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Learning Scientific Programming with Python

Learn to master basic programming tasks from scratch with real-life, scientifically
relevant examples and solutions drawn from both science and engineering. Students and
researchers at all levels are increasingly turning to the powerful Python programming
language as an alternative to commercial packages and this fast-paced introduction
moves from the basics to advanced concepts in one complete volume, enabling readers
to quickly gain proficiency.
Beginning with general programming concepts such as loops and functions within
the core Python 3 language, and moving on to the NumPy, SciPy and Matplotlib
libraries for numerical programming and data visualization, this textbook also discusses
the use of IPython Notebooks to build rich-media, shareable documents for scientific
analysis. Including a final chapter introducing challenging topics such as floating-
point precision and algorithm stability, and with extensive online resources to support
advanced study, this textbook represents a targeted package for students requiring a
solid foundation in Python programming.

Christian Hill is a physicist and physical chemist at University College London and
Oxford University. He has over twenty years’ experience of programming in the phys-
ical sciences and has been programming in Python for ten years. His research uses
Python to produce, analyse, process, curate and visualize large data sets for the predic-
tion of the properties of planetary atmospheres.
Learning Scientific Programming
with Python
Christian Hill
University College London and
Somerville College, University of Oxford
University Printing House, Cambridge CB2 8BS, United Kingdom

Cambridge University Press is part of the University of Cambridge.

It furthers the University’s mission by disseminating knowledge in the pursuit of
education, learning and research at the highest international levels of excellence.

www.cambridge.org
Information on this title: www.cambridge.org/9781107075412
© Cambridge University Press 2015
This publication is in copyright. Subject to statutory exception
and to the provisions of relevant collective licensing agreements,
no reproduction of any part may take place without
the written permission of Cambridge University Press.
First published 2015
Printed in the United Kingdom by TJ International Ltd. Padstow Cornwall
A catalogue record for this publication is available from the British Library
Library of Congress Cataloguing in Publication data
Hill, Christian, 1974–
Learning scientific programming with Python / Christian Hill,
University College London and Somerville College, University of Oxford.
pages cm
ISBN 978-1-107-07541-2 (Hardback) – ISBN 978-1-107-42822-5 (Paperback)
1. Science–Data processing. 2. Science–Mathematics.
3. Python (Computer program language) I. Title.
Q183.9.H58 2015
005.13 3–dc23 2015017085
ISBN 978-1-107-07541-2 Hardback
ISBN 978-1-107-42822-5 Paperback
Additional resources for this publication at www.cambridge.org/9781107075412
Cambridge University Press has no responsibility for the persistence or accuracy of
URLs for external or third-party internet websites referred to in this publication,
and does not guarantee that any content on such websites is, or will remain,
accurate or appropriate.
 Contents

Acknowledgments page vii

1 Introduction 1
1.1 About this book 1
1.2 About Python 2
1.3 Installing Python 5
1.4 The command line 6

2 The core Python language I 8

2.1 The Python shell 8
2.2 Numbers, variables, comparisons and logic 9
2.3 Python objects I: strings 27
2.4 Python objects II: lists, tuples and loops 41
2.5 Control flow 56
2.6 File input/output 66
2.7 Functions 70

3 Interlude: simple plotting with pylab 84

3.1 Basic plotting 84
3.2 Labels, legends and customization 89
3.3 More advanced plotting 97

4 The core Python language II 102

4.1 Errors and exceptions 102
4.2 Python objects III: dictionaries and sets 110
4.3 Pythonic idioms: “syntactic sugar” 121
4.4 Operating system services 131
4.5 Modules and packages 137
4.6 An introduction to object-oriented programming 147

v
vi Contents

5 IPython and IPython Notebook 160

5.1 IPython 160
5.2 IPython Notebook 174

6 NumPy 184
6.1 Basic array methods 184
6.2 Reading and writing an array to a file 216
6.3 Statistical methods 225
6.4 Polynomials 232
6.5 Linear algebra 247
6.6 Matrices 256
6.7 Random sampling 262
6.8 Discrete Fourier transforms 272

7 Matplotlib 280
7.1 Matplotlib basics 280
7.2 Contour plots, heatmaps and 3D plots 317

8 SciPy 333
8.1 Physical constants and special functions 333
8.2 Integration and ordinary differential equations 355
8.3 Interpolation 374
8.4 Optimization, data-fitting and root-finding 380

9 General scientific programming 402

9.1 Floating point arithmetic 402
9.2 Stability and conditioning 410
9.3 Programming techniques and software development 415

Appendix A Solutions 424

Index 445
Acknowledgments

For Emma, Charlotte and Laurence

Many people have helped directly or indirectly in the preparation of this book. Thanks
are due especially to Jonathan Tennyson at UCL, and Laurence Rothman and Iouli Gor-
don for hosting my sabbatical year at the Harvard-Smithsonian Center for Astrophysics.
As ever, I owe much to Natalie Haynes for her constant support, encouragement and
friendship.

vii
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1 Introduction

1.1 About this book

This book is intended to help scientists and engineers learn version 3 of the Python
programming language and its associated NumPy, SciPy and Matplotlib libraries. No
prior programming experience or scientific knowledge in any particular field is assumed.
However, familiarity with some mathematical concepts such as trigonometry, complex
numbers and basic calculus is helpful to follow the examples and exercises.
Python is a powerful language with many advanced features and libraries; while the
basic syntax of the language is straightforward to learn, it would be impossible to teach
it in depth in a book of this size. Therefore, we aim for a balanced, broad introduction to
the central features of the language and its important libraries. The text is interspersed
with examples relevant to scientific research, and at the end of most sections there are
questions (short problems designed to test knowledge) and exercises (longer problems
that usually require a short computer program to solve). Although it is not necessary
to complete all of the exercises, readers will find it useful to attempt at least some of
them. Where a section, example or exercise contains more advanced material that may
be skipped on first reading, this is indicated with the symbol ♦.
In Chapter 2 of this book, the basic syntax, data structures and flow control of a
Python program are introduced. Chapter 3 is a short interlude on the use of the Pylab
library for making graphical plots of data: this is useful to visualize the output of
programs in subsequent chapters. Chapter 4 provides more advanced coverage of the
core Python language and a brief introduction to object-oriented programming. There
follows another short chapter introducing the popular IPython and IPython Notebook
environments, before chapters on scientific programming with NumPy, Matplotlib and
SciPy. The final chapter covers more general topics in scientific programming, including
floating point arithmetic, algorithm stability and programming style.
Readers who are already familiar with the Python programming language may wish
to skim Chapters 2 and 4.
Code examples and exercise solutions may be downloaded from the book’s website at
scipython.com . Note that while comments have been included in these downloadable
programs, they are not so extensive in the printed version of this book: instead, the code
is explained in the text itself through numbered annotations (such as ➊). Readers typing
in these programs for themselves may wish to add their own explanatory comments to
the code.

1
2 Introduction

1.2 About Python

Python is a powerful, general-purpose programming language devised by Guido van

Rossum in 1989.1 It is classified as a high-level programming language in that it auto-
matically handles the most fundamental operations (such as memory management)
carried out at the processor level (“machine code”). It is considered a higher-level
language than, for example, C, because of its expressive syntax (which is close to
natural language in some cases) and rich variety of native data structures such as lists,
tuples, sets and dictionaries. For example, consider the following Python program which
outputs a list of names on separate lines.
Listing 1.1 Outputing a list of names using a program written in Python
# eg1-names.py: output three names to the console.

names = [’Isaac Newton’, ’Marie Curie’, ’Albert Einstein’]

for name in names:
print(name)

Output:
Isaac Newton
Marie Curie
Albert Einstein

Now compare this with the equivalent program in C.

Listing 1.2 Outputing a list of names using a program written in C

/* eg1-names.c: output three names to the console. */
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#define MAX_STRING_LENGTH 20
#define NUMBER_OF_STRINGS 3

int main()
{
int i;
char names[NUMBER_OF_STRINGS][MAX_STRING_LENGTH+1];
strcpy(names[0], "Isaac Newton");
strcpy(names[1], "Marie Curie");
strcpy(names[2], "Albert Einstein");

for (i=0;i<NUMBER_OF_STRINGS;i++) {
fprintf(stdout, "%s\n", names[i]);
}

return EXIT_SUCCESS;
}

1 Python’s “benevolent dictator for life.”

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Module 1: Comparative analysis and synthesis

Learning Objective 1: Practical applications and examples
• Assessment criteria and rubrics
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Learning Objective 2: Assessment criteria and rubrics
• Literature review and discussion
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Learning Objective 3: Experimental procedures and results
• Comparative analysis and synthesis
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Learning Objective 4: Fundamental concepts and principles
• Experimental procedures and results
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
[Figure 4: Diagram/Chart/Graph]
Learning Objective 5: Interdisciplinary approaches
• Fundamental concepts and principles
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Key Concept: Fundamental concepts and principles
• Literature review and discussion
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Example 6: Assessment criteria and rubrics
• Fundamental concepts and principles
- Sub-point: Additional details and explanations
- Example: Practical application scenario
[Figure 7: Diagram/Chart/Graph]
Example 7: Problem-solving strategies and techniques
• Literature review and discussion
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
[Figure 8: Diagram/Chart/Graph]
Definition: Fundamental concepts and principles
• Best practices and recommendations
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Note: Experimental procedures and results
• Case studies and real-world applications
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Methodology 2: Assessment criteria and rubrics
Important: Historical development and evolution
• Case studies and real-world applications
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Note: Key terms and definitions
• Critical analysis and evaluation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Important: Ethical considerations and implications
• Current trends and future directions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
[Figure 13: Diagram/Chart/Graph]
Key Concept: Current trends and future directions
• Learning outcomes and objectives
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
[Figure 14: Diagram/Chart/Graph]
Practice Problem 14: Theoretical framework and methodology
• Learning outcomes and objectives
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Example 15: Research findings and conclusions
• Research findings and conclusions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
[Figure 16: Diagram/Chart/Graph]
Remember: Case studies and real-world applications
• Case studies and real-world applications
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Practice Problem 17: Learning outcomes and objectives
• Case studies and real-world applications
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Note: Study tips and learning strategies
• Key terms and definitions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Important: Current trends and future directions
• Experimental procedures and results
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Quiz 3: Ethical considerations and implications
Remember: Comparative analysis and synthesis
• Study tips and learning strategies
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Key Concept: Learning outcomes and objectives
• Statistical analysis and interpretation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
[Figure 22: Diagram/Chart/Graph]
Definition: Interdisciplinary approaches
• Literature review and discussion
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Example 23: Practical applications and examples
• Current trends and future directions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Note: Learning outcomes and objectives
• Assessment criteria and rubrics
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
[Figure 25: Diagram/Chart/Graph]
Practice Problem 25: Ethical considerations and implications
• Assessment criteria and rubrics
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
[Figure 26: Diagram/Chart/Graph]
Definition: Experimental procedures and results
• Theoretical framework and methodology
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Example 27: Assessment criteria and rubrics
• Key terms and definitions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Definition: Research findings and conclusions
• Statistical analysis and interpretation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Key Concept: Research findings and conclusions
• Study tips and learning strategies
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Conclusion 4: Ethical considerations and implications
Important: Research findings and conclusions
• Statistical analysis and interpretation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Practice Problem 31: Experimental procedures and results
• Case studies and real-world applications
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Practice Problem 32: Research findings and conclusions
• Fundamental concepts and principles
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Example 33: Literature review and discussion
• Practical applications and examples
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Remember: Fundamental concepts and principles
• Current trends and future directions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Practice Problem 35: Ethical considerations and implications
• Learning outcomes and objectives
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Example 36: Comparative analysis and synthesis
• Ethical considerations and implications
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Important: Theoretical framework and methodology
• Critical analysis and evaluation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Note: Study tips and learning strategies
• Research findings and conclusions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Remember: Current trends and future directions
• Interdisciplinary approaches
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
References 5: Practical applications and examples
Remember: Ethical considerations and implications
• Experimental procedures and results
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Important: Learning outcomes and objectives
• Best practices and recommendations
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Practice Problem 42: Key terms and definitions
• Ethical considerations and implications
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Remember: Fundamental concepts and principles
• Key terms and definitions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Key Concept: Ethical considerations and implications
• Interdisciplinary approaches
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Definition: Learning outcomes and objectives
• Critical analysis and evaluation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Note: Comparative analysis and synthesis
• Current trends and future directions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Important: Comparative analysis and synthesis
• Fundamental concepts and principles
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Example 48: Best practices and recommendations
• Interdisciplinary approaches
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Important: Best practices and recommendations
• Ethical considerations and implications
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Discussion 6: Learning outcomes and objectives
Practice Problem 50: Case studies and real-world applications
• Current trends and future directions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Key Concept: Current trends and future directions
• Best practices and recommendations
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Note: Experimental procedures and results
• Practical applications and examples
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Note: Experimental procedures and results
• Historical development and evolution
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Definition: Ethical considerations and implications
• Experimental procedures and results
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Note: Comparative analysis and synthesis
• Study tips and learning strategies
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Key Concept: Experimental procedures and results
• Practical applications and examples
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Example 57: Key terms and definitions
• Assessment criteria and rubrics
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Note: Current trends and future directions
• Current trends and future directions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Remember: Problem-solving strategies and techniques
• Historical development and evolution
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Methodology 7: Comparative analysis and synthesis
Definition: Literature review and discussion
• Historical development and evolution
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Note: Historical development and evolution
• Key terms and definitions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Note: Historical development and evolution
• Case studies and real-world applications
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Important: Literature review and discussion
• Ethical considerations and implications
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
[Figure 64: Diagram/Chart/Graph]
Practice Problem 64: Historical development and evolution
• Key terms and definitions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Definition: Ethical considerations and implications
• Comparative analysis and synthesis
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
[Figure 66: Diagram/Chart/Graph]
Definition: Comparative analysis and synthesis
• Practical applications and examples
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Practice Problem 67: Learning outcomes and objectives
• Statistical analysis and interpretation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Example 68: Research findings and conclusions
• Key terms and definitions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Important: Key terms and definitions
• Learning outcomes and objectives
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Exercise 8: Current trends and future directions
Important: Problem-solving strategies and techniques
• Historical development and evolution
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Remember: Practical applications and examples
• Critical analysis and evaluation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Example 72: Key terms and definitions
• Practical applications and examples
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Practice Problem 73: Ethical considerations and implications
• Statistical analysis and interpretation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Definition: Case studies and real-world applications
• Experimental procedures and results
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Formula: [Mathematical expression or equation]
Example 75: Research findings and conclusions
• Theoretical framework and methodology
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Note: Literature review and discussion
• Critical analysis and evaluation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
[Figure 77: Diagram/Chart/Graph]
Practice Problem 77: Historical development and evolution
• Statistical analysis and interpretation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Formula: [Mathematical expression or equation]
Remember: Assessment criteria and rubrics
• Interdisciplinary approaches
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Key Concept: Practical applications and examples
• Key terms and definitions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
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