Effective Computation in Physics (Python).pdf PDF

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SCIENCEPROGRAMMING

Effective Computation in Physics

ISBN: 978-1-491-90153-3

US $49.99

CAN $57.99

" - Fernando Perez

Staff Scientist,

Lawrence Berkeley National Laboratory

Twitter: @oreillymedia

facebook.com/oreilly More physicists today are taking on the role of software developer as part of their research, but software development isn"t always easy or obvious, even for physicists. This practical book teaches essential software development skills to help you automate and accomplish nearly any aspect of research in a physics-based field. Written by two PhDs in nuclear engineering, this book includes practical

examples drawn from a working knowledge of physics concepts. You"ll learn how to use the Python programming language to perform everything

from collecting and analyzing data to building software and publishing your results.

In four parts, this book includes:

Getting Started: Jump into Python, the command line, data containers, functions, flow control and logic, and classes and objects Getting It Done: Learn about regular expressions, analysis and visualization, NumPy, storing data in files and HDF5, important data structures in physics, computing in parallel, and deploying software Getting It Right: Build pipelines and software, learn to use local and remote version control, and debug and test your code Getting It Out There: Document your code, process and publish your ndings, and collaborate eciently; dive into software licenses, ownership, and copyright procedures Kathryn Huff is a fellow with the Berkeley Institute for Data Science and a postdoctoral scholar with the Nuclear Science and Security Consortium at the University of California Berkeley. She received her Ph.D. in Nuclear Engineering from the University of Wisconsin-Madison. Anthony Scopatz, a computational physicist and longtime Python developer, holds a Ph.D. in Mechanical/Nuclear Engineering from the University of Texas at Austin. In August 2015, he'll start as a professor in Mechanical Engineering at the

University of South Carolina.

Anthony Scopatz &

Kathryn D. Hu

Effective

FIELD GUIDE TO RESEARCH

WITH PYTHONEffective Computation

Scopatz & Hu

SCIENCEPROGRAMMING

Effective Computation in Physics

ISBN: 978-1-491-90153-3

US $49.99

CAN $57.99

" - Fernando Perez

Staff Scientist,

Lawrence Berkeley National Laboratory

Twitter: @oreillymedia

examples drawn from a working knowledge of physics concepts. You"ll learn how to use the Python programming language to perform everything

from collecting and analyzing data to building software and publishing your results.

In four parts, this book includes:

University of South Carolina.

Anthony Scopatz &

Kathryn D. Hu

Effective

FIELD GUIDE TO RESEARCH

WITH PYTHONEffective Computation

Scopatz & Hu

Anthony Scopatz and Kathryn D. Hufff

Boston

Efffective Computation in Physics

978-1-491-90153-3

Printed in the United States of America.

Published by O'Reilly Media, Inc., 1005 Gravenstein Highway North, Sebastopol, CA 95472.

O'Reilly books may be purchased for educational, business, or sales promotional use. Online editions are

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institutional sales department: 800-998-9938 or corporate@oreilly.com.Editor: Meghan Blanchette

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Illustrator: Rebecca DemarestJune 2015:

First Edition

Revision History for the First Edition

2015-06-09: First Release

See http://oreilly.com/catalog/errata.csp?isbn=9781491901533 for release details. The O'Reilly logo is a registered trademark of O'Reilly Media, Inc.

Efffective Computation in Physics, the

cover image, and related trade dress are trademarks of O'Reilly Media, Inc. While the publisher and the authors have used good faith efforts to ensure that the information and

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thereof complies with such licenses and ghts. To THW and friends: gonuke, animal1, kmo, redbeard, spidr, slayer, nicopresto, wolfman, blackbeard, johnnyb, jdangerx, punkish, radio, crbates, 3rdbit, fastmath, and others, this one is for you.

Foreword. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

. . . . . xv

Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

. . . . . . xvii

Part I. Getting Started

Introduction to the Command Line. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Navigating the Shell 1

The Shell Is a Programming Language 2

Paths and pwd 3

Home Directory (~) 5

Listing the Contents (ls) 6

Changing Directories (cd) 7

File Inspection (head and tail) 10

Manipulating Files and Directories 11

Creating Files (nano, emacs, vi, cat, >, and touch) 11

Copying and Renaming Files (cp and mv) 17

Making Directories (mkdir) 18

Deleting Files and Directories (rm) 18

Flags and Wildcards 20

Getting Help 21

Reading the Manual (man) 21

Finding the Right Hammer (apropos) 24

Combining Utilities with Redirection and Pipes (>, >>, and |) 25

Permissions and Sharing 26

Seeing Permissions (ls -l) 26

Setting Ownership (chown) 28

Setting Permissions (chmod) 29

Creating Links (ln) 29

Connecting to Other Computers (ssh and scp) 30

The Environment 31

Saving Environment Variables (.bashrc) 33

Running Programs (PATH) 34

Nicknaming Commands (alias) 36

Scripting with Bash 36

Command Line Wrap-up 382.

Programming Blastofff with Python. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Running Python 40

Comments 41

Variables

Special Variables 44

Boolean Values 45

None Is Not Zero! 45

NotImplemented Is Not None! 45

Operators 46

Strings

String Indexing 50

String Concatenation 53

String Literals 54

String Methods 55

Modules

Importing Modules 58

Importing Variables from a Module 58

Aliasing Imports 59

Aliasing Variables on Import 59

Packages 60

The Standard Library and the Python Ecosystem 62

Python Wrap-up 63

Essential Containers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

Lists 66

Tuples

70
Sets 71

Dictionaries

Containers Wrap-up 75

Flow Control and Logic. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

Conditionals

77
vi | Table of C ontents

if-else Statements 80

if-elif-else Statements 81

if-else Expression 82

Exceptions

Raising Exceptions 84

Loops 85

while Loops 86

for Loops 88

Comprehensions 90

Flow Control and Logic Wrap-up 935.

Operating with Functions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95

Functions in Python 96

Keyword Arguments 99

Variable Number of Arguments 101

Multiple Return Values 103

Scope 104

Recursion

107

Lambdas

108

Generators 109

Decorators 112

Function Wrap-up 116

Classes and Objects. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117

Object Orientation 118

Objects

119

Classes

123

Class Variables 124

Instance Variables 126

Constructors 127

Methods 129

Static Methods 132

Duck Typing 133

Polymorphism 135

Decorators and Metaclasses 139

Object Orientation Wrap-up 141

Part II. Getting It Done

Analysis and Visualization. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145

Preparing Data 145

Table of Contents | vii

Experimental Data 149

Simulation Data 150

Metadata 151

Loading Data 151

NumPy 152

PyTables 153

Pandas 153

Blaze 155

Cleaning and Munging Data 155

Missing Data 158

Analysis

159

Model-Driven Analysis 160

Data-Driven Analysis 162

Visualization 162

Visualization Tools 164

Gnuplot 164

matplotlib 167

Bokeh 172

Inkscape 174

Analysis and Visualization Wrap-up 1758.

Regular Expressions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177

Messy Magnetism 178

Metacharacters on the Command Line 179

Listing Files with Simple Patterns 180

Globally Finding Filenames with Patterns (find) 182

grep, sed, and awk 187

Finding Patterns in Files (grep) 188

quotesdbs_dbs20.pdfusesText_26

[PDF] Effective Computation in Physics (Python).pdf

SCIENCEPROGRAMMING

Effective Computation in Physics

ISBN: 978-1-491-90153-3

US $49.99

CAN $57.99

Staff Scientist,

Lawrence Berkeley National Laboratory

Twitter: @oreillymedia

In four parts, this book includes:

University of South Carolina.

Anthony Scopatz &

Kathryn D. Hu

Effective

FIELD GUIDE TO RESEARCH

WITH PYTHONEffective Computation

Scopatz & Hu

SCIENCEPROGRAMMING

Effective Computation in Physics

ISBN: 978-1-491-90153-3

US $49.99

CAN $57.99

Staff Scientist,

Lawrence Berkeley National Laboratory

Twitter: @oreillymedia

In four parts, this book includes:

University of South Carolina.

Anthony Scopatz &

Kathryn D. Hu

Effective

FIELD GUIDE TO RESEARCH

WITH PYTHONEffective Computation

Scopatz & Hu

Anthony Scopatz and Kathryn D. Hufff

Boston

Efffective Computation in Physics

978-1-491-90153-3

Printed in the United States of America.

Production Editor: Nicole Shelby

Copyeditor: Rachel Head

Interior Designer: David Futato

Cover Designer: Ellie Volckhausen

Illustrator: Rebecca DemarestJune 2015:

First Edition

Revision History for the First Edition

2015-06-09: First Release

Efffective Computation in Physics, the

Table of Contents

Part I. Getting Started

Variables

Strings

Modules

Tuples

Dictionaries

Conditionals

Exceptions

Recursion

Lambdas

Objects

Classes

Part II. Getting It Done

Table of Contents | vii

Analysis