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 Earth Observation Using Python

0005078634.3D 1 12/7/2021 12:32:26 PM

 Special Publications 75

EARTH OBSERVATION
USING PYTHON
A Practical Programming Guide
Rebekah B. Esmaili

This Work is a co-publication of

the American Geophysical Union and John Wiley and Sons, Inc.

0005078634.3D 3 12/7/2021 12:32:26 PM

 This edition first published 2021
© 2021 American Geophysical Union

All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted,
in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as
permitted by law. Advice on how to obtain permission to reuse material from this title is available at
http://www.wiley.com/go/permissions.

Published under the aegis of the AGU Publications Committee

Brooks Hanson, Executive Vice President, Science
Carol Frost, Chair, Publications Committee
For details about the American Geophysical Union visit us at www.agu.org.

The right of Rebekah B. Esmaili to be identified as the author of this work has been asserted in accordance with law.

Registered Office
John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, USA

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For details of our global editorial offices, customer services, and more information about Wiley products visit us at
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other commercial damages, including but not limited to special, incidental, consequential, or other damages.

Library of Congress Cataloging-in-Publication Data

Name: Esmaili, Rebekah Bradley, author.
Title: Earth observation using Python : a practical programming guide /
Rebekah B. Esmaili.
Description: Hoboken, NJ : Wiley, [2021] | Includes bibliographical
references and index.
Identifiers: LCCN 2021001631 (print) | LCCN 2021001632 (ebook) | ISBN
9781119606888 (hardback) | ISBN 9781119606895 (adobe pdf) | ISBN
9781119606918 (epub)
Subjects: LCSH: Earth sciences–Data processing. | Remote sensing–Data
processing. | Python (Computer program language) | Information
visualization. | Artificial satellites in earth sciences. | Earth
sciences–Methodology.
Classification: LCC QE48.8 .E85 2021 (print) | LCC QE48.8 (ebook) | DDC
550.285/5133–dc23
LC record available at https://lccn.loc.gov/2021001631
LC ebook record available at https://lccn.loc.gov/2021001632

Cover Design: Wiley

Cover Image: © NASA

Set in 10/12pt Times New Roman by Straive, Pondicherry, India

10 9 8 7 6 5 4 3 2 1

0005078634.3D 4 12/7/2021 12:32:26 PM

 CONTENTS

Foreword ......................................................................................................... vii

Acknowledgments ............................................................................................ ix

Introduction ...................................................................................................... 1
Part I: Overview of Satellite Datasets ............................................................... 5
1 A Tour of Current Satellite Missions and Products .................................. 7
2 Overview of Python................................................................................ 17
3 A Deep Dive into Scientific Data Sets.................................................... 25

Part II: Practical Python Tutorials for Remote Sensing................................... 45

4 Practical Python Syntax .......................................................................... 47
5 Importing Standard Earth Science Datasets ........................................... 67
6 Plotting and Graphs for All.....................................................................95
7 Creating Effective and Functional Maps...............................................125
8 Gridding Operations.............................................................................155
9 Meaningful Visuals through Data Combination ................................... 177
10 Exporting with Ease ..............................................................................207

Part III: Effective Coding Practices ...............................................................219

11 Developing a Workflow .......................................................................221
12 Reproducible and Shareable Science ...................................................239

Conclusion..................................................................................................... 253

Appendix A: Installing Python.......................................................................255

Appendix B: Jupyter Notebook .....................................................................259
Appendix C: Additional Learning Resources.................................................267
Appendix D: Tools......................................................................................... 269
Appendix E: Finding, Accessing, and Downloading Satellite Datasets .........271
Appendix F: Acronyms ..................................................................................279

Index.............................................................................................................. 283

0005078635.3D 5 12/7/2021 12:35:39 PM

 FOREWORD

When I first met the author a few years ago, she was eager to become more
involved in the Joint Polar Satellite System’s Proving Ground. The Proving
Ground by definition assesses the impact of a product in the user’s environment;
this intrigued Rebekah because as a product developer, she wanted to understand
the user’s perspective. Rebekah worked with the National Weather Service to
demonstrate how satellite-derived atmospheric temperature and water vapor
soundings can be used to describe the atmosphere’s instability to support severe
weather warnings. Rebekah spent considerable time with users at the Storm Pre-
diction Center in Norman, Oklahoma, to understand their needs, and she found
their thirst for data and the need for data to be easily visualized and understand-
able. This is where Rebekah leveraged her expert skills in Python to provide NWS
with the information they found to be most useful. Little did I know at the time she
was writing a book.
As noted in this book, a myriad of Earth-observing satellites collect critical
information of the Earth’s complex and ever-changing environment and land-
scape. However, today, unfortunately, all that information is not effectively being
used for various reasons: issues with data access, different data formats, and the
need for better tools for data fusion and visualization. If we were able to solve these
problems, then suddenly there would be vast improvements in providing societies
with the information needed to support decisions related to weather and climate
and their impacts, including high-impact weather events, droughts, flooding, wild-
fires, ocean/coastal ecosystems, air quality, and more. Python is becoming the uni-
versal language to bridge these various data sources and translate them into useful
information. Open and free attributes, and the data and code sharing mindset of
the Python communities, make Python very appealing.
Being involved in a number of international collaborations to improve the
integration of Earth observations, I can certainly emphasize the importance
of working together, data sharing, and demonstrating the value of data
fusion. I am very honored to write this Foreword, since this book focuses on these

vii

0005078636.3D 7 14/6/2021 5:41:00 PM

 viii Foreword

issues and provides an excellent guide with relevant examples for the reader to
follow and relate to.

Dr. Mitch Goldberg

Chief Program Scientist
NOAA-National Environmental Satellite, Data,
and Information Service
June 22, 2020

0005078636.3D 8 14/6/2021 5:41:00 PM

 ACKNOWLEDGMENTS

This book evolved from a series of Python workshops that I developed with
the help of Eviatar Bach and Kriti Bhargava from the Department of Atmospheric
and Oceanic Science at the University of Maryland. I am very grateful for their
assistance providing feedback for the examples in this book and for leading several
of these workshops with me.
This book would not exist without their support and contributions from
others, including:
The many reviewers who took the time to read versions of this book, several of
whom I have never met in person. Thanks to modern communication systems,
I was able to draw from their expertise. Their constructive feedback and insights
not only helped to improve this quality and breadth of the book but also helped me
hone my technical writing skills.
Rituparna Bose, Jenny Lunn, Layla Harden, and the rest of the team at AGU
and Wiley for keeping me informed, organized, and on track throughout this
process. They were truly a pleasure to work with.
Nadia Smith and Chris Barnet, and my other colleagues at Science and Tech-
nology Corp., who provided both feedback and conversations that helped shape
some of the ideas and content in this book.
Catherine Thomas, Clare Flynn, Erin Lynch, and Amy Ho for their endless
encouragement and support.
Tracie and Farid Esmaili, my parents, who encouraged me to aim high even if
they were initially confused when their atmospheric scientist daughter became
interested in “snakes.”

ix

0005078636.3D 9 14/6/2021 5:41:00 PM

 INTRODUCTION

Python is a programming language that is rapidly growing in popularity. The

number of users is large, although difficult to quantify; in fact, Python is currently
the most tagged language on stackoverflow.com, a coding Q&A website with
approximately 3 million questions a year. Some view this interest as hype, but
there are many reasons to join the movement. Scientists are embracing Python
because it is free, open source, easy to learn, and has thousands of add-on
packages. Many routine tasks in the Earth sciences have already been coded
and stored in off-the-shelf Python libraries. Users can download these libraries
and apply them to their research rather than simply using older, more primitive
functions. The widespread adoption of Python means scientists are moving toward
a common programming language and set of tools that will improve code share-
ability and research reproducibility.
Among the wealth of remote sensing data available, satellite datasets are par-
ticularly voluminous and tend to be stored in a variety of binary formats. Some
datasets conform to a “standard” structure, such as netCDF4. However, because
of uncoordinated efforts across different agencies and countries, such standard
formats bear their own inconsistencies in how data are handled and intended to
be displayed. To address this, many agencies and companies have developed
numerous “quick look” methods. For instance, data can be searched for and
viewed online as Jpeg images, or individual files can be displayed with free,
open-source software tools like Panoply (www.giss.nasa.gov/tools/panoply/)
and HDFView (www.hdfgroup.org/downloads/hdfview/).
Still, scientists who wish to execute more sophisticated visualization techni-
ques will have to learn to code. Coding knowledge is not the only limitation for
users. Not all data are “analysis ready,” i.e., in the proper input format for visu-
alization tools. As such, many pre-processing steps are required to make the data
usable for scientific analysis. This is particularly evident for data fusion, where two
datasets with different resolutions must first be mapped to the same grid before
they are compared. Many data users are not satellite scientists or professional

Earth Observation Using Python: A Practical Programming Guide, Special Publications 75,
First Edition. Rebekah B. Esmaili.
© 2021 American Geophysical Union. Published 2021 by John Wiley & Sons, Inc.
DOI: 10.1002/9781119606925.introduction

cintro.3d 1 13/7/2021 9:13:41 AM

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