oahu and in the nights
of Kane, we will come. When
you see two narrow pointed
clouds hanging in the horizon
make sure that the clouds are
ourselves and we will come soon
after that.” The two then asked
Keliimalolo: “Let us all make a
circuit of Kauai in one day.” This
was consented to by Keliimalolo.
[Contents]
Legend of Opelemoemoe. He Kaao no Opelemoemoe.
1 Sleeping Opele. ↑
2 Pokai (pronounced ko-ka-ee), a
place in Waianae. ↑
3 Anahulu, a ten day period, as we
speak of a dozen for twelve. ↑
4 Another deserting father’s token of
identity. ↑
[Contents]
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