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Maurizio Petrelli

Introduction
to Python
in Earth Science
Data Analysis
From Descriptive Statistics
to Machine Learning
Springer Textbooks in Earth Sciences,
Geography and Environment
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Maurizio Petrelli

Introduction to Python
in Earth Science Data
Analysis
From Descriptive Statistics to Machine
Learning
Maurizio Petrelli
Department of Physics and Geology
University of Perugia
Perugia, Italy

ISSN 2510-1307 ISSN 2510-1315 (electronic)

Springer Textbooks in Earth Sciences, Geography and Environment
ISBN 978-3-030-78054-8 ISBN 978-3-030-78055-5 (eBook)
https://doi.org/10.1007/978-3-030-78055-5

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To my daughters Agata, Anna, and Caterina,
my wife Arianna, and Atomo who completes
the family
Preface

The idea of writing this book came to me in 2015 when I started teaching a course
entitled “Data Analysis and Interpretation in Earth Science” at the Department of
Physics and Geology of Perugia University. From the beginning of the course, I
realized that many of my students were strongly interested in data managing, visu-
alizing, and modeling in Python. I also realized that no reference book was avail-
able for teaching Python to geologists. Although numerous books present Python
to programmers at all levels, from beginners to experts, they mostly focus solely on
programming techniques, without discussing real applications, especially in geology.
In other words, a book devoted to Earth Scientists was missing. The project grew
and became structured while teaching the basics of Python to Earth Scientists at
the Eötvös University Budapest (Hungary) and at Leibniz Universität of Hannover
(Germany) in December 2018 and February 2020, respectively. Sadly, by the begin-
ning of March 2020, the COVID-19 pandemic had dramatically spread to all regions
of Italy and, on March 4th, the Italian government shut down all schools and univer-
sities nationwide, forcing me to stay at home like most Italians. In one of the most
confusing and insecure moments of my life, I decided to start writing this book.
“Introduction to Python in Earth Science Data Analysis” is devoted to Earth Scien-
tists, at any level, from students to academics and professionals, who would like to
harness the power of Python to visualize, analyze, and model geological data. No
experience in programming is required to use this book. If you are working in the
Earth Sciences, are a novice programmer, and would like to exploit the power of
Python in your projects, this is the right place for you.

Assisi, Italy Maurizio Petrelli

March 2021

vii
Acknowledgments

I would like to acknowledge all the people who encouraged me when I started
planning this project and all those who supported me during the writing. The first
one is Diego Perugini, who allowed me to re-enter academia in 2014 through the
Chronos project after a hiatus of three years. I also thank the Erasmus Plus (E+)
program that supported my foreign teaching excursions in Hungary and Germany,
including Roberto Rettori and Sabrina Nazzareni, who oversaw the E+ program for
my department, and the local E+ officers at the University of Perugia (Sonia Trinari
and Francesca Buco) and at the Tiber Umbria Comett Education Programme (Maria
Grazia Valocchia). Professor Francois Holtz (Leibniz Universität Hannover) and
Professor Szabolcs Harangi (Eötvös University Budapest) are also kindly acknowl-
edged for allowing me to run the “Python in Earth Sciences” courses at their insti-
tutions. The Department of Physics and Geology at University of Perugia, who
supported this book through the Engage FRB2019 project, also has my gratitude. I
also give my heartfelt thanks to my family, who put up with me as I wrote this book.
Finally, I sincerely thank Aviva Loew (Academic Language Experts), Giuseppe la
Spina, Eleonora Carocci, and Diego González-García for their critical suggestions,
which have largely improved this book.
Just before I starting writing these acknowledgments, I received a message on
my smartphone stating that I had an appointment for a COVID-19 vaccination the
following day (March 3, 2021), exactly a year to the day after the initial lockdown in
Italy. I interpreted this notification as a message of belief. I hope that the worldwide
vaccination campaigns that have been launched will signal the beginning of a new era
of beloved “normality” in our lives and that the time for resilience against COVID-19
is coming to an end. Now should be a time of empathy, cooperation, and rebirth.

ix
Overview

Let me Introduce Myself

Hi and welcome. My name is Maurizio Petrelli and I currently work at the Depart-
ment of Physics and Geology, University of Perugia (UniPg). My research focuses
on the petrological characterization of volcanoes with an emphasis on the dynamics
and timescales of pre-eruptive events. For this work, I combine classical and uncon-
ventional techniques. Since 2002, I’ve worked intensely in the laboratory, mainly
focusing on the development UniPg’s facility for Laser Ablation Inductively Coupled
Plasma Mass Spectrometry (LA-ICP-MS). In February 2006, I obtained my Ph.D.
degree with a thesis entitled “Nonlinear Dynamics in Magma Interaction Processes
and their Implications on Magma Hybridization.” Currently, I am developing a new
line of research at UniPg, Department of Physics and Geology, for applying Machine
Learning techniques in Geology. Finally, I also manage the LA-ICP-MS laboratory
at UniPg.

Organization of Book

The book is organized into five parts plus three appendixes. The Part I, entitled
“Python for Geologists: A Kickoff,” focuses on the very basics of Python program-
ming, from setting up an environment for scientific computing to solving your first
geology problems using Python. The Part II is entitled “Describing Geological Data”
and explains how to start visualizing (i.e., making plots) and generating descriptive
statistics, both univariate and bivariate. The Part III, entitled “Integrals and Differ-
ential Equations in Geology,” discusses integrals and differential equations while
highlighting various applications in geology. The Part IV deals with “Probability
Density Functions and Error Analysis” applied to the evaluation and modeling of
Earth Science data. Finally, the Part V, entitled “Robust Statistics and Machine Learn-
ing” analyzes data sets that depart from normality (statistically speaking) and the
application of machine learning techniques to data modeling in the Earth Sciences.

xi
xii Overview

Styling Conventions

I use conventions throughout this book to identify different types of information. For
example, Python statements, commands, and variables used within the main body of
the text are set in italics.
Consider the following quoted text as an example “There are many options to
create multiple subplots in matplotlib. In my opinion, the easiest approach is to
create an empty figure [i.e., fig = plt.figure(), then add multiple axes (i.e., subplots)
by using the method fig.add_subplot(nrows, ncols, index)]. The parameters nrows,
ncols, and index indicate the numbers of rows and columns (ncols) and the positional
index. In detail, index starts at 1 in the upper-left corner and increases to the right.
To better understand, consider the code listing 4.4.”
A block of Python code is highlighted as follows:

Listing 1 Example of code listing in Python

Shared Codes

All code presented in this book is tested on the Anaconda Individual Edition ver.
2021.5 (Python 3.8.8) and is available at my GitHub repository ( Petrelli-m):
http://bit.ly/python_earth_science

Involvement and Collaborations

I am always open to new collaborations worldwide. Feel free to contact me by mail

to discuss new ideas or propose a collaboration. You can also reach me through
my personal website or by Twitter. I love sharing the content of this book in short
courses everywhere. If you are interested, please contact me to organize a visit to
your institution.
Personal contacts:
[email protected]
@mauripetre
https://www.mauriziopetrelli.info
Contents

Part I Python for Geologists: A Kickoff

1 Setting Up Your Python Environment, Easily . . . . . . . . . . . . . . . . . . . . 3
1.1 The Python Programming Language . . . . . . . . . . . . . . . . . . . . . . . . 3
1.2 Programming Paradigms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.3 A Local Python Environment for Scientific Computing . . . . . . . . 5
1.4 Remote Python Environments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.5 Python Packages for Scientific Applications . . . . . . . . . . . . . . . . . . 8
1.6 Python Packages Specifically Developed for Geologists . . . . . . . . 9
2 Python Essentials for a Geologist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.1 Start Working with IPython Console . . . . . . . . . . . . . . . . . . . . . . . . 11
2.2 Naming and Style Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.3 Working with Python Scripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
2.4 Conditional Statements, Indentation, Loops, and Functions . . . . . 17
2.5 Importing External Libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
2.6 Basic Operations and Mathematical Functions . . . . . . . . . . . . . . . . 21
3 Solving Geology Problems Using Python: An Introduction . . . . . . . . 25
3.1 My First Binary Diagram Using Python . . . . . . . . . . . . . . . . . . . . . 25
3.2 Making Our First Models in Earth Science . . . . . . . . . . . . . . . . . . . 32
3.3 Quick Intro to Spatial Data Representation . . . . . . . . . . . . . . . . . . . 36

Part II Describing Geological Data

4 Graphical Visualization of a Geological Data Set . . . . . . . . . . . . . . . . . 43
4.1 Statistical Description of a Data Set: Key Concepts . . . . . . . . . . . . 43
4.2 Visualizing Univariate Sample Distributions . . . . . . . . . . . . . . . . . . 44
4.3 Preparing Publication-Ready Binary Diagrams . . . . . . . . . . . . . . . 47
4.4 Visualization of Multivariate Data: A First Attempt . . . . . . . . . . . 66
5 Descriptive Statistics 1: Univariate Analysis . . . . . . . . . . . . . . . . . . . . . 67
5.1 Basics of Descriptive Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
5.2 Location . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

xiii
xiv Contents

5.3 Dispersion or Scale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72

5.4 Skewness . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
5.5 Descriptive Statistics in Pandas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
5.6 Box Plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
6 Descriptive Statistics 2: Bivariate Analysis . . . . . . . . . . . . . . . . . . . . . . . 83
6.1 Covariance and Correlation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
6.2 Simple Linear Regression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
6.3 Polynomial Regression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
6.4 Nonlinear Regression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

Part III Integrals and Differential Equations in Geology

7 Numerical Integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
7.1 Definite Integrals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
7.2 Basic Properties of Integrals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
7.3 Analytical and Numerical Solutions of Definite Integrals . . . . . . . 101
7.4 Fundamental Theorem of Calculus and Analytical Solutions . . . . 101
7.5 Numerical Solutions of Definite Integrals . . . . . . . . . . . . . . . . . . . . 103
7.6 Computing the Volume of Geological Structures . . . . . . . . . . . . . . 109
7.7 Computing the Lithostatic Pressure . . . . . . . . . . . . . . . . . . . . . . . . . 110
8 Differential Equations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
8.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
8.2 Ordinary Differential Equations . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
8.3 Numerical Solutions of First-Order Ordinary Differential
Equations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
8.4 Fick’s Law of Diffusion—A Widely Used Partial
Differential Equation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126

Part IV Probability Density Functions and Error Analysis

9 Probability Density Functions and Their Use in Geology . . . . . . . . . . 137
9.1 Probability Distribution and Density Functions . . . . . . . . . . . . . . . 137
9.2 The Normal Distribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
9.3 The Log-Normal Distribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
9.4 Other Useful PDFs for Geological Applications . . . . . . . . . . . . . . . 144
9.5 Density Estimation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
9.6 The Central Limit Theorem and Normal Distributed Means . . . . 152
10 Error Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
10.1 Dealing with Errors in Geological Measurements . . . . . . . . . . . . . 155
10.2 Reporting Uncertainties in Binary Diagrams . . . . . . . . . . . . . . . . . 162
10.3 Linearized Approach to Error Propagation . . . . . . . . . . . . . . . . . . . 168
10.4 The Mote Carlo Approach to Error Propagation . . . . . . . . . . . . . . . 172
Contents xv

Part V Robust Statistics and Machine Learning

11 Introduction to Robust Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
11.1 Classical and Robust Approaches to Statistics . . . . . . . . . . . . . . . . 181
11.2 Normality Tests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
11.3 Robust Estimators for Location and Scale . . . . . . . . . . . . . . . . . . . . 186
11.4 Robust Statistics in Geochemistry . . . . . . . . . . . . . . . . . . . . . . . . . . 192
12 Machine Learning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
12.1 Introduction to Machine Learning in Geology . . . . . . . . . . . . . . . . 195
12.2 Machine Learning in Python . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
12.3 A Case Study of Machine Learning in Geology . . . . . . . . . . . . . . . 197

Appendix A: Python Packages and Resources for Geologists . . . . . . . . . . . 209

Appendix B: Introduction to Object Oriented Programming . . . . . . . . . . 211
Appendix C: The Matplotlib Object Oriented API . . . . . . . . . . . . . . . . . . . . 215
Appendix D: Working with Pandas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219
Further Readings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223
 Part I
Python for Geologists: A Kickoff
Chapter 1
Setting Up Your Python Environment,
Easily

1.1 The Python Programming Language

Python is a high-level, modular, interpreted programming language.1 What does this

mean? A high-level programming language is characterized by a strong abstraction
that cloaks the details of the computer so that the code is easy to understand for
humans. Python is modular, which means that it supports modules and packages that
allow program flexibility and code reuse. In detail, Python is composed of a “core”
that deals with all basic operations plus a wide ecosystem of specialized packages
to perform specific tasks. To be clear, a Python package or library is a reusable
portion of code, which is a collection of functions and modules (i.e., a group of
functions) allowing the user to complete specialized tasks such as reading an excel
file or drawing a publication-ready diagram.
Python is an interpreted language (like MATLAB, Mathematica, Maple, and R).
Conversely, C or FORTRAN are compiled languages. What is the difference between
compiled and interpreted languages? Roughly speaking, with compiled languages, a
translator compiles each code listing in an executable file. Once compiled, any target
machine can directly run the executable file. Interpreted languages compile code in
real time during each execution. The main difference for a novice programmer is that
interpreted code typically runs slower than compiled executable code. However, per-
formance is not an issue in most everyday operations. Performance starts becoming
significant in computing-intensive tasks such as complex fluid dynamic simulations
or three-dimensional (3D) graphical applications. If needed, the performance of
Python can be significantly improved with the support of specific packages such as
Numba, which can compile Python code. In this case, Python code approaches the
speed of C and FORTRAN.
Being an interpreted language, Python facilitates code exchange over different
platforms (i.e., cross-platform code exchange), fast prototyping, and great flexibility.

1 https://www.python.org.
© The Author(s), under exclusive license to Springer Nature Switzerland AG 2021 3
M. Petrelli, Introduction to Python in Earth Science Data Analysis,
Springer Textbooks in Earth Sciences, Geography and Environment,
https://doi.org/10.1007/978-3-030-78055-5_1
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