MATLAB® and Design Recipes for Earth Sciences

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The overall aim of the book is to introduce students to the typical course followed by a data analysis project in earth sciences. A project usually involves searching relevant literature, reviewing and ranking published books and journal articles, extracting relevant information from the literature
Martin h. Trauth. Elisabeth sillmann MATLAB and design Recipes for earth Sciences How to collect. Process and present Geoscientific Information Springer Martin h. trauth Elisabeth sillmann Inst fur erd- und umweltwissenschaften BlaetterwaldDesign Universitat potsdam Potsdam German Germany Additionalmaterialtothisbookcanbedownloadedfromhttp:/extras.springer.com ISBN978-3-642-32543-4 ISBN978-3-642-32544-1( eBook) DOI10.1007/978-3-642-32544-1 Springer Heidelberg New York Dordrecht London Library of Congress Control Number: 2012945735 g idelberg 2013 This work is subject to copyright. All rights are reserved 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 mission o information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar nethodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publishers location, in its current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through rightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law 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 While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein Printed on acid-free paper SpringerispartofSpringerScience+businessMedia(www.springer.com) Preface The book matlab and Design Recipes for Earth Sciences is designed to help undergraduate and postgraduate students, doctoral students, post-doc toral researchers, and professionals find quick solutions for common prob lems when starting out on a new research project. A project usually starts with searching and reviewing the relevant literature and data, and then ex tracting relevant information as text data or graphs from the literature fol- lowed by searching, processing and visualizing the data, and finally, compi ing and presenting the results as posters, abstracts and talks at conferences The course on which this book is based was first taught by M.H.T.as a bachelor's module for second-year students during the 2010/ll winter se mester,three years after the introduction of bachelor's and master's pro grams at the University of Potsdam. The initial design of the bachelor's program included an introductory course on data analysis, scheduled for the second year, which was based on the sister book to this one: MATLAB Recipes for earth Sciences-3rd Edition(Trauth 2010). This course was a complete failure, probably because the second-year bachelor students were not well enough prepared for an advanced course on data analysis, even after two semesters of mathematics during the first year. A few weeks later, the course for students at masters and doctoral levels on the same topic which M.H.T. was invited to give at the university of ghent in belgium was a great success. The difference between the undergraduate students in Potsdam and the graduate students in Belgium was, of course, the greater motivation that students already working on their own projects had to learn the statistical and numerical methods offered by MatlaB, in order to be able to analyze their data As a consequence, M.H.T. moved the course into the masters program and designed a completely new course on how to Collect, Process and Present Geoscientific Information, which was very well received by the second-year students, despite the very large number of participants. The course was not presented as a complete package, but evolved during the months of teaching, taking into consideration the suggestions made by stu dents attending the course during the course and very much motivated by PREFACE its success, the idea for this new book quickly emerged and the first outline for the text was drafted in late December 2010. Most of the text was written immediately following completion of the first course and before the start of the second course in spring 2011. Fortunately, the graphic design specialist E.S., who is the owner of blaetterwaldDesign, joined the project to con- tribute to the design sections in the book as well as the books layout, after having designed the layout of all three editions of the sister book, as well as many other books, for Springer. The publisher quickly agreed to assist in realizing the book and contracts were signed in summer 2011 While undergraduates participating in a course on data analysis might wish to work their way through the entire book, more experienced readers might refer to only one particular method in the book, in order to solve a specific problem. The concept of the book and its contents are therefore out lined below in order to make it easier for readers with a variety of different requirements to decide how they wish to approach the book Chapter 1-This chapter is about initiating, planning and organizing a project. It introduces the Internet resources used in the following chap ters to search for geoscientific information, as well as the software and online tools used to manage projects to process data to exchange infor- mation, and to present project results Chapters 2 and 3- These chapters deal with searching and reviewing scientific literature and data on the Internet. Chapter 2 provides a com prehensive tutorial-style introduction to Internet literature resources.It also demonstrates how to extract information from the literature for use within the readers own projects, and introduces software for managing large collections of electronic journal articles and books. Chapter 3 in- troduces the most popular data formats on the internet, and methods to store and transfer such data. Data access and management is demon strated by means of typical examples Chapters 4 to 7-The first of these chapters starts with a tutorial-style in troduction to MAtLAB, designed for earth scientists(as in Chapter 2 of the sister book). Chapters 5 and 6 introduce advanced visualization tech niques with MATLAB, for example, how to create sophisticated two-and three-dimensional graphs from data collected in Chapter 3. Chapter 7 is on processing and displaying images with MATLAB, including satellite images(as in Chapter 8 of the sister book) PREFACE Chapter 8- The graphs created with MATLAB in the previous chap ters are now handed over to the graphic design unit of the project. Even though the advanced plotting features of matlab presented in chapters 5 and 6 are able to create sophisticated figures, all graphs will require fur ther editing with vector and image processing software before they can be included, together with text and tables, in conference presentations and manuscripts Chapters 9 to 11-These chapters are about creating conference presen tations such as talks and posters, and various types of manuscripts for publication. They cover the preparation of colorful flyers and brochures relating to projects, as well as theses or project reports with relatively modest designs, and also deal with assembling books and their layout design. Both Chapters 9 and 10 close with some remarks on practicing for conference presentations, and their final delivery The book contains MATLAB scripts, or M-files for visualizing typical earth sciencedatasets(http://mathworks.com).TheMatlabcodescanbeeasily adapted to the reader's data and projects. M. H.T. developed these recipes us- ing MatlaB Version 7(R2011b), but most of them will also work with ear- lier software releases. Furthermore, the book relies on numerous other soft wareproductsfirstandforemosttheadobeCreativeSuite(http:adobe com), which is used to edit all the graphs created with MATLAB. Although most examples are also explained with open-source alternatives, the use of the adobe Creative Suite produces consistently high quality results for all g raphics to be included in project presentations. The book provides brief introductions to the use of these graphics editors by means of step-by-step tutorials, supplemented by screenshots documenting the workflows that are provided as supplementary electronic material to this book. We are plan ning to make all vector materials available online as soon as an appropriate digital rights management is provided by the publisher We hope that our readers will appreciate our efforts to introduce open source software tools in addition to the commercial products that the au thors of this book use during their daily work. during the course at the University of Potsdam, students asked about free alternatives to MAtLaB such as Python, R and Octave. Some students also liked to use laTeX for typesetting, and GMT for creating xy and xyz plots. Students' financial re sources are often limited and many therefore use open-source software on their computers. For professionals, however, time is by far the more im- portant limiting factor. When trying to meet a strict deadline for the sub- VIll PREFACE mission of a research proposal or report, one quickly learns to appreciate complete and concise software manuals and the short response time of the software vendor's support line In putting together this book we have benefited from the comments offered by many people, in particular Nina Bosche, Verena Forster, Oliver Korup, Oliver Oswald, and Marius Walter. It is expected that this book will be constantly changing and evolving over time, as has been the case through the various editions of its sister book. Please send us your com ments and criticisms on the text, suggestions for correction and expansion of the text, and comments on any experiences that you may have had with Similar courses or books PleasevisitthewebpagesofM.h.t.(hTtp://www.geo.uni-potsdam.de/ palaeoklimadynamik. html)and E.s.(Http: //blaetterwald-design. de)from time to time, in order to check for updates and errata files for this book Te are much obliged to Ed Manning for professional proofreading of the text We would like to thank christian witschel. Chris bendall and their team at springer, and also andreas bohlen, brunhilde schulz and their team at UP Transfer gmbh for their support. M. H.T. acknowledges the book program and the Academic Support at The MathWorks Inc,as well as claudia olrogge, Kremen Radeva, and annegret Schumann at The MathWorks gmbh Deutschland. E.S. thanks adobe Systems Inc for their support and the permission to include screenshots of Adobe software in the book. M.H.T. would also like to thank Nasa/ gsfC metiersdacl JAROS and the U.S. / Japan Aster Science Team, and their team leader Mike abrams, for permission to include their aster images in the book Potsdam/Landau, June 2012 Martin trauth Elisabeth sillmann Earth Scientist, University of Potsdam Designer(AgD), blaetterwaldDesign de apl. Prof Dr Martin H. Trauth Dipl-Ing (FH)Elisabeth Sillmann Institute of earth and Environmental science blaetterwaldDesign University of potsdam Biro fur Medien und Gestaltung Karl-Liebknecht-Strasse 24-25 Emich-von-Leiningen-Strasse 38 D-14476 Potsdam D-76829 Landau in der pfalz Germany ermany Contents Preface 1 Scientific Information in earth sciences 1.1 Introduction 1.2 Collecting and Managing Information in Earth Sciences 1.3 Methods for Processing Scientific Information 1.4 Presenting Geoscientific Information 16 Recommended Reading 18 2 Searching and Reviewing Scientific Literature 19 21 Introduction 19 2.2 Resources for literature reviews 19 2.3 Finding the Relevant Literature 21 2.4 Extracting the relevant Information from Literature 2.5 Extracting Text, Data and Graphs from Literature 2.6 Organizing Literature in a Computer 46 Recommended reading 50 3 Internet resources for earth science data 51 3.1 Introduction 51 3.2 Data Storage in a Computer 51 3.3 Data Formats in earth sciences 53 3.4 Data Transfer between Computers 56 3.5 Internet Resources: When was the Younger di 60 3.6 Internet Resources: Calibrating Radiocarbon Ages 3.7 Internet resources: Insolation data 66 3.8 Internet Resources: Tephrabase 71 3.9 Organizing Data in a Computer 72 Recommended Reading 74 4 MATLAB as a visualization too 4.1 Introduction 4.2 Getting started with MATLAB 78 X CONTENTS 4.3 The Syntax of MAtlab 4.4 Data Storage and Handling 84 4.5 Data Structures and classes of objects 86 4.6 Scripts and Functions 91 4.7 Basic Visualization tools 95 4.8 Generating M-Files to Regenerate Graphs 98 4.9 Publishing M-Files 100 Recommended reading 102 5 Visualizing 2D Data in Earth Sciences 103 5.1 Introduction 103 5.2 Line Graphs: Plotting Time Series in Earth Sciences 5.3 Bar Graphs Plotting Histograms in Earth Sciences 108 5.4 Pie Charts: Illustrating proportion in earth Sciences 111 5.5 Rose Diagrams Plotting Directional Data 113 5.6 plots Plotting Scaled Multiple Area Graphs 5.7 Stratplots: Plotting Stratigraphic Columns 118 6 Visualizing 3D Data in Earth Sciences 125 6.1 Introduction 125 6.2 The gshhs shoreline data set .126 6.3 The 2-Minute gridded global relief data etopo2 129 6.4 The global 30-Arc Second elevation data gtoPo30 136 6.5 The Shuttle radar topography mission SRtm 38 6.6 Interpolating and visualizing Irregularly-Spaced Data 143 Recommended reading 148 7 Processing and Displaying Images in Earth Sciences 149 7.1 Introduction 149 7.2 Storing Images on a Computer 149 7.3 Importing, Processing and Exporting Images 153 7.4 Processing and Printing Satellite Images 157 7.5 Georeferencing satellite Images 158 7.6 Digitizing from the Screen From Pixel to Vector 162 Recommended Reading 164 8 Editing Graphics, Text, and Tables 165 8.1 Introduction 165 8.2 Editing Vector Graphics 166 8.3 Processing Images 187 8.4 Editing text 194 8.5 Editing tables 198

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