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José Unpingco

Python
Programming
for Data
Analysis
Python Programming for Data Analysis
José Unpingco

Python Programming
for Data Analysis
José Unpingco
University of California
San Diego
CA, USA

ISBN 978-3-030-68951-3 ISBN 978-3-030-68952-0 (eBook)

https://doi.org/10.1007/978-3-030-68952-0

© The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland
AG 2021
This work is subject to copyright. All rights are solely and exclusively licensed by the Publisher, whether
the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse
of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and
transmission or information storage and retrieval, electronic adaptation, computer software, or by similar
or dissimilar methodology now known or hereafter developed.
The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication
does not imply, even in the absence of a specific statement, that such names are exempt from the relevant
protective laws and regulations and therefore free for general use.
The publisher, the authors, and the editors are safe to assume that the advice and information in this book
are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or
the editors give a warranty, expressed or implied, with respect to the material contained herein or for any
errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional
claims in published maps and institutional affiliations.

This Springer imprint is published by the registered company Springer Nature Switzerland AG
The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland
To Irene, Nicholas, and Daniella, for all their
patient support.
Preface

This book grew out of notes for the ECE143 Programming for Data Analysis class
that I have been teaching at the University of California, San Diego, which is a
requirement for both graduate and undergraduate degrees in Machine Learning and
Data Science. The reader is assumed to have some basic programming knowledge
and experience using another language, such as Matlab or Java. The Python idioms
and methods we discuss here focus on data analysis, notwithstanding Python’s
usage across many other topics. Specifically, because raw data is typically a mess
and requires much work to prepare, this text focuses on specific Python language
features to facilitate such cleanup, as opposed to only focusing on particular Python
modules for this.
As with ECE143, here we discuss why things are the way they are in Python
instead of just that they are this way. I have found that providing this kind of
context helps students make better engineering design choices in their codes, which
is especially helpful for newcomers to both Python and data analysis. The text is
sprinkled with little tricks of the trade to make it easier to create readable and
maintainable code suitable for use in both production and development.
The text focuses on using the Python language itself effectively and then moves
on to key third-party modules. This approach improves effectiveness in different
environments, which may or may not have access to such third-party modules. The
Numpy numerical array module is covered in depth because it is the foundation
of all data science and machine learning in Python. We discuss the Numpy array
data structure in detail, especially its memory aspects. Next, we move on to Pandas
and develop its many features for effective and fluid data processing. Because data
visualization is key to data science and machine learning, third-party modules such
as Matplotlib are developed in depth, as well as web-based modules such as Bokeh,
Holoviews, Plotly, and Altair.
On the other hand, I would not recommend this book to someone with no
programming experience at all, but if you can do a little Python already and want to
improve by understanding how and why Python works the way it does, then this is
a good book for you.

vii
viii Preface

To get the most out of this book, open a Python interpreter and type-along with
the many code samples. I worked hard to ensure that all of the given code samples
work as advertised.

Acknowledgments I would like to acknowledge the help of Brian Granger and Fernando Perez,
two of the originators of the Jupyter Notebook, for all their great work, as well as the Python
community as a whole, for all their contributions that made this book possible. Hans Petter
Langtangen was the author of the Doconce [1] document preparation system that was used to
write this text. Thanks to Geoffrey Poore [2] for his work with PythonTeX and LATEX, both key
technologies used to produce this book.

San Diego, CA, USA José Unpingco

February, 2020

References

1. H.P. Langtangen, DocOnce markup language. https://github.com/hplgit/doconce

2. G.M. Poore, Pythontex: reproducible documents with latex, python, and more. Comput. Sci.
Discov. 8(1), 014010 (2015)
Contents

1 Basic Programming . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.1 Basic Language . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.1.1 Getting Started . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.1.2 Reserved Keywords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.1.3 Numbers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.1.4 Complex Numbers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.1.5 Strings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
1.1.6 Loops and Conditionals. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
1.1.7 Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
1.1.8 File Input/Output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
1.1.9 Dealing with Errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
1.1.10 Power Python Features to Master . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
1.1.11 Generators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
1.1.12 Decorators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
1.1.13 Iteration and Iterables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
1.1.14 Using Python Assertions to Pre-debug Code . . . . . . . . . . . . . . . 60
1.1.15 Stack Tracing with sys.settrace . . . . . . . . . . . . . . . . . . . . . . 61
1.1.16 Debugging Using IPython . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
1.1.17 Logging from Python . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
2 Object-Oriented Programming. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
2.1 Properties/Attributes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
2.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
2.3 Inheritance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
2.4 Class Variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
2.5 Class Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
2.6 Static Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
2.7 Hashing Hides Parent Variables from Children . . . . . . . . . . . . . . . . . . . . . . 76
2.8 Delegating Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
2.9 Using super for Delegation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
2.10 Metaprogramming: Monkey Patching . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

ix
x Contents

2.11 Abstract Base Classes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80

2.12 Descriptors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
2.13 Named Tuples and Data Classes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
2.14 Generic Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
2.15 Design Patterns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
2.15.1 Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
2.15.2 Singleton . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
2.15.3 Observer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
2.15.4 Adapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
3 Using Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
3.1 Standard Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
3.2 Writing and Using Your Own Modules. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
3.2.1 Using a Directory as a Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
3.3 Dynamic Importing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
3.4 Getting Modules from the Web . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
3.5 Conda Package Management . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
4 Numpy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
4.1 Dtypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
4.2 Multidimensional Arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
4.3 Reshaping and Stacking Numpy Arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
4.4 Duplicating Numpy Arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
4.5 Slicing, Logical Array Operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
4.6 Numpy Arrays and Memory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
4.7 Numpy Memory Data Structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
4.8 Array Element-Wise Operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
4.9 Universal Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
4.10 Numpy Data Input/Output. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
4.11 Linear Algebra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
4.12 Broadcasting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
4.13 Masked Arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
4.14 Floating Point Numbers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
4.15 Advanced Numpy dtypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
5 Pandas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
5.1 Using Series . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
5.2 Using DataFrame . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
5.3 Reindexing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
5.4 Deleting Items . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
5.5 Advanced Indexing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
5.6 Broadcasting and Data Alignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
5.7 Categorical and Merging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
Contents xi

5.8 Memory Usage and dtypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143

5.9 Common Operations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
5.10 Displaying DataFrames. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
5.11 Multi-index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
5.12 Pipes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
5.13 Data Files and Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
5.14 Customizing Pandas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
5.15 Rolling and Filling Operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
6 Visualizing Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
6.1 Matplotlib . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158
6.1.1 Setting Defaults . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
6.1.2 Legends . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
6.1.3 Subplots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
6.1.4 Spines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
6.1.5 Sharing Axes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
6.1.6 3D Surfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
6.1.7 Using Patch Primitives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
6.1.8 Patches in 3D . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
6.1.9 Using Transformations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
6.1.10 Annotating Plots with Text . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
6.1.11 Annotating Plots with Arrows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
6.1.12 Embedding Scalable and Non-scalable Subplots . . . . . . . . . . . 173
6.1.13 Animations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
6.1.14 Using Paths Directly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177
6.1.15 Interacting with Plots Using Sliders . . . . . . . . . . . . . . . . . . . . . . . . 179
6.1.16 Colormaps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
6.1.17 Low-Level Control Using setp and getp . . . . . . . . . . . . . . . 183
6.1.18 Interacting with Matplotlib Figures . . . . . . . . . . . . . . . . . . . . . . . . . 183
6.1.19 Keyboard Events . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
6.1.20 Mouse Events . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
6.2 Seaborn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
6.2.1 Automatic Aggregation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190
6.2.2 Multiple Plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194
6.2.3 Distribution Plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
6.3 Bokeh. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
6.3.1 Using Bokeh Primitives. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
6.3.2 Bokeh Layouts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206
6.3.3 Bokeh Widgets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
6.4 Altair . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
6.4.1 Detailing Altair. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
6.4.2 Aggregations and Transformations. . . . . . . . . . . . . . . . . . . . . . . . . . 217
6.4.3 Interactive Altair . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222
6.5 Holoviews . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224
6.5.1 Dataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230
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