Performing Science with Open Source Software: Utilizing Python(xy)

Welcome to Python in Science! A few short stories will introduce you to some very versatile tools, which might well support you in daily life as an engineer or scientist: visualization, image processing, statistics, differential equations, optimization, symbolic algebra, etc.. Emphasis is put on realistic applications, not so much on language skills. Nevertheless, you will learn some basic Python on the fly. The book intends to help you to master the first hurdles. Once, your appetite is whetted, you'll become addicted, I'm sure! Chapter 1 To whom it may concern 1.1 Who are you? 1.2 Who am I? 1.3 Then, why Python? 1.4 "Should I learn Python before I start with this book?" 1.5 Why Python(x,y)? 1.6 Why Open Source Software? 1.7 Where to find what? 1.8 Load down! 1.9 Alternative: Anaconda Chapter 2 Brave New World 2.1 The launcher 2.2 Route A: for Python beginners 2.3 If you can't wait: Python's basic Basics 2.4 Strings 2.5 Integer and floating point numbers 2.6 Simple Operations 2.7 Sequences 2.8 Do not get surprised! 2.9 Route B: for Python(x,y) starters 2.10 Cheat sheets Chapter 3 All strings in your hand! 3.1 Your IDE 3.2 Spyder 3.3 The 'Editor' 3.4 Editor vs. Interpreter 3.5 Do it yourself Chapter 4 Paint it black! 4.1 Aim: a publishable figure 4.2 Jump into cold water ... and ask for help! 4.3 Getting confused 4.4 Getting serious 4.5 My trick 4.6 Continuing getting serious 4.7 Not yet perfect 4.8 Finally perfect! 4.9 Do it yourself! Chapter 5 Dress to impress! 5.1 Aim: Color, 3D, interaction, and animation 5.2 Searching for an example 5.3 Analyze this file 5.4 Some tricks with arrays 5.5 Do it yourself Chapter 6 Bake your own .py! 6.1 Aim: creating a package with your own programs 6.2 Step by step, starting simple 6.3 Class with style! 6.4 Remote control 6.5 Do it yourself! Chapter 7 Will you still feed me? 7.1 Aim: make external data available for your programs 7.2 Point by point 7.3 Pixel by pixel 7.4 Beat by beat 7.5 Do it yourself! Chapter 8 Like a Nobel laureate 8.1 Aim: Solving a system of ordinary differential equations 8.2 First Example: The Hodgkin and Huxley equations 8.3 Putting everything together 8.4 Nobel 2.0 8.5 Do it yourself! Chapter 9 Let it roll! 9.1 Aim: Visualizing 9.2 Get started 9.3 Color your life 9.4 Where are the data? 9.5 Another twist 9.6 Do it yourself! Chapter 10 Some physics 10.1 Aim: Handling vectors; example: Biot-Savart law 10.2 Preliminaries 10.3 Sidestepping by a few units 10.4 Vectorization 10.5 Do it yourself! Chapter 11 Perfect fit? 11.1 Aim: Image registration - or: how to understand the ITK user guide 11.2 Hello World Registration: from .cxx to .py 11.3 Intermezzo I: an odyssey 11.4 Continuation I: 11.5 Intermezzo II: on pixel types 11.6 Continuation II: 11.7 Observer 11.8 The final move 11.9 Do it yourself: very very demanding! Chapter 12 Glue 12.1 Aim: exploit the best of two worlds 12.2 Reading a DICOM image 12.3 Involving ITK 12.4 Interacting! 12.5 Smooth control by comparison 12.6 Interactive segmentation 12.7 Do it yourself: remove the arm Chapter 13 Back to school 13.1 Aim: Doing some symbolic math 13.2 Before we really start: preliminaries 13.3 Three points and a plane in 3D 13.4 Bistability 13.5 Do yourself symbolics! Chapter 14 Optimistic optimization 14.1 Aim: Looking for the best, considering circumstances 14.2 Looks simple, but ... 14.3 Step, print, understand ... 14.4 Do it yourself Chapter 15 Are you certain? 15.1 Aim: Quantifying uncertainties 15.2 The robot 15.3 Frightening conventional 15.4 Matrix formulation, more professional but even more frightening 15.5 More intuitive: the Monte Carlo approach 15.6 Easy going and very fast 15.7 Do it yourself! Chapter 16 Your own statistics 16.1 Aim 1: Learning from R 16.2 Aim 2: Learning from NIST/SEMATECH 16.3 Preparatory action: involving 'pandas' and 'patsy' 16.4 The ceramics example 16.5 How to reproduce? 16.6 Back to the sources 16.7 Do it yourself! Chapter 17 Publish or perish! 17.1 Aim: documentation, publication, poster creation 17.2 Collecting and debugging the codes 17.3 Building a pdf poster 17.4 How I prepared the cover of this book 17.5 Do it yourself! Chapter 18 Table of tools