Programming for Cognitive and Brain

Sciences

Christophe Pallier

Nov 14, 2023

 CONTENTS:

1 Foreword 3

2 Software Installation 5
2.1 Instructions for native Windows (without WSL) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.2 Instructions for Windows using the Windows Subsystem for Linux (WSL) . . . . . . . . . . . . . . . 9
2.3 Instructions for MacOS X . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
2.4 Instructions for Ubuntu Linux . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

3 Check your installation 15

3.1 Check R and Rstudio . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
3.2 Check if Python can be executed in a Terminal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
3.3 Check Git . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
3.4 Check Python . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
3.5 Check basic graphics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
3.6 Check matplotlib . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
3.7 Check pygame . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
3.8 Check Expyriment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
3.9 Appendices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
3.10 Keep your local copy of the course material up to date . . . . . . . . . . . . . . . . . . . . . . . . . . 22
3.11 Basic surviving skill: how to enter command lines in a Terminal . . . . . . . . . . . . . . . . . . . . . 23

4 Starting from Scratch 25

4.1 First steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
4.2 Concepts learned so far . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
4.3 Loops . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
4.4 Two sprites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
4.5 Conditional execution or branching . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
4.6 First series of exercices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
4.7 Variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
4.8 Second series of exercices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

5 Fun programming language 37

6 Interacting with a computer (in a Nutshell) 39

6.1 The shell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
6.2 Disks, Directories and files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
6.3 filenames, directory structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
6.4 Working directory. Absolute pathnames vs. relative pathnames (..) . . . . . . . . . . . . . . . . . . . 42
6.5 What is the PATH? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
6.6 What is a library (or module/package)? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

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7 Running Python 45
7.1 Running a python script from the command line . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
7.2 Testing a short piece of python code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
7.3 Write code with a text editor (Edit-run cycle) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
7.4 Using an Integrated Development Environment (IDE) . . . . . . . . . . . . . . . . . . . . . . . . . . 49
7.5 Perform an interactive data analysis with jupyter-notebook or jupyter-lab . . . . . . . . . . . . . . . . 49
7.6 Developping in Python with Emacs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

8 Coding Exercises 53
8.1 Flow control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
8.2 Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
8.3 Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
8.4 Strings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
8.5 Dictionaries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
8.6 File reading and writing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

9 Automata and Computers 61

9.1 The Computational Theory of Mind . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
9.2 What is computation anyway ? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
9.3 The ancestors of the computer: the automata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
9.4 Formal description of an automaton . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
9.5 Examples of transition diagrams . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
9.6 What is a Computer? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
9.7 Register machines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
9.8 The Seven secrets of computers revealed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
9.9 Programmable computers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
9.10 Compilation and interpretation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
9.11 Operating systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
9.12 What is a Terminal? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72

10 Representations of numbers, text, images 75

10.1 Representation of integers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
10.2 Representation of text . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
10.3 Representation of images . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83

11 Creating stimuli 87
11.1 Static visual stimuli . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
11.2 Dynamic visual stimuli . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
11.3 Creating and playing sounds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
11.4 More illusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101

12 Experiments 103
12.1 Simple reaction times . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
12.2 Decision times . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
12.3 Numerical distance effect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
12.4 Lexical Decision . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
12.5 Posner’s attentional cueing task . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
12.6 Stroop Effect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
12.7 A general audio visual stimulus presentation script . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
12.8 Sound-picture matching using a touchscreen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
12.9 More examples using Expyriment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111

13 Programming a Lexical decision task 113

13.1 Step 1: stimuli in constants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
13.2 Step 2: read stimuli from a csv file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113

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 13.3 Select words in a lexical dabatase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
13.4 Automatising database searches with R and Python . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
13.5 Generate nonwords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
13.6 Create a stimuli file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
13.7 Use sys.argv to pass the name of the file containing the list of stimuli . . . . . . . . . . . . . . . . . . 115
13.8 Improving the pseudowords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
13.9 Data analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
13.10 Finally . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116

14 Data Analyses 117

14.1 Permutation tests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
14.2 Bootstrap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
14.3 Basic Data Analysis with R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
14.4 Comparing means using Easy ANOVA (Analysis of Variance) . . . . . . . . . . . . . . . . . . . . . 118
14.5 Frequency Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118

15 Lexical Statistics 119

15.1 Zipf law . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
15.2 Benford’s law . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
15.3 Neuroimaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120

16 Online experiments 121

16.1 HTML Basics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
16.2 Simple shapes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
16.3 Combining shapes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
16.4 Combining shapes with JS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
16.5 Using JsPsych . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128

17 Regular Expressions 137

17.1 Tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
17.2 Example in Cognitive Science research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
17.3 More on the Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138

18 Simulations 139
18.1 Monte Carlo Estimation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
18.2 Fractals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
18.3 Formal systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
18.4 Artificial Neural networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141

19 Hopfield Networks 143

19.1 Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
19.2 Computing the weight matrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
19.3 Encoding images . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
19.4 Simulations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
19.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146

20 Web Scraping 147

21 Tools to do Reproducible Science 161

21.1 Two tools: literate programming and version control . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
21.2 Lesson 101: how to compare files or directories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
21.3 Introducing git . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
21.4 Working with remotes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167

22 Resources to learn Git 171

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23 How to solve problems 173
23.1 How to think like a programmer: lessons in problem solving . . . . . . . . . . . . . . . . . . . . . . . 173
23.2 How to report bugs effectively . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
23.3 How to solve it by Polya . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177
23.4 Computer Science Distilled . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177

24 Writing clean code 179

24.1 Names . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
24.2 Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
24.3 Successive refinement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
24.4 General . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
24.5 Comments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
24.6 Testing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181

25 Building abstractions with recursive functions and higher-order functions 183

25.1 Recursive functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
25.2 Higher-order functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
25.3 Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185

26 Sending TTL triggers 187

26.1 Parallel Port . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
26.2 DLP-IO8-G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
26.3 Python . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
26.4 Reading an input line . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190
26.5 Arduino . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
26.6 Raspberry Pi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191

27 Cogmaster Lectures 193

27.1 Course description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
27.2 Prerequisites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194
27.3 Projects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194

28 Projects 197

29 Resources 199
29.1 Learning Python3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
29.2 Programming skills . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
29.3 Books relevant to Cognitive and Brain Sciences Programming . . . . . . . . . . . . . . . . . . . . . . 200
29.4 Stimulus/Experiment generation modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
29.5 Data analyses, Statistics in Python . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
29.6 Simulations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201

iv
 Programming for Cognitive and Brain Sciences

PDF version of this document

https://media.readthedocs.org/pdf/pcbs/latest/pcbs.pdf
Git repository on github (contains slides, solutions to exercices, and more)
https://github.com/chrplr/PCBS
Discord (discussion forum)
https://discord.gg/9hKDQmRu
Self-evaluation quizz (do you need to attend PROG101?):
https://forms.gle/iq7CN41DZMA6XJC59

CONTENTS: 1
Programming for Cognitive and Brain Sciences

2 CONTENTS:
 CHAPTER

ONE

FOREWORD

Students in cognitive/neuro science need to learn programming in order to:

• have a basic understanding of how computers work because of the importance of the Computational Theory of
Mind in Cognitive Science.
• prepare and run experiments on humans or animals, analyze data, run computational simulations, …
• automate the boring stuff such as, repetitive work on files, web scraping, …
This book gathers various lectures given at the Master in Cognitive Science in Paris (“Cogmaster3 ”) over the last 15
years.1 (Students enrolled in the current course, Programming for Cognitive and Brain Sciences, will find more information
about it in the chapter Cogmaster Lectures).
This book can also be used as a self-teaching tool. Depending on the Reader’s prior programming experience and interests,
different sections are relevant. I have tried to keep the sections as independent as possible to facilitate the study, but you
will find some cross referencing when needed. Although we cover many topics, some are only touched superficially; the
reader should definitely check the Resources section to go further.
The latest version of this document is always available at https://pcbs.readthedocs.io and can be downloaded as a single
pdf file4 .
Dear Reader, suggestions for corrections are very appreciated! You can just send me an email at
[email protected], or open an issue on the PCBS github repository5 .
Christophe Pallier <http://www.pallier.org>

3 https://cogmaster.ens.psl.eu/en
1 These lectures come from various courses (Atelier d’experimentation humaine, Atelier d’Analyse de données expérimentales, Introduction to R,
Introduction to Programming with Python, …) taught by me and my colleages and friends Mark Wexler6 , Christophe Lalanne7 , Sylvain Charron8 , Ewan
Dunbar9 , Cédric Foucault10 , Henri van den Driessche11 .
6 http://wexler.free.fr/
7 https://aliquote.org
8 https://fr.linkedin.com/in/sylvain-charron-410a9810
9 http://individual.utoronto.ca/ewan_dunbar
10 https://cedricfoucault.github.io/
11 https://fr.linkedin.com/in/henri-vandendriessche-07784548
4 https://media.readthedocs.org/pdf/pcbs/latest/pcbs.pdf
5 https://github.com/chrplr/PCBS

3
Programming for Cognitive and Brain Sciences

4 Chapter 1. Foreword
 CHAPTER

TWO

SOFTWARE INSTALLATION

We explain below how to install:

• a code editor: Visual Studio Code
• a version control system: Git
• the statistical programming language R
• the integrated development environment RStudio
• The programming language Python (version 3.7 !)
• The experiment generator Expyriment (python module)
After the installation, you will need to check that everything works (see Check your installation

Warning:
• You will need to download several GB of software from the Internet. Therefore, make sure to have a decent
connection.
• Make sure that you have at least 5GB of free space on your hard drive to unpack the various software.
• You will need to have administrator rights to install some of the software. If you are using a computer from an
institution, check with the IT support team.

Contents

• Software Installation
– Instructions for native Windows (without WSL)
– Instructions for Windows using the Windows Subsystem for Linux (WSL)
– Instructions for MacOS X
– Instructions for Ubuntu Linux

5
Programming for Cognitive and Brain Sciences

2.1 Instructions for native Windows (without WSL)

Please follow these instructions carefully! If you do not, many things could go wrong and you might need to run the
installers again.

2.1.1 R and Rstudio

R is a programming language specialized for statistical data analyses; Download and install it from https://cran.rstudio.
com/bin/windows/base/ (accepting all the default options proposed by the installer)
Rstudio is an Integrated Developpement Environment for R which greatly simplifies the use of RMarkdown. You can
download and install the free version of RStudio Desktop from https://posit.co/download/rstudio-desktop/ (accepting all
the default options)
Lauch RStudio, go to the “Tools” menu, select “install packages” and in the dialog window that opens, in the ‘packages’
box, type:

tidyverse lme4 ez

This will take a while to download packages from the internet and install them. Do not close rstudio until the process
is finished (no more scrolling messages in the console). Meanwhile, you can start the installation of the other software
below.

2.1.2 Code editor

A code editor is a program that allows you to edit pure text files such as Python programs, Markdown12 or LaTeX13
documents, etc.
If you do not already have a code editor that you like, download and install Visual Studio Code14 (accepting the default
options proposed by the installer)

2.1.3 Python3 using the Anaconda distribution

You will need to install Python version 3.7 (because the expyriment module, to be installed later, requires this specific
version)
There exists various Python distributions. Under Windows, we recommend the Anaconda3 distribution15 as it already
contains many of the packages needed for cognitive science (but it is very large. If you you lack disk space, you can install
miniconda, but later you will need to install many python packages manually)
1. Go to <https://www.anaconda.com/products/individual>, click on Download and select the 64-bit installer for
Windows.
2. Execute the Anaconda3 installer. Pay special attention to the options:
• To the question ‘Install for’, select Just Me (recommended)
• Accept the default Destination folder and click on Next
12 https://daringfireball.net/projects/markdown/
13 https://www.latex-project.org/
14 https://code.visualstudio.com/
15 https://www.anaconda.com/distribution

6 Chapter 2. Software Installation

 Programming for Cognitive and Brain Sciences

• VERY IMPORTANT: Check the boxes in front Add Anaconda3 to my PATH (ignore the warning
that this is not recommended) and Register Anaconda as my default Python (all the other
default options are fine). Click on Install.
• upon completion, click on Next, then Finish

2.1.4 The Git version control system

Git is a version control tool for software development, an indispensable tool to do reproducible science.
IMPORTANT: you must wait for the installation of Anaconda to finish before trying to install Git.
Download the installer of Git for Windows16 and launch it.
1. When the GNU Licence is displayed, press Next;
2. Accept the default installation folder and press Next;
3. Accept all the Components selected by default and press Next
4. Accept the creation of a start menu folder named ‘Git’: press Next;
5. VERY IMPORTANT: When proposed a default editor, select ‘Use the nano editor’ (unless you want
to learn Vim)
6. VERY IMPORTANT: When proposed to adjust the PATH environment variable, tick the box “Use
Git and optional unix tools from the command line prompt”.
You can accept all the other defaults.
Now, to finish the installation of git, launch Git bash (use the “Search box”), and on type:

conda init bash

then press ‘Return’

If the computer replies with an error message of the type conda: command not found, you did not properly
install Anaconda (you did not check the box that made sure it is added to the PATH). If you know how to do correct the
PATH, correct it now, otherwise, reinstall anaconda.
Now, type:

echo "alias python='winpty python.exe'" >> ~/.bash_profile

and press ‘Return’

Close the Git Bash Terminal, and reopen a new Git Bash.
Type:

which python

And then:

python

It should print a message ‘Python 3.x.xx…’ and a give a prompt ‘>>>’. You are talking to the python interpreter. Type:

2**100

16 https://git-scm.com/download/win

2.1. Instructions for native Windows (without WSL) 7

Programming for Cognitive and Brain Sciences

This should display the 100 power of 2. To exit python, type:

quit()

If python does not start, there is something wrong. Most probably, you forgot to check the boxe Add Anaconda to
my PATH during the installation of Anaconda. do it again. If it still does not work, ask for help.
Finally, you must configure Git: Within a Git Bash terminal, type the following commands (replacing
your_first_and_last_name_here and your_email_here by relevant personal information)

git config --global user.name "your_first_and_last_names_here"

git config --global user.email your_email_here
git config --global core.editor nano

You can close Git Bash by typing the command exit or, faster, by pressing Ctrl-D, or by just closing its window.

2.1.5 The Pygame and Expyriment python modules

We will rely on the Pygame module17 to create stimuli and the Expyriment Python Library18 to program behavorial
experiments.
Start Git bash and, in the Terminal that opens, type:

conda create -n expyriment python=3.7

And press ‘Return’ to accept the installation.

Then, type:

conda activate expyriment

conda install ipython
pip install expyriment[all]

To check the installation, type:

ipython

and then:

import expyriment

If a message Experiment 0.10.0 … is displayed and no error message, the installation worked. Press Ctrl-D to quit ipython,
and Ctrl-D again to qui Git Bash.
17 https://www.pygame.org
18 http://www.expyriment.org

8 Chapter 2. Software Installation

 Programming for Cognitive and Brain Sciences

2.1.6 Checking everything

Now you should check if everything works, following the instructions in chapter Check your installation.

2.2 Instructions for Windows using the Windows Subsystem for

Linux (WSL)

As an alternative to installing Python et coll. as native Windows applications, you can install Ubuntu Linux under Win-
dows, relying on Microsoft’s Windows Subsystem for Linux (aka WSL) and then install Python and coll. within Ubuntu.
The interest of having WSL is that it gives you the opportunity to learn to use Linux, which may come handy if one day
you need to access remote computational facilities such as the Jean Zay supercomputer.
If you already have WSL Ubuntu installed on your Windows PC, you can just open an Ubuntu terminal and jump directly
to the linux section.
If not, and want to try it, keep reading.

2.2.1 Installing the Microsoft’s Windows Subsystem for Linux

If you want to install Linux under Windows using the WSL, follow the instructions at https://docs.microsoft.com/en-us/
windows/wsl/install but be aware that the download is large (several GB) and the installation can be lengthy, depeding on
the power of your PC (30min-1h)
Here is an overview of the process:
• If you have Windows 11:
1. Install the vGPU driver for your graphics card (Intel19 , AMD20 or Nvidia21 )2 if it not already installed.
2. Launch “Windows PowerShell” as administrator, and execute the command:

wsl --install -d ubuntu

• If you have Windows 10, follow these instructions22 . (You may have to enable Hyper-V23 )
This downloads the full Ubuntu Linux distribution which may take a while. Some versions of Windows may even ask
you to reboot during the installation process. At some point during the install, a new Terminal window entitled “Ubuntu”
will open and will require a new user name and password. You can type anything but it is crucial that you note down the
password as it will be needed to install software under Ubuntu.

Note: If anything goes wrong during the installation check the Troubleshoting WSL24 section.

Now that the WSL installation is finished, jump to the linux section in order to install the required software.
19 https://www.intel.com/content/www/us/en/download/19344/intel-graphics-windows-dch-drivers.html?
20 https://www.amd.com/en/support/kb/release-notes/rn-rad-win-wsl-support
21 https://developer.nvidia.com/cuda/wsl
2 To determine which type of GPU (Intel, AMD, Nvidia) is installed on your computer, under Windows, open the Task Manager, e.g. with

Ctrl-Alt-Del, and search for GPU under the Performance tab.

22 https://omgubuntu.co.uk/how-to-install-wsl2-on-windows-10
23 https://www.zdnet.com/article/windows-10-tip-find-out-if-your-pc-can-run-hyper-v/
24 https://docs.microsoft.com/en-us/windows/wsl/troubleshooting

2.2. Instructions for Windows using the Windows Subsystem for Linux (WSL) 9
Programming for Cognitive and Brain Sciences

2.3 Instructions for MacOS X

2.3.1 Code editor

A code editor is a program that allows you to edit pure text files such as Python programs, Markdown25 or LaTeX26
documents, etc.
Unless you already use a code editor that you are familiar and happy with, we recommend that you download and install
Visual Studio Code27 . Follow the instructions specific to MacOS.

2.3.2 The Git version control system

Download and install Xcode28 , either from the App store, or by using the command line xcode-select --install.
This will provide git.
To finish the installation of git, open a Terminal window1 and type the following command lines, making sure to replace
your_first_and_last_name_here and your_email_here by the relevant personal information:

git config --global user.name "your_first_and_last_names_here"

git config --global user.email your_email_here
git config --global core.editor nano

2.3.3 The R statistical software

Download and install the latest version of R from https://cran.rstudio.com/bin/macosx/

2.3.4 Rstudio Desktop

Download and install the latest version of RStudio Desktop from https://posit.co/download/rstudio-desktop/. Make sure
to select the MacOS version!
25 https://daringfireball.net/projects/markdown/
26 https://www.latex-project.org/
27 https://code.visualstudio.com/
28 https://developer.apple.com/xcode/
1 To open a Terminal:
• Windows with the WSL: launch the “Ubuntu” app.
• Windows with Git for Windows: launch “Git bash”.
• Linux: Launch Terminal or press Ctrl-Alt-T (Gnome or Xfce) or Win-Return (i3).
• MacOS: Type terminal in the Spotlight search field. Alternatively, you can open a Finder window and select the Application folder,
then the Utilities folder, then double-click on the Terminal icon..

10 Chapter 2. Software Installation

 Programming for Cognitive and Brain Sciences

2.3.5 Python

Download and install Anaconda3 Python from https://www.anaconda.com/products/individual

2.3.6 The Pygame and Expyriment python modules

1. Install XQuartz29 . Download the .dmg file from the official website and open it to install.
2. Open a Terminal and type /bin/bash -c "$(curl -fsSL https://raw.
githubusercontent.com/Homebrew/install/HEAD/install.sh)" to install
Homebrew30 (which is needed to install SDL).
• If you see “Password: “, this means the Terminal is prompting you to type your computer’s ad-
ministrator account password. Type your password and press the return key to continue.
• If you see an error message such as “Error: /usr/local/Cellar is not writable. You should change
the ownership and permissions of /usr/local/Cellar back to your user account: sudo chown -R
$(whoami) /usr/local/Cellar”, run in the Terminal the command that was suggested (here sudo
chown -R $(whoami) /usr/local/Cellar), and then run the previous command to
try installing Homebrew once again
3. In the same Terminal, type brew install sdl2 sdl2_image sdl2_mixer sdl2_ttf
pkg-config to install SDL (which is needed to install expyriment). This may take a while.
4. In the same Terminal, type pip install "expyriment[all]" to install expyriment.
5. In the same Terminal, type pip install -U pygame to upgrade pygame (version >= 2.0 is
required on recent versions of macOS, but this must be done after installing expyriment otherwise the
install of expyriment will fail).
Now you should check if everything works, following the instructions in chapter Check your installation.

2.4 Instructions for Ubuntu Linux

These instructions were tested with Ubuntu 20.04

Open a TerminalPage 10, 1 .
Then, for each software section below, copy and paste in the terminal the lines that are in the boxes and press Enter to
execute them.

2.4.1 Git

Git31 is a free distributed version control system.

sudo apt install git -y

Now, type the following command lines, making sure to replace your_first_and_last_name_here and
your_email_here by the relevant personal information:

29 https://www.xquartz.org/
30 https://brew.sh/
31 https://git-scm.com/

2.4. Instructions for Ubuntu Linux 11

Programming for Cognitive and Brain Sciences

git config --global user.name "your_first_and_last_names_here"

git config --global user.email your_email_here
git config --global core.editor nano

2.4.2 Visual Studio Code editor

Install Visual Studio Code32 :

snap install code

2.4.3 R language for statistics

R33 is a free software environment for statistical computing and graphics.

sudo apt update -qq

sudo apt install –no-install-recommends software-properties-common dirmngr wget -qO- https://cloud.r-project.org/bin/

linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc sudo add-apt-repository “deb
https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/”
sudo apt install –no-install-recommends r-base sudo add-apt-repository ppa:c2d4u.team/c2d4u4.0+ sudo apt install –no-
install-recommends r-cran-tidyverse
(in case of trouble, check the latest instructions at https://cran.rstudio.com/bin/linux/ubuntu/)

2.4.4 Rstudio Desktop

Rstudio is an Integrated Developpement Environment for R which greatly simplifies the use of RMarkdown. You can
download and install the latest version of RStudio Desktop from https://posit.co/download/rstudio-desktop/ Make sure
to select the ubuntu version!

wget https://download1.rstudio.org/electron/jammy/amd64/rstudio-2023.06.2-561-amd64.
,→deb

sudo apt install ./rstudio-2023.06.2-561-amd64.deb -y

2.4.5 Python3

Python34 is the main programming language used in these courses. The following commands install various modules that
will be needed.

sudo apt install -y python3 ipython3 python3-dev python-is-python3 python3-future \

python3-opengl python3-pip python3-ipython python3-pygame python3-numpy \
python3-matplotlib python3-skimage python3-pandas python3-scipy \
python3-imageio python3-ipython

32 https://code.visualstudio.com/
33 https://www.r-project.org/
34 https://www.python.org/

12 Chapter 2. Software Installation

 Programming for Cognitive and Brain Sciences

2.4.6 Expyriment

We now need to install the Expyriment module35 .

Try:

sudo apt-get install -y python3-dev libasound2-dev

sudo pip install simpleaudio

sudo pip install expyriment[all]

Check the installation by typing:

python

and then, after >>>:

import expyriment

If you see No module named expyriment, there was a problem (most probably due a version of pygame). Forcing the using
of python version 3.7 should solve it.
First install pyenv36 , then:

pyenv install 3.7.6

pyenv virtualenv 3.7.6 expyriment
pyenv activate expyriment
pip install expyriment[all]

Note: Later, when you will need to run python scripts importing expyriment, you will need first to activate the virtual
environment with:

pyenv activate expyriment

2.4.7 Psychtoolbox

(This is optional: we do not make use of the Psychtoolbox in this course)

Psychtoolbox-337 is a set Octave functions which is very popular in vision and neuroscience research. This installation is
optional as the Psychtoolbox is not used in this book.
First, add the [Neurodebian](https://neuro.debian.net/) repository.

wget -O- http://neuro.debian.net/lists/focal.de-m.full | sudo tee /etc/apt/sources.

,→list.d/neurodebian.sources.list

sudo apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com␣

,→0xA5D32F012649A5A9

Then activate the sources and install the required packages:

35 http://expyriment.org
36 https://linuxpip.org/pyenv-ubuntu/
37 http://psychtoolbox.org/

2.4. Instructions for Ubuntu Linux 13

Programming for Cognitive and Brain Sciences

sudo sed -Ei 's/^# deb-src /deb-src /' /etc/apt/sources.list

sudo apt update

sudo apt build-dep octave-psychtoolbox-3 -y

sudo apt install subversion libdc1394-22-dev libfreenect* libgstreamer1.0-dev␣
,→libgstreamer-plugins-* -y

Download the psychtoolbox installation script:

wget https://raw.github.com/Psychtoolbox-3/Psychtoolbox-3/master/Psychtoolbox/
,→DownloadPsychtoolbox.m.zip

unzip DownloadPsychtoolbox.m.zip

mkdir ~/PTB3

Finally, start octave and, on Octave’s command line, type:

DownloadPsychtoolbox('/home/neurostim/PTB3')
PsychLinuxConfiguration()

# test
DrawingSpeedTest()

Now you should check if everything works, following the instructions in chapter Check your installation.

14 Chapter 2. Software Installation

 CHAPTER

THREE

CHECK YOUR INSTALLATION

Contents

• Check your installation

– Check R and Rstudio
– Check if Python can be executed in a Terminal
– Check Git
– Check Python
– Check basic graphics
– Check matplotlib
– Check pygame
– Check Expyriment
– Appendices
– Keep your local copy of the course material up to date
– Basic surviving skill: how to enter command lines in a Terminal

3.1 Check R and Rstudio

Launch Rstudio, and in the Console (left window), type:

example(density)

This should display a series of graphics (Press <Return> to advance).

Then type:

require(tidyverse)

If the package tidyyverse is not found, you need to install it with:

install.packages('tidyverse')

Close RStudio. That will be all.

15
Programming for Cognitive and Brain Sciences

3.2 Check if Python can be executed in a Terminal

Open a Terminal (that is, Git Bash for Windows users) and type:

which python

This should print the location of the python interpreter, e.g. something like /home/macron/anaconda3/python
If no message is displayed, the PATH environment variable — which lists the directories where programs can be found
— is messed up, most probably due not following closely the installation instructions (for Windows users, check the
Anaconda and Git for Windows instructions)
Type python and press ‘Enter’.
You should see a prompt >>> followed by a blinking cursor. Python is waiting for your commands! Type:

2**100

This should display the 100 power of 2. Type quit() to leave Python and press Ctrl-D to close the Terminal. Basic
Python is working.

3.3 Check Git

Download the course materials using Git by entering the following command line in a Terminal:

git clone https://github.com/chrplr/PCBS.git

You should see a message Cloning into 'PCBS'... and, if everything goes well, all the course materials (python
scripts, data files, …) should be downloaded in a new subdirectory called PCBS, within the current working directory.
You can cd into it and list its content:

cd PCBS
pwd
ls

Your Terminal window should more or less look like this:

16 Chapter 3. Check your installation

 Programming for Cognitive and Brain Sciences

Warning: If a folder named PCBS already exists in the current working directory, git will stop and will not download
the content of the remote PCBS repository. In that case, you must delete or move the existing PCBS folder before
running the git clone command above.
When you open a Terminal, the current working directory is your “home”, or “user”, directory, until you start navigat-
ing in the filesystem with the cd (change directory) command. If you are lost at this point, read Navigating
the file system38 .

3.4 Check Python

This tests if Python3 is installed and correctly configured.

cd ~/PCBS/games
python human-guess-a-number.py

38 http://linuxcommand.sourceforge.net/lc3_lts0020.php

3.4. Check Python 17

Programming for Cognitive and Brain Sciences

Warning: If you receive an error message such as bash: python: No such file or directory,
and you are sure that python is installed, the most likely reason is that the problems lies with the PATH environment
variable39 ) listing all the directories: the directory containing the python executable file may be missing from the list.
This happens for example, if you run the Anaconda3 installer and did not check the relevant box.

3.5 Check basic graphics

cd ~/PCBS/simulations/fractals
python koch0.py

You can launch the Visual Code editor and open the python file PCBS/simulations/fractals/koch0.py to
check the code.

3.6 Check matplotlib

matplotlib is a python library to create and display graphics. Here, we try to generate some graphical effects to check that
this library has been correctly installed.

cd ~/PCBS/stimuli/visual

python bullseye.py

39 https://linuxhint.com/path_in_bash/

18 Chapter 3. Check your installation

 Programming for Cognitive and Brain Sciences

python contrast_modulated_grating.py

python gabor.py

3.6. Check matplotlib 19

Programming for Cognitive and Brain Sciences

python image-manipulation.py

python wedgering.py

20 Chapter 3. Check your installation

 Programming for Cognitive and Brain Sciences

3.7 Check pygame

Pygame40 is a Python library to create simple audio visual games. It was installed along with expyriment. If you had to
create a Python virtual environment when you installed expyriment, you need to activate it:

conda activate expyriment # if you use conda

pyenv activate expyriment # if you use standard python with pyenv

You can then check if pygame is installed by starting python on a command line and typing import pygame a the
>>>` prompt. A message ``Hello from the pygame community. should be displayed.

cd ~/PCBS/stimuli/visual-illusions/
python kanizsa_triangle.py

python hering.py

40 http://www.pygame.org

3.7. Check pygame 21

Programming for Cognitive and Brain Sciences

python extinction-rotated.py

3.8 Check Expyriment

Expyriment41 is a Python library for designing and conducting behavioural and neuroimaging experiments.
If you had to create a Python virtual environment when you installed expyriment, you need to activate it (unless it is
already activated in your current Terminal):

conda activate expyriment # if you use conda

pyenv activate expyriment # if you use standard python with pyenv

Try to run the following experiment (Note that the programs can be interrupted at any time by pressing the Esc key).

cd ~/PCBS/experiments/xpy_parity_decision
python parity_feedback.py

This should run a small exepriment where the participant must chech the parity (odd or even) of numbers.
That’s all folks !

3.9 Appendices

3.10 Keep your local copy of the course material up to date

The course materials are often updated. To make sure you have the latest version, you can synchronize your local copy
with the github repository http://github.com/chrplr/PCBS, with the commands:

cd ~/PCBS
git pull

41 http://expyriment.org

22 Chapter 3. Check your installation

 Programming for Cognitive and Brain Sciences

Notes:
• if the PCBS directory is not in your home directory (-), you will need to use the appropriate path in the first cd
command.
• do not manually modify or create new files in the PCBS folder. If you do so, git will notice it and might prevent an
automatic upgrade and ask you to ‘resolve conflicts’. If you get such a message, the simplest course of action, for
beginners, is to delete the PCBS folder (or move it if you wnat to keep a copy of your modifications) and reissue
the git clone command above to reload the full folder.)

3.11 Basic surviving skill: how to enter command lines in a Terminal

Watch the video at https://www.youtube.com/watch?v=2yhcWvBt7ZE&t and try to perform the activities in it (the in-
structions also work for Mac or Linux: you just need to open a standard Terminal while in Windows you start ‘Git Bash’).
Note: the game scripts mentioned in the video are available at https://github.com/chrplr/PCBS/tree/master/games/games.
zip
For the moment, you mostly need to know the following three commands:
• ls: list the content of the current working directory
• pwd: path of current working directory
• cd: change directory
Read about them in http://linuxcommand.sourceforge.net/lc3_lts0020.php
Here are some resources to learn more about how to control your computer from a terminal:
• Learning the Shell http://linuxcommand.org/lc3_learning_the_shell.php
• OpenClassRoom : https://openclassrooms.com/en/courses/43538-reprenez-le-controle-a-laide-de-linux/
37813-la-console-ca-se-mange

3.11. Basic surviving skill: how to enter command lines in a Terminal 23

Programming for Cognitive and Brain Sciences

24 Chapter 3. Check your installation

 CHAPTER

FOUR

STARTING FROM SCRATCH

To begin our journey into programming, we will use Scratch42 , a system developed the MIT media lab to teach how to
program to kids.
A great advantage of Scratch43 is that programs are created using a graphical interface, preventing syntactic errors. Thus,
you can learn the language without having to learn its grammar!
One can either work online at https://scratch.mit.edu/projects/editor/?tip_bar=home or offline, by downloading Scratch44
at
• https://scratch.mit.edu/scratch_1.4/ (version 1)
• https://scratch.mit.edu/scratch2download/ (version 2)
We recommend the reader to run the tutorial “Getting Started with Scratch”45

4.1 First steps

4.1.1 Program 001

In the motion group, take the instruction turn 15 degrees and drag it onto the Scripts panel.
42 http://scratch.mit.edu
43 http://scratch.mit.edu
44 http://scratch.mit.edu
45 https://scratch.mit.edu/projects/editor/?tip_bar=home

25
Programming for Cognitive and Brain Sciences

Double-Click repeatedly on the block turn 15 degrees, you should see the cat (sprite 1) rotate.
In Scratch, when one double-clicks an instruction in the Scripts panel, the computer executes it.

4.1.2 Program 002

Drag the instruction move 10 steps from the motion group, and add it to the bottom of the instruction turn 15
degrees. Change the value 10 into 50.

You have just created a block of instructions, that is, your first program or script, Bravo!
• Double-Click on the block and see the sprite moving.
• Note that inside a block, instructions are exectuted sequentially, one after the other. Can you prove it?
• Experiment with changing the argument of the instruction move (Tip: to clear the drawing area, move the in-
struction pen/clear to the script window and execute it)

4.1.3 Program 003

Click on the pen group, and add pen down at the top of the block.

26 Chapter 4. Starting from Scratch

 Programming for Cognitive and Brain Sciences

Run it.

4.1.4 Program 004

Construct the following scripts and play with them until you are sure to understand the behavior of the computer..

4.2 Concepts learned so far

• Instruction
• Argument of an instruction (change 10 in move 10 steps)
• Block of instructions and sequential execution

4.3 Loops

4.3.1 repeat (for loop)

Computers are good at doing tasks repeatedly (as they do not get tired).
Click on the “Control” group, and try to construct the following script:

4.2. Concepts learned so far 27

Programming for Cognitive and Brain Sciences

• Clicking on the green flag will execute the block of instructions

• The Repeat instruction executes the inner block of instruction a number of times specified as an argument. This
is called a loop
• Adjust the parameter of the Repeat instruction so that the sprite draws a full circle when you click once on the green
flag.
• Replace the repeat instruction by forever.

4.3.2 Repeat until

Modify the script as follows:

Tip: the condition key space pressed? is in the Sensing group.

This illustrates a repeat…until loop: the inner block is executed until the condition is satisfied.

28 Chapter 4. Starting from Scratch

 Programming for Cognitive and Brain Sciences

4.4 Two sprites

Add a new sprite, and duplicate the script from sprite1. Click on the green flag. You should see the two sprites running
in circles.

Remark that the scripts associated to the two sprites run in parallel (rather than sequentially).

4.4. Two sprites 29

Programming for Cognitive and Brain Sciences

4.5 Conditional execution or branching

Create a new scratch project, and change the costume of the sprite into a ball.
Then write and execute the following script.

You should see the ball bounce on the edges.

4.6 First series of exercices

1. With Scratch, use the instructions “pen down” and “move” and “turn” to (a) make the cat draw a square (with sides
measuring 100 steps) (b) draw an hexagon (c) draw a circle
2. Using the Control/Forever, make the cat turn continuously along a circle.
3. Bouncing ball
• Delete the cat. Using new sprite/open, add a ball.
• Make the ball move automatically horizontally from left to right and bounce when it touches an edge (tip: use
Control/forever)
• Make the ball follow the mouse.
• Add a second ball that follows the first.
4. Create a script that asks for your name and then displays “Hello !”. Tip: use the instructions sensing/ask,
looks/say and operator/join and the variable sensing/answer.
…

30 Chapter 4. Starting from Scratch

 Programming for Cognitive and Brain Sciences

4.7 Variables

Using the group variable, we are going to create a variable a and make it display continuously the x-coordinate of
the ball.

The concept of variable is very important. You can think of it as a name for a object that can change (here the object is
a number).
Now study the following script:

4.7. Variables 31
Programming for Cognitive and Brain Sciences

The loop is executed 100 times. Each time, the value of the variable a is incremented by 1, and is used to compute new
x and y coordinates where to sprite is instructed to moved to.

32 Chapter 4. Starting from Scratch

 Programming for Cognitive and Brain Sciences

4.8 Second series of exercices

4.8.1 Multiplication

“Multiply by adding”: Write a program that reads in two integer numbers and displays their sum.

4.8.2 Guess a number

“Guess a number”. Make Scratch pick up a random number in the interval [1,100], and loop asking you for a guess and
reply either too low, too high, or you win! depending on your answer.

4.8. Second series of exercices 33

Programming for Cognitive and Brain Sciences

4.8.3 Estimate PI

3. We are going to estimate the number PI by a Monte Carlo method.:

• Repeatly (e.g. 2000 times) picks up two random numbers on the interval [-1, 1]. This corresponds to a dot inside
a square of size 2x2.
• Count how many times the dot falls within the circle of radius 1 centered on the origin (Pythagore helps you here:
the dot is within the circle iff (x * x + y * y) < 1.)
• The proportion of dots falling within the circle, multiplied by four (the area of the square), is an estimate of teh
area of the disk, that is, the number pi.

34 Chapter 4. Starting from Scratch

 Programming for Cognitive and Brain Sciences

4.8. Second series of exercices 35

Programming for Cognitive and Brain Sciences

36 Chapter 4. Starting from Scratch

 CHAPTER

FIVE

FUN PROGRAMMING LANGUAGE

If you liked Scratch, but found it too much child-oriented, you may enjoy:
• Processing46 a language for learning how to code within the context of the visual arts.
• Sonic Pi47 a code-based music creation and performance tool.
Give them a look: these are two great programming tools to create visual and audio effects and, being designed for non
programmers, they are very good to learn the bases of programming without pain.

46 https://www.processing.org
47 https://sonic-pi.net

37
Programming for Cognitive and Brain Sciences

38 Chapter 5. Fun programming language

 CHAPTER

SIX

INTERACTING WITH A COMPUTER (IN A NUTSHELL)

Contents

• Interacting with a computer (in a Nutshell)

– The shell
∗ Why learn the command shell?
– Disks, Directories and files
– filenames, directory structure
– Working directory. Absolute pathnames vs. relative pathnames (..)
– What is the PATH?
– What is a library (or module/package)?

Nowadays, most interactions with the operating system (the “conductor of the orchestra” of the programs installed on
your computer) are achieved by clicking on icons that represents programs or data files. When you click on a program,
you start it; when you click on a document, you open it within its associated program.
The is convenient but limited. Imagine you could “talk” to your computer and ask it: “Slave ! find all the jpg graphics
files in this folder, make copy that you reduce to size 512x512 pixels, and place them in a new folder”. This is actually
possible, by typing a single line in a Terminal running the bash shell:

mkdir thumbnails; for f in *.jpg; do convert "$f" -resize 512x512 thumbnails/"${f%.

,→jpg}-512x512.jpg"; done

6.1 The shell

Inside the terminal, you are interacting with a program which runs an infinite loop where it prints a ‘prompt’, wait for you
to type some instructions and, when you press the Enter or Return Key, interprets the line and execute the instructions.
This program is called a Shell. Various Shells exist: bash, zsh, poweshell. they speak slightly different languages.
There even is a shell that speaks python: it is called ipython (for interactive python).
One difficulty is that you need to know the language of the shell and, also, the available programs on your computer. By
contrast with Graphical User Interfaces that display Windows/Icons/Menus, Textual shells have a poor ergonomy in that
there is no visual way of discovering the potential actions. Yet, because they are languages providing variables, loops, …
shells facilitate the automation of tasks.
For example, to create 20 directories in a single bash command under linux:

39
Programming for Cognitive and Brain Sciences

for f in 01 02 03 04 05 06 07 08 09 10; do mkdir -p subject_$f/data subject_$f/

,→results; done

The good news is: in these lectures, you will need to use only three shell commands: * cd (change directory) * ls (list)
* pwd (path of working directory).
I recommend that you read the web page at http://linuxcommand.org/lc3_lts0020.php which provides very clear expla-
nations.
You do not have to learn more about the shell for these lecture, but learning more about it may be good idea in the long
run.

6.1.1 Why learn the command shell?

“To properly understand the role of a shell, it’s necessary to visualize what a computer does for you. Basically,
a computer is a tool; in order to use that tool, you must tell it what to do—or give it “commands.” These
commands take many forms, such as clicking with a mouse on certain parts of the screen. But that is only
one form of command input.
By far the most versatile way to express what you want the computer to do is by using an abbreviated lan-
guage called script. In script, instead of telling the computer, “list my files, please”, one writes a standard
abbreviated command word—‘ls’. Typing ‘ls’ in a command shell is a script way of telling the computer to
list your files.1
The real flexibility of this approach is apparent only when you realize that there are many, many different
ways to list files. Perhaps you want them sorted by name, sorted by date, in reverse order, or grouped by
type. Most graphical browsers have simple ways to express this. But what about showing only a few files,
or only files that meet a certain criteria? In very complex and specific situations, the request becomes too
difficult to express using a mouse or pointing device. It is just these kinds of requests that are easily solved
using a command shell.
For example, what if you want to list every Word file on your hard drive, larger than 100 kilobytes in size,
and which hasn’t been looked at in over six months? That is a good candidate list for deletion, when you go
to clean up your hard drive. But have you ever tried asking your computer for such a list? There is no way
to do it! At least, not without using a command shell.
The role of a command shell is to give you more control over what your computer does for you. Not everyone
needs this amount of control, and it does come at a cost: Learning the necessary script commands to express
what you want done. A complicated query, such as the example above, takes time to learn. But if you find
yourself using your computer frequently enough, it is more than worthwhile in the long run. Any tool you
use often deserves the time spent learning to master it.”
(Extracted from Emacs’ eshell documentation)
To learn more about how to control the computer by interacting with the shell, I can only highly recommend two resources:
• Learning the Shell http://linuxcommand.org/lc3_learning_the_shell.php
• OpenClassRoom https://openclassrooms.com/en/courses/43538-reprenez-le-controle-a-laide-de-linux/
37813-la-console-ca-se-mange

40 Chapter 6. Interacting with a computer (in a Nutshell)

 Programming for Cognitive and Brain Sciences

6.2 Disks, Directories and files

Most computers (not all) have two kinds of memories:

• volatile, fast, memory, which is cleared when the computer is switched off (processor’s caches, RAM)
• ‘permanent’, slow, memory, which is not erased when the computer is switched off (DISKS, Flashdrives (=solid-
state drives))
The unit of storage is the file.
Files are nothing but blobs of bits stored “sequentially” on disks.
A first file could be stored between location 234 and 256, a second file could be stored at location 456 on your disk.

6.3 filenames, directory structure

To access a file, one would need to know its location on the disk. To simplify human users’ life, the OS provide a system
of “pointers”, that is filenames , organised in directories.
To help users further, the directories are organised in a hierarchical structure: a directory can contain filenames and other
(sub)directories. The top-level directory is called the root.

Fig. 1: Linux directory structure

To locate a file, you must know:

• its location in the directory structure
• its basename
See absolute or relative pathnames48
48 https://www.geeksforgeeks.org/absolute-relative-pathnames-unix/

6.2. Disks, Directories and files 41

Programming for Cognitive and Brain Sciences

Remark: a given file can have several names in the same or various directories (remember: a filename is nothing but a
link between a human readable charachter string to a location on the disk)

6.4 Working directory. Absolute pathnames vs. relative pathnames

(..)

It would be tedious to always have to specify the full path of a files (that is, the list of all subdirs from the root)
Here comes the notion of working directory: A running program has a working directory and filenames can specified
relative to this directory.
Suppose you want to access the file pointed to by /users/pallier/documents/thesis.pdf. If the current
working directory is /users/pallier, you can just use documents/thesis.pdf (notice the absence of ‘/’ at
the beginning).
To determine the current working directory in a shell, list its content, and change it:
• under bash (or ipython):

pwd
ls
cd Documents

6.5 What is the PATH?

A command can simply consists of a program’s name: typing it and pressing Enter will start the program.
The shell knows where to look for programs thanks to an environment variable49 called PATH.
The PATH variable lists all the directories that contains programs. Try the following commands:

echo $PATH
which ls
which python

Under bash, to add new directories to the PATH:

export PATH="newdirectory":"$PATH"

For example, under Git Bash for Windows, to be able to start sublime text from the command line, by just typing subl,
you must add its folder to the PATH, as follows:

export PATH="/c/Program Files/SublimeText 3/":"$PATH"

To make this setting permanent, you must copy this line within a file .bash_profile in your home directory.
49 https://www.twilio.com/blog/2017/01/how-to-set-environment-variables.html

42 Chapter 6. Interacting with a computer (in a Nutshell)

 Programming for Cognitive and Brain Sciences

6.6 What is a library (or module/package)?

A library is a set of new functions that extend a language.

Libraries can be used simultaneously by several processes.
E.g. the function @@sqrt@@ can be defined once, and called by several programs.
In Python, one uses import to be able to access functions from a library (a.k.a. module), for example:

import math
math.srqt(2)

6.6. What is a library (or module/package)? 43

Programming for Cognitive and Brain Sciences

44 Chapter 6. Interacting with a computer (in a Nutshell)

 CHAPTER

SEVEN

RUNNING PYTHON

Contents

• Running Python
– Running a python script from the command line
– Testing a short piece of python code
– Write code with a text editor (Edit-run cycle)
– Using an Integrated Development Environment (IDE)
– Perform an interactive data analysis with jupyter-notebook or jupyter-lab
– Developping in Python with Emacs

They are several ways to work with Python, each of which is best adapted to a certain type of task:
• To write reusable python scripts, use a code editor (e.g. subl` (Sublime Text)), or an Integrated Development
Environment (e.g. spyder), save the script and run it from a shell command line inside a Terminal.
• To quickly test short pieces of code in an interactive manner, or to access the documentation of some functions or
mudles, open a terminal and run ipython
• To write a data analysis report use jupyter notebook

7.1 Running a python script from the command line

To run a python script, that is, a text file containing python code, you need to:
1. Open a Terminal
• MacOSX: Search for terminal in Spotlight.
• Windows: Launch Git Bash (This assumes that you have installed
Git for windows as described in Instructions for software installation)
• Linux: Launch Terminal from your application menu or use
Ctrl-Alt-T in Gnome, Xfce or Win+Return in i3.
2. If the script is not located in your home directory, use the cd command to navigate to the directory that contains
the script (to learn about this, read Navigation in the shell50 ).
3. Type python followed by the script’s filename, then press the return/enter key.
50 http://linuxcommand.sourceforge.net/lc3_lts0020.php

45
Programming for Cognitive and Brain Sciences

For example, let us suppose that you want to execute a script named matches.py located in a subdirectory PCBS/
games of your home directory. Open a terminal and type:

cd PCBS/games
python matches.py

Remarks:
• When the script has run to completion, you will be back to interacting with the shell51 .
• It you need to interrupt a running python script, you can press Ctrl-C in the Terminal.
• You can specify absolute or relative pathnames52 to specify the location of the script:

python ~/PCBS/games/matches.py

Note: The directory from which you started the script is the current working directory: it will
be the root for any relative path names that may be used within the script.
• A good practice is to systematically take a glance to the code before running it. Depending on your
system, you might be able to do this with the commands cat filename.py or less filename.
py or micro filename.py.

7.2 Testing a short piece of python code

To quickly test some Python code, type ipython (“interactive Python”) on a command line.
Then press ‘Return’; you should obtain a should display like the following:
A blinking cursor after [1]: indicates that ipython is ready and waiting for you to enter a Python statement that it will
execute as soon as you press the “Return” key. For example, try:

2 ** 5
2 ** 64

import turtle
turtle.circle(50)
turtle;forward(100)
turtle.circle(50)

turtle.right(90)
turtle.forward(100)
turtle.right(90)
turtle.heading()

import matplotlib.pyplot as plt

import numpy as np
t = np.linspace(0, 30, num=3001)
plt.plot(t, np.sin(t))

A Window should open with a graphical representation of the sine function, You can press ‘q’ in this Window to close it.
It is possible to execute a python script from within ipython. While in ipython, try:
51 https://linuxcommand.sourceforge.net/lc3_learning_the_shell.php)
52 https://www.geeksforgeeks.org/absolute-relative-pathnames-unix/

46 Chapter 7. Running Python

 Programming for Cognitive and Brain Sciences

7.2. Testing a short piece of python code 47

Programming for Cognitive and Brain Sciences

pwd
cd PCBS/games
%run matches.py

Finally, To quit ipython, type quit() or press Ctrl-D .

This approach is fine if you need to quickly test an idea. But as soon as you quit ipython, you lose all what you have
done.
To keep track of your work, you need to use a code editor and the Edit-Run approach.

7.3 Write code with a text editor (Edit-run cycle)

A script is nothing but a pure text file, that is, a sequence of characters.
A Python script is written with a text editor, saved on the disk, and then executed.
1. Open a Text-Editor (e.g. Sublime Text) and a Terminal window side-by-side:

2. Create a New File in the Editor and enter the following text:

import turtle
turtle.forward(50)
turtle.left(120)
turtle.forward(100)
turtle.left(120)
turtle.forward(100)
turtle.left(120)
turtle.forward(50)

3. Using ‘File/Save as’, save the this text under the filename myscript.py in your personal (home) directory

48 Chapter 7. Running Python

 Programming for Cognitive and Brain Sciences

• run with a python interpreter, by typing python myscript.py on a command line of the Terminal. Try it
now.
Important: you must make sure that the current working directory of the terminal is the same directory where the file
myscript.py has been saved. Otherwise, you will get an error message such as ‘No such file or directory’. To fix this
problem, you must use the cd command to navigate the directory structure53 .
Remarks:
• You can learn more about Turtle graphics by reading the documentation at https://docs.python.org/2/library/turtle.
html
• WINDOWS Only: To be able to start ‘Sublime Text’ from the command line by just typing subl, copy the
following command:
export PATH=”/c/Program Files/SublimeText 3/”:”$PATH”
in the file $HOME/.bash_profile (create it if necessary)

7.4 Using an Integrated Development Environment (IDE)

Some people like to work within a single application and avoid going back and forth from the text editor to the terminal.
The Anaconda Python distribution comes with and integrated development environment (IDE), Spyder54 , which provides
an environment somewhat similar to the MATLAB IDE. PyCharm55 and Microsoft Visual Code56 are two other popular
(and more powerful) IDEs.
Visual Code, PyCharm, Spyder… are very nice IDEs but you should not use them to run python scripts that open new
graphics windows (e.g. scripts using tkinter, pygame, …) because, when such scripts crash, they can leave the IDE
in an unstable state. It is always safer to run a script directly from the command line in a terminal windows.
One commendable approach is to use an IDE to edit python code, but use the command line to run the scripts.

7.5 Perform an interactive data analysis with jupyter-notebook or

jupyter-lab

To perform data analyses and produce nicely formatted reports, one can use jupyter-notebook or jupyter-lab
(see https://jupyter.org/).
In practice, launch Jupyter Notebook from the Start Menu/Anaconda3 (in Windows) or type jupyter notebook in
a terminal (Linux, MacOS). The “Jupyter homepage” should then open in your browser:
Clicking New and selecting Python [root] will open a new tab containing a notebook where you can enter python
code inside so-called ‘cells’. To execute the code in a cell, just move the cursor there and press Ctrl+Enter
A nice feature of the Jupyter notebooks is persistence, i.e. they are saved automatically (in .ipynb files) and you can go
on working on the same notebook whn you reopen it. This is also very handy, for example, to send a data analysis report
by email.
Jupyter’s documentation is available at http://jupyter.readthedocs.io/en/latest/index.html
53 http://linuxcommand.sourceforge.net/lc3_lts0020.php
54 https://www.spyder-ide.org/
55 https://www.jetbrains.com/pycharm/
56 https://code.visualstudio.com/

7.4. Using an Integrated Development Environment (IDE) 49

Programming for Cognitive and Brain Sciences

Fig. 1: The “Spyder” Integrated Development Environment

50 Chapter 7. Running Python

 Programming for Cognitive and Brain Sciences

7.6 Developping in Python with Emacs

Action Shortcut Function

Comment or Uncomment M-; comment-dwim
cleverly
Indent C-> python-indent-shift-right
Unindent C-< python-indent-shift-left
Navigate the function defi- C-c C-j imenu
nitions
Move backward to block M-a python-nav-backward-block
Move forward to block M-e python-nav-forward-block
Checking for errors, etc. flymake
Checking for errors, etc. flycheck
Reformat code to best yapify
practices
Launch the Python Debug- pdb
ger (Pdb57 )

Note: I am actually using Spacemacs58 with the python layer59

See also https://realpython.com/emacs-the-best-python-editor/

57 https://realpython.com/python-debugging-pdb/#essential-pdb-commands
58 https://www.spacemacs.org/
59 https://develop.spacemacs.org/layers/+lang/python/README.html

7.6. Developping in Python with Emacs 51

Programming for Cognitive and Brain Sciences

52 Chapter 7. Running Python

 CHAPTER

EIGHT

CODING EXERCISES

Contents

• Coding Exercises
– Flow control
∗ Shining
∗ Multiplication tables
∗ Taxis
∗ Estimation of PI by a Monte-Carlo method
∗ Computer-guess-a-number
– Lists
∗ Prime numbers
∗ Pascal triangle
– Functions
∗ Convert temperatures from Fahrenheit to Celcius and vice-versa.
∗ Permutations
∗ Eight queens puzzle
– Strings
∗ Pseudowords
– Dictionaries
∗ unique
∗ word count
∗ Anagrams
– File reading and writing
∗ head
∗ tail
∗ string-detector
∗ Kaprekar numbers

53
Programming for Cognitive and Brain Sciences

∗ RPN Calculator
∗ Rodrego-simulator
∗ Cellular automata
∗ Analysis of a Signal Detection Experiment

(Note: Solutions to most exercises are available in https://github.com/chrplr/PCBS/tree/master/coding-exercises )

8.1 Flow control

You can read about loops in Python60 , and more generally about flow control61 .

8.1.1 Shining

Write a python script that prints 1000 times the line All work and no play makes Jack a dull boy.
Check a solution at shining.py

8.1.2 Multiplication tables

Write a script that displays the tables of multiplication from 1 to 10 as a table:

1 2 3 4 5 6 7 8 9 10
2 4 6 8 10 12 14 16 18 20
3 6 9 12 15 18 21 24 27 30
4 8 12 16 20 24 28 32 36 40
5 10 15 20 25 30 35 40 45 50
6 12 18 24 30 36 42 48 54 60
7 14 21 28 35 42 49 56 63 70
8 16 24 32 40 48 56 64 72 80
9 18 27 36 45 54 63 72 81 90
10 20 30 40 50 60 70 80 90 100

Check out multiplication_table.py for a solution.

8.1.3 Taxis

Two taxi companies propose differents pricing schemes:

• Company A charges 4.80€ plus 1.00€/km
• Company B charges 3.20€ plus 1.20€/km
Write code to find which company is the cheapest as a function of the distance to travel.
Check out taxis.py
60 https://wiki.python.org/moin/ForLoop
61 https://automatetheboringstuff.com/chapter2/

54 Chapter 8. Coding Exercises

 Programming for Cognitive and Brain Sciences

8.1.4 Estimation of PI by a Monte-Carlo method

One way to estimate the value of the π is to generate a large number of random points in the unit square and see how
many fall within the unit circle; their proportion is an estimate of the area of the circle. See https://academo.org/demos/
estimating-pi-monte-carlo/
Implement the proposed algorithm to estimate the value of π.
Check out pi_monte_carlo.py

8.1.5 Computer-guess-a-number

Read chapter 3 of Invent your own games with Python62 where the author presents a game where the computer chooses
a random number that the user must guess. Study the code.
Now, your task is to write another program, where the roles are inverted: the computer tries to guess a number that the
user has in mind. The computer proposes a number and the user answers with ‘+’ (the number he has is mind is larger),
‘-’ (if it is smaller), ‘y’ (if the guess is correct)
Check a solution at computer-guess-a-number.py

8.2 Lists

These exercises require list manipulations. If you do not know Lists in Python, you can read:
• Python Lists63
• List comprehensions64
• https://automatetheboringstuff.com/2e/chapter4/
Try to solve the following exercices:
• Given a list of numbers, print their sum
• Given a list of numbers, print their product
• Given a list of numbers, print the sum of their squares
• Given a list of numbers, print the largest one.
• Given a list of numbers, print the second largest one.
After you have tried to solve these problems, you can check lists.py
62 https://inventwithpython.com/invent4thed/chapter3.html
63 https://www.w3schools.com/python/python_lists.asp
64 https://www.pythonforbeginners.com/basics/list-comprehensions-in-python

8.2. Lists 55
Programming for Cognitive and Brain Sciences

8.2.1 Prime numbers

Write a script that lists all prime numbers between 1 and 10000 (A prime number is a integer that has no divisors except
1 and itself). You can use the following function:

def is_factor(d, n):

""" True if `d` is a divisor of `n` """
return n % d == 0

Check a solution at prime-numbers.py

8.2.2 Pascal triangle

Write a program that prints the first N rows of Pascal’s triangle (see https://www.youtube.com/watch?v=
XMriWTvPXHI). For example:

1
1 1
1 2 1
1 3 3 1
1 4 6 4 1
1 5 10 10 5 1
1 6 15 20 15 6 1
1 7 21 35 35 21 7 1
1 8 28 56 70 56 28 8 1
1 9 36 84 126 126 84 36 9 1

To solve this problem, one solution is to store the values of the current line in a Python list, and write a function that given
a list as an argument, calculates and returns the following line in a new list.
Proposed solutions:
• Pascal-triangle_v1.py
• Pascal-triangle_v2.py

8.3 Functions

Read about functions in Python: - https://www.w3schools.com/python/python_functions.asp - https:

//automatetheboringstuff.com/2e/chapter3/).

8.3.1 Convert temperatures from Fahrenheit to Celcius and vice-versa.

• Read https://en.wikipedia.org/wiki/Fahrenheit and write a function that converts a temperature from Fahrenheit
to Celsius, and another one that converts from Celsius to Fahrenheit
• Add code that reads temperatures from the standard input and print the converted numbers.
A solution is available here: Fahrenheit_celsius.py.

56 Chapter 8. Coding Exercises

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8.3.2 Permutations

Generate all the permutations of a set, e.g. (1..n).

Note: This is an advanced exercise, which requires mastery of recursive functions (functions that call themselves)
A solution is proposed at generate_all_permutations.py.
To run it:

python generate_all_permutations.py 4

8.3.3 Eight queens puzzle

The eight queens puzzle is the problem of placing eight chess queens on an 8×8 chessboard so that no two queens threaten
each other; thus, a solution requires that no two queens share the same row, column, or diagonal. See https://en.wikipedia.
org/wiki/Eight_queens_puzzle
As there can be only one queen per column and per row, a winning solution can be represented by a set of 8 numbers,
one per line, which represent the column in which there is a queen. Because the columns must be different, the solutions
are a subset of the permutations of 8 numbers. We just have to check that no two queens are in the same diagonal.
In Python, you can get all the permutations of a set, with the permutations function from the itertools module

from itertools import permutations

list(permutations(range(3))

For a solution to the eight queens problem, check out https://code.activestate.com/recipes/

576647-eight-queens-six-lines/
The code is available at eight_queens.py.

8.4 Strings

8.4.1 Pseudowords

• Search the internet to find out how to generate a random integer number in a interval in Python
• Read about strings in Python at https://realpython.com/python-strings/
• Write functions that generate pseudowords from words. The first function will delete a character in a random
position from a string passed as argument. The second will insert a random character at a random position. The
third will swap two characters at random location.
• If you know about file input/output (see https://automatetheboringstuff.com/2e/chapter9/), you can read a dictio-
nary (e.g. http://www.pallier.org/extra/liste.de.mots.francais.frgut.txt) and use it to filter out any actual words.

8.4. Strings 57
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8.5 Dictionaries

8.5.1 unique

Given a list of words, print how many different words are in that list (hint: use a dictionary or a set)

liste = ['bonjour', 'chat', 'chien', 'bonjour']

n = 0
d = dict()
for e in liste:
if not e in d.keys():
d[e] = 1
n = n + 1
print(n)

print(len(set(liste))) # shortest solution using a set

8.5.2 word count

Given a list of words, count the number of times each word appears in the list. Eg. [Jim, Alan, Jim, Joe] ->
Jim:2, Alan:1, Joe:1 (hint: use a dictionary)

liste = ['Jim', 'Alan', 'Jim', 'Joe']

counts = dict()
for word in liste:
if word in counts.keys():
counts[word] += 1
else:
counts[word] = 1
print(counts)

8.5.3 Anagrams

Two words are anagrams if they contain the same letters in different orders, e.g., binary and brainy.
• write a function that take two strings as arguments and returns True if they are anagrams.
• Given a list of words, print all subsets that form anagrams.
Check my solution at anagrams.py. Running:

python anagrams.py < liste.de.mots.francais.frgut.txt

will list all anagrams in French! (liste.de.mots.francais.frgut.txt contains a list of French words)

58 Chapter 8. Coding Exercises

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8.6 File reading and writing

Read the chapter about files reading and writing at https://automatetheboringstuff.com/2e/chapter9/

8.6.1 head

Write a script that prints the first 10 lines of a file (or the whole file is it is less than 10 lines long).

with open('aga.txt', 'r', encoding='utf-8') as f:

for l in f.readlines()[:10]:
print(l, end='')

8.6.2 tail

Write a script that prints the last 10 lines of a file (or the whole file is it is less than 10 lines long).

with open('aga.txt', 'r', encoding='utf-8') as f:

all_lines = f.readlines()
for l in all_lines[-10:]:
print(l, end='')

8.6.3 string-detector

Read Chap. 8 of Automate the boring stuff65 .

Write a script that opens and read a text file, and print all the lines that contain a given target word, say, cogmaster.
Check out search-file.py

8.6.4 Kaprekar numbers

A Kaprekar number is a number whose decimal representation of the square can be cut into a left and a right part (no nil)
such that the sum of these two parts gives the number initial. For example:
• 703 is a number of Kaprekar in base 10 because 703² = 494 209 and that
494 + 209 = 703.
• 4879 is a number of Kaprekar in base 10 because 4879² = 23 804 641 and
04641 + 238 = 4879
Write a program that returns all Kaprekar numbers between 1 and N.
Solution: Kaprekar-numbers.py
65 http://automatetheboringstuff.com/chapter8/

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Programming for Cognitive and Brain Sciences

8.6.5 RPN Calculator

Write a reverse Polish arithmetic expression evaluator (See https://en.wikipedia.org/wiki/Reverse_Polish_notation).

E.g. 3 4 * 5 - evaluate to 7.
Solution: rpn-calculator.py

8.6.6 Rodrego-simulator

Write a Python script that simulates a RodRego machine66 with 10 registers. The program is stored in a string or in file
that is read and then executed. Your program must contain a function which, given the 10 initial values of the registers,
and the program, returns the new register values when the END command is reached.
Check two possible solutions: - rodrego_maxime_caute.py - rodrego_christophe_pallier.py

8.6.7 Cellular automata

Implement a 1-dimension elementay cellular automata67 . (Further reading: https://en.wikipedia.org/wiki/A_New_Kind_

of_Science)
Solution: 1d-ca.py

8.6.8 Analysis of a Signal Detection Experiment

In a signal detection experiment, a faint stimulus (e.g. a faint sound or a faint visual target) is presented or not at each
trial and the participant must indicate whether he has perceived it or not. There are four possible outcomes for each trial:
• A hit occurs when the participant correctly detects the target.
• A miss occurs when the target was there but the participant did not detect it.
• A false alarm occurs when the participant reports the presence of the target when it was not actually there.
• A correct rejection occurs when the participant correctly reports that the target was not present.
One defines;
• The hit rate, equal to #hits / (#hits + #misses)
• The false alarm rate, equal to #false alarms / (#false alarms + # correct rejections)
Let us first suppose that the data from a participant is represented as a string. This string represents a series of trials, each
trial being represented by two characters indicating the trial type (1=target present, 0=target absent) and the participant’s
response (Y=target perceived, N=No target perceived). For example:
data = "0Y,0N,1Y,1Y,0N,0N,0Y,1Y,1Y"

Exercise:
• Write a function which, given such a string, returns the Hit rate and the False rate.
• Now, the results from different participants are stored in different files subj*.dat (download the files from
https://github.com/chrplr/PCBS/tree/master/coding-exercises/subjdat.zip`) Write a script that computes the hit
rates and false alarms for each subject, and displays the group averages and standard deviations.
Solution sdt.py
66 http://sites.tufts.edu/rodrego/
67 https://en.wikipedia.org/wiki/Elementary_cellular_automaton

60 Chapter 8. Coding Exercises

 CHAPTER

NINE

AUTOMATA AND COMPUTERS

Contents

• Automata and Computers

– The Computational Theory of Mind
– What is computation anyway ?
– The ancestors of the computer: the automata
– Formal description of an automaton
– Examples of transition diagrams
– What is a Computer?
– Register machines
∗ Exercice: implementation of a Register machine
– The Seven secrets of computers revealed
– Programmable computers
– Compilation and interpretation
– Operating systems
– What is a Terminal?

9.1 The Computational Theory of Mind

Cognitive science founding disciplines :

• Psychology
• Linguistics
• Philosophy of mind
• Neurosciences
• Computer science (Cybernetics + AI)
Could a machine think? Could the mind itself be a machine?

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Programming for Cognitive and Brain Sciences

Computers were designed to simulate the mental operations realized by a human mathematician performing a… compu-
tation (see Alan Turing)
The Computational Theory of Mind has been defended and attacked many times.
More readings:
• Zylberberg, Ariel, Stanislas Dehaene, Pieter R. Roelfsema, and Mariano Sigman. 2011. “The Human Turing
Machine: A Neural Framework for Mental Programs.” Trends in Cognitive Sciences
• Van Gelder, Tim. 1995. “What Might Cognition Be, If Not Computation?:” Journal of Philosophy 92 (7): 345–81.
• Jerry Fodor The Mind does not work that way
• Douglas Hoftstader Gödel, Escher & Bach: an eternal golden braid and I am a strange loop

9.2 What is computation anyway ?

One common answer is:

“Computation is what a Turing machine can do”
But what is a Turing machine?

9.3 The ancestors of the computer: the automata

An automaton is a device designed to automatically follow a predetermined sequence of operations.

(see Descartes’ Les Animaux Machines Lettre au Marquis de Newcastle68

9.4 Formal description of an automaton

At a abstract level, an automaton can be formally described by:

• a set of internal states
• a transition table (or diagram) that describes the events that lead to changes from one state to the other state.

9.5 Examples of transition diagrams

A Finite State Automaton can be used to generate or recognize regular languages.

In Formal Language Theory, a language is a set of strings.
Examples:
• { a, aa, ab, ba, aab, bab, …}
• { ha!, haha!, hahaha!, hahahaha!, …}
• { ab, aabb, aaabbb, … }
• { the set of grammatical English sentences}
68 http://www.ac-grenoble.fr/PhiloSophie/logphil/oeuvres/descarte/newcastl.htm

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9.5. Examples of transition diagrams 63

Programming for Cognitive and Brain Sciences

Fig. 1: Examples of Automata: A vending machine, A clock, Vaucanson’s duck

Fig. 2: Diagram and Tabular representation of a finite state automaton

Fig. 3: The change counter of a vending machine

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Fig. 4: Transition Diagram for the lyrics of Hey Jude

9.5. Examples of transition diagrams 65

Programming for Cognitive and Brain Sciences

Fig. 5: Algorithm to decide if you must use “du” or “sie” in German

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 Programming for Cognitive and Brain Sciences

Fig. 6: A (Probabilistic) Finite state diagram for Bengalese Finch songs (Berwick et al., 2011 Trends in Cognitive Sciences)

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Programming for Cognitive and Brain Sciences

9.6 What is a Computer?

A computer is basically an automaton augmented with a memory store.

This is particularly clear in the case of the Turing machine, a mathematical model of computation (Turing offered the
Turing machine as an analysis of the activity of an (idealised) human mathematician engaged in computing).

Fig. 7: A Turing machine = FSA + memory store

A Turing machine is a finite state machine augmented with a tape and a mechanism to read/write on it.
Read Roger Penrose’s chapter’s on Turing machines and https://en.wikipedia.org/wiki/Turing_machine. You may laos
read the Alan Turing’s seminal paper69 .

Fig. 8: A table describing a Turing machine: try to simulate it.

Other computing machines have been invented, yet:

“All attempts to give an exact analysis of the intuitive notion of an effectively calculable function have turned out to be
equivalent, in the sense that each analysis offered has been proved to pick out the same class of functions, namely those
that are computable by Turing machine.
The concept of effective calculability has turned out to be formalism-independent, in that all these different formalisms
pick out exactly the same class of functions.” (B. Jack Copeland “The Church-Turing thesis” in Stanford Encyclopedia of
Philosophy Archive)
Another computing model which is closer to actual computers, is the register machine.
69 https://londmathsoc.onlinelibrary.wiley.com/doi/pdf/10.1112/plms/s2-42.1.230

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9.7 Register machines

Read The seven secrets of computer power revealed (Chapter 24 from Daniel Dennett’s Intuition Pumps and other tools
for thinking)
The RogRego computer possesses:
• a bank of registers, or memory locations, each with a unique address (1, 2, 3, …), and each able to have, as content,
a single integer (0, 1, 2, …)
• a processing unit can execute instructions in a stepwise, one-at-a-time fashion. The processor knows only 3 in-
structions:
1. End: finishes the programs
2. Increment register with 2 arguments:
– a register number to increment by 1
– a step (line) number to jump to when the increment is complete
3. Decrement register and Branch with 3 arguments:
– a register number to decrement by 1
– a step number to jump if the register contains a non null value.
– a step number to jump if the register contains 0
An online demo is available at http://proto.atech.tufts.edu/RodRego/
You can enter the following program “ADD[0,1]”, on a machine where Reg0 contains 4 and Reg1 contains 7. Try to
explain what it is doing:

1 DEB 0 2 3
2 INC 1 1
3 END

…
This program adds the content of register 0 to register 1 (destroying the content of 0)
…
Exercice: write a program Program 2 “MOVE[4,5]” that moves the content of reg4 intro reg5
…

1 DEB 5 1 2
2 DEB 4 3 4
3 INC 5 2
4 END

…
Program 3 “COPY[1,3]” copies the content of reg1 into reg3, leaving reg1 unchanged:

1 DEB 3 1 2
2 DEB 4 2 3
3 DEB 1 4 6
4 INC 3 5
5 INC 4 3
6 DEB 4 7 8
(continues on next page)

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Programming for Cognitive and Brain Sciences

(continued from previous page)

7 INC 1 6
8 END

Program 4 (NON DESTRUCTIVE ADD[1,2,3]):

1 DEB 3 1 2
2 DEB 4 2 3
3 DEB 1 4 6
4 INC 3 5
5 INC 4 3
6 DEB 4 7 8
7 INC 1 6
8 DEB 2 9 11
9 INC 3 10
10 INC 4 11
11 DEB 4 12 13
12 INC 2 11
13 END

…
Note that conditional branching is the key instruction that gives the power to the machine. Depending on the content of
memory, the machine can do either (a) or (b).

9.7.1 Exercice: implementation of a Register machine

Write a Python script that simulates a RodRego machine70 with 10 registers. The program is stored in a string or in file
that is read and then executed. Your program must contain a function which, given the 10 initial values of the registers,
and the program, returns the new register values when the END command is reached.
Check two possible solutions: - rodrego_maxime_caute.py - rodrego_christophe_pallier.py
—

9.8 The Seven secrets of computers revealed

1. Competence without comprehension. A machine can do perfect arithmetic without having to comprehend what it
is doing.
2. What a number in a register stands for depends on the program
3. The register machine can be designed to discriminate any pattern that can be encoded with numbers (e.g. figures,
text, sensory inputs,…)
4. Programs can be encoded by numbers.
5. All programs can be given a unique number which can be treated as a list of instructions by a Universal Machine.
6. all improvements in computers over Turing machine (or Register machine), are simply ways of making them faster
7. There is no secret #7
70 http://sites.tufts.edu/rodrego/

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9.9 Programmable computers

• The first computers were not programmable. They were hardwired!

• An important milestone was the invention of the programmable computer:
– a program is a set of instructions stored in memory.
– Loaded and executed by a processor.
– Such programs are written in machine langage (the language of the processor)

9.10 Compilation and interpretation

Programs written in higher=level languages (rather than Machine language) can be either:
= compiled, or = interpreted
In both cases, you write the program as text files called source files.
A compiler translates the program into an executable file in machine language. The executable file is standalone, that is,
the source code is not needed.
An interpreter reads the file and execute the commands one by one. It is slower, but easier to interact with. Disatvantage:
you need the interpreter to exectute it.

Fig. 9: Interpretation and compilation

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9.11 Operating systems

In the first computers, there was only one program running. One would load the program into memory, then run it until
it halted. Several Programs were ran in batch mode, in a sequence.
Then, it was realized that computers could time-share between programs, allowing several users (or programs) to share
the computer.
This requires an operating systems (O.S.). The O.S. is the first program that loads into the computer during the boot.
When running:
• The OS controls the hardware (screen/printer/disk/keybord/mouse,…) (drivers)
• The OS manages all the other programs (processes/tasks/applications).
– sharing memory
– allocating processors and cores
– allocating time
Check out Task Manager (Windows)/System Monitor (Linux)/ Activity Monitor (Mac)

Fig. 10: Three popular operating systems

Different OSes offer different “views” of the computer (e.g. 1 button mouse in Mac, 2 in Windows, 3 in Linux), so often
programs are designed to work on one OS (bad!). Prefer multiplatform software (like Python).
Several OS can be installed in a given machine:
• choice at boot (multiboot)
• an OS can run inside a virtual machine, that is a program running in another (or the same) OS, and emulating a
full computer.

9.12 What is a Terminal?

Terminal (or console): originaly, a device comprising a keyboard and screen, allowing a human to interact with a com-
puter.
Remarks:
Before keyboards and screens, there were punchcards and printers:
Historically, terminals used to be a dumb screen/keyboard connected to a central computer.

72 Chapter 9. Automata and Computers

 Programming for Cognitive and Brain Sciences

Fig. 11: Terminals

Fig. 12: Early computers had no keyboard, no screen. The input was done through punched cards and output would be
printed out

9.12. What is a Terminal? 73

Programming for Cognitive and Brain Sciences

In the mainframe era, many terminals were connected to a single, powerful, computer. Everybody was sharing the same
computer
With the advent of Personal Computers, the terminal and the computer became a single apparatus.
However, terminals can be virtual. A terminal is a program that let you run text programs. You interact by typing and
displaying text. No graphical interface/no mouse.
When you open a terminal, a program called a shell71 is started that displays a prompt, waiting for you to enter commands
with the keyboard.

Fig. 13: Picture of a ‘virtual’ terminal in Linux

71 http://en.wikipedia.org/wiki/Shell_%28computing%29

74 Chapter 9. Automata and Computers

 CHAPTER

TEN

REPRESENTATIONS OF NUMBERS, TEXT, IMAGES

Contents

• Representations of numbers, text, images

– Representation of integers
∗ From binary to decimal
∗ From decimal to binary
– Representation of text
∗ Strings
∗ search/replace a substring within a string
∗ splitting a strings at delimiters
∗ Interactive input from the command line
∗ Reading and writing to text files
∗ Counting lines and words in a text file
– Representation of images
∗ Grey level pictures
∗ Colored bitmaps

10.1 Representation of integers

There are 10 kinds of people: those who count in binary and the others.
Computers represent everything as series of 0 and 1, also known as bits (for “binary digits”).
A number represented in basis ‘b’ by four digits ‘d3 d2 d1 d0 ’, has a value of: d3 .b3 + d2 .b2 + d1 .b1 + d0 .b0
• In binary, there are only two possibilities for the digits: {0, 1}
• In decimal, there are 10 possible characters
• In hexadecimal, 16 possible characters 0-9, A, B, C, D, E, F:: D8F1 = 14*16^3 + 8*10^2 + 15*16^1
+ 1*16^0
Just like a number can be written in base 10, it can be written in base 2 (or in any other base):

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Programming for Cognitive and Brain Sciences

12 = 10 + 2 = 1.(10^1) + 2.(10^0) => '12' in base 10

12 = 8 + 4 = 2^3 + 2^1 => '1010' in base 2

33 = 30 + 3 = 3.(10^1) + 3.(10^0) => '33' in base 10

33 = 32 + 1 = 2^5 + 2^0 => '100001' in base 2

Here are the binary representions of the first integers:

0 : 0
1 : 1
2 : 10
3 : 11
4 : 100
5 : 101
6 : 110
7 : 111
...

To learn more about how integer numbers are represented in binary format, you can check out http://csunplugged.org/
binary-numbers
Exercise 1: Convert (manually) into decimal the following binary numbers:
• 101
• 1000
• 1011
• 11111111
…
Answers: 5, 8, 11, 255

10.1.1 From binary to decimal

Exercise 2: Let us write a function that, given the binary representation of a

number as a string of 0 and 1, returns its value as a integer.
1. Let us first suppose that we want to convert a string containing exactly 8 binary digits (e.g. ‘01011010’) into decimal.
How would you do that?
…

def todec8bits(s):
""" converts a 8 bits string (binary representation)into a integer """
return int(s[0])*128 + int(s[1])*64 + int(s[2])*32 + \
int(s[3])*16 + int(s[4])*8 + int(s[5])*4 + \
int(s[6])*2 + int(s[7])

todec8bits("00001010")
todec8bits("01010101")

One issue with this code is that it handles only 8 bits strings

todec8bits("0101010")
todec8bits("010101010")

76 Chapter 10. Representations of numbers, text, images

 Programming for Cognitive and Brain Sciences

A better version of the fonction would be:

def todec8bits(s):
""" converts a 8 bits string (binary representation)into a integer """
assert len(s) == 8 # 's' should be exactly 8 bits long
return int(s[0])*128 + int(s[1])*64 + int(s[2])*32 + \
int(s[3])*16 + int(s[4])*8 + int(s[5])*4 + \
int(s[6])*2 + int(s[7])

Remark: On your computers, integers are represented either as 32 or 64 bits, depending on your processor/operating
system.
Why is this is relevant? Suppose you perform an EEG recording with 256 electrodes every milliseconds for one hour.
How large is the data?
Beware: in some programming languages, the computer can make mistakes if you add too large numbers!
Here is another solution demonstrating several python features (list comprehensions, zip constructions, increment operator,
…):

def todec(s):
""" converts a 8 bit strings into an integer """
assert len(s) == 8 # 's' should be exactly 8 bits long
pow2 = [2 ** n for n in range(7, -1, -1)]
n = 0
for b, p in zip(s, pow2):
n += int(b) * p
return n

…
Exercise: modify the function above to handle strings of any size as input.
Here is a code that works with strings of unlimited size:

def todec(s):
""" convert a string of 0 and 1 representing a binary number into an integer """
n = 0
for b in s:
n = n * 2 + int(b)
return n

for i in ['101', '1000', '1011', '11111111']:

print(todec(i))

Can you understand how/why it works ?

10.1.2 From decimal to binary

Now we will go in the other direction: Our aim is to write a program that, given a number (in decimal), computes its
binary representation.
Exercise: If you have an idea how to program it, please proceed. Else, I propose that you follow the following steps:
Examine the script below and execute it for various values of the variable num. Note that the sign % stands for the modulo
division operation which produces the remainder of an integer division. If x and y are integers, then the expression x %
y yields the remainder when x is divided by y.
Do you understand the last line? Do you see a limitation of this program?

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Programming for Cognitive and Brain Sciences

num = 143
d3 = int(num/1000) % 10 # thousands
d2 = int(num/100) % 10 # hundreds
d1 = int(num/10) % 10 # dec
d0 = num % 10
print(str(d3) + str(d2) + str(d1) + str(d0))

Adapt the above program to print the binary representation of num

…

num = 17
b0 = num % 2
b1 = int(num/2) % 2
b2 = int(num/4) % 2
b3 = int(num/8) % 2
b4 = int(num/16) % 2
b5 = int(num/32) % 2
b6 = int(num/64) % 2
b7 = int(num/128) % 2
b8 = int(num/256) % 2
print(str(b8) + str(b7) + str(b6) + str(b5) + str(b4) + str(b3) + str(b2) + str(b1)␣
,→+ str(b0))

…
(6) Modify the above program to print the binary representations of all the integers between 0 and 255.
…

def tobin(num):
""" Returns the binary represention (strings of bits) of a 0 <= num <= 255 """
b7 = int(num/128) % 2
b6 = int(num/64) % 2
b5 = int(num/32) % 2
b4 = int(num/16) % 2
b3 = int(num/8) % 2
b2 = int(num/4) % 2
b1 = int(num/2) % 2
b0 = num % 2
return (str(b7) + str(b6) + str(b5) + str(b4) + \
str(b3) + str(b2) + str(b1) + str(b0))

for n in range(256):
print(n, ':', tobin(n))

…
(7) (Advanced) Write an improved version that uses a loop and does not have a limitation in size.
…

def binary(n):
""" returns the binary representation of ``n`` """
if n == 0:
return '0'
s = ''
while n > 0:
b = str(n % 2)
(continues on next page)

78 Chapter 10. Representations of numbers, text, images

 Programming for Cognitive and Brain Sciences

(continued from previous page)

s = b + s
n = n // 2
return s

…
(8) Study the following code. Do you understand why it works?

def binary(num):
""" returns the binary representation of ``num`` """
if num == 0:
return '0'
if num == 1:
return '1'
return(binary(int(num /2)) + binary(num % 2))

print(binary(1234))

…
Answer: It is a recursive function which calls itself. See http://en.wikipedia.org/wiki/Recursion_%28computer_
science%29
…
Remark: measures of memory size
• 1 byte = 8 bits
• 1 Kilobyte (KB) = 1024 bytes
• 1 Megabyte (MB) = 1024 kbytes = 1048576 bytes
• 1 Gigabytes (GB) = 1024 Mbytes
• Terabyte, Petabyte, Exabyte…
Exercise (advanced): Write a function that return the hexadecimal representation (base 16) of a number.
To go further:
• If you want to know how negative integer numbers are represented, see http://en.wikipedia.org/wiki/Two%27s_
complement
• To understand how real numbers (a.k.a. “floats”) are encoded, read What Every Programmer Should Know About
Floating-Point Arithmetic72 and https://docs.python.org/2/tutorial/floatingpoint.html#tut-fp-issues

10.2 Representation of text

A text file is nothing but a sequences of characters.

For a long time, characters were encoded using ASCII code.
In Python, you can know the code of a character with the function ord:

print(ord('a'))
print(ord('@'))

72 http://floating-point-gui.de/

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Fig. 1: ascii table

The inverse of ord is chr.

(9) lookup the ASCII representation of your first name in the table and use the chr function of Python to print it.
…
For example, if you name is ‘ZOE’, you would type:

print(chr(90)+chr(79)+chr(69))

Remark: ASCII codes use one byte (=8bits) per character. This is fine for English, but cannot cover all the caracters of
all alphabets. It cannot even encode french accented letters.
Unicode was invented that associate a unique 2 bytes number to each character of any human script. It is possible to
write text files using these number, but more economic to encode the most common letters with one byte, and keep the
compatibility with ASCII (UTF-8).

print("".join([chr(c) for c in range(20000, 21000)]))

10.2.1 Strings

In Python, text can be stored in objects called strings.

String constants are enclosed between single quotes:

'Bonjour le monde!'

Or double quotes:

80 Chapter 10. Representations of numbers, text, images

 Programming for Cognitive and Brain Sciences

"Bonjour le monde !"

Or “triple” quotes for multilines strings:

"""
Bonjour le monde!

Longtemps je me suis levé de bonne heure,

Les sanglots longs des violons,
...
"""

They have a type str:

type('bonjour')

To convert an object to a string representation:

str(10)
a = dict((("a",1), ("b",2)))
str(a)

A string is nothing but a sequence of characters:

a = 'bonjour'
print(a[0])
print(a[1])
print(a[2])
print(a[2:4])
print(len(a))

for c in 'bonjour':
print(c)

Operations on strings:
a = 'bonjour'
b = 'hello'
a + b
a + ' ' + b

A set of functions to manipulate strings is available in the module ‘string’:

str.upper(a)
str.lower('ENS')

10.2.2 search/replace a substring within a string

a = 'alain marie jean marc'

print(a.find('alain'))
print(a.find('marie'))
print(a.find('ma'))
print(a.find('marc'))
print(a.find('o'))

(continues on next page)

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(continued from previous page)

a.replace('marie','claude')
print(a)

10.2.3 splitting a strings at delimiters

a = 'alain marie jean marc'

a.split(" ")

Read https://docs.python.org/3/library/stdtypes.html#string-methods to learn about more string functions.

10.2.4 Interactive input from the command line

name = input('Comment vous appelez-vous ? ')

print("Bonjour " + name + '!')

10.2.5 Reading and writing to text files

1. With Atom, create a text file containing a few lines of arbitrary content, an save it under the filename ‘test.txt’
2. with ipython running in the same directory where you saved test.txt

with open('test.txt', 'r') as f:

o = f.read()
print(o)
lines = o.split("\n")
print(lines)

10.2.6 Counting lines and words in a text file

Download Alice in Wonderland73

with open('alice.txt') as f:
o = f.read()
print(o)
lines = o.split("\\n")
print(lines)

Exercise: Write a program that counts the number of lines, and number of
words in alice.txt (we suppose that words are separated by spaces).
…

with open('alice.txt') as f:
o = f.read()
print(o)
lines = o.split("\n")

nlines = len(lines)
(continues on next page)
73 http://www.umich.edu/~umfandsf/other/ebooks/alice30.txt

82 Chapter 10. Representations of numbers, text, images

 Programming for Cognitive and Brain Sciences

(continued from previous page)

nw = 0
for l in lines:
nw += len(l.split(" "))

print(nlines)
print(nw)

(11) Write a program that detects if a text file contains the word ‘NSA’
…

def spot_nsa(filename):
""" detects if the text file pointed to by filename contains 'NSA' """
with open(filename) as f:
o = f.read()
lines = o.split("\n")
found = False
for l in lines:
if "NSA" in l.split(" "):
found = True
break
return found

10.3 Representation of images

Images can be stored either:

• as bitmaps, that is a two dimensional arrays of dots (formats: bmp, png, gif, jpeg…)
• as vectorized formats, the image contain instruction for drawing objects (eps, pdf, svg, …).
Here we are just going to manipulate bitmaps.
Each dot (pixel) is either ‘0’ (black) or ‘1’ (white).

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Programming for Cognitive and Brain Sciences

(12) What is the size in kilobytes of a 1024x768pixels black and white image ?
…
Answer: 1024*768/8/1024=96 KB
(13) Execute the following code in ipython:

import numpy as np
import matplotlib.pyplot as plt

a = np.array([[0, 0, 0, 0, 0, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 0, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0]])
plt.imshow(a, cmap=plt.cm.gray, interpolation='nearest')
plt.show()

Numpy’s arrays are a new type of object. There are similar to lists, but optimised for mathematical computations. Notably,
they can be multidimensional (i.e. you can use a[i,j] notation). You can learn more about arrays in the documents https:
//scipy-lectures.org/ and https://www.projectpro.io/data-science-in-python-tutorial/numpy-python-tutorial
Here is another example:
…

a = np.zeros((200,200))
for i in range(200):
a[i, i] = 1
plt.imshow(a, cmap=plt.cm.gray, interpolation='nearest')
plt.show()

a[0:200:2,] = 1
plt.imshow(a, cmap=plt.cm.gray, interpolation='nearest')
plt.show()

84 Chapter 10. Representations of numbers, text, images

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10.3.1 Grey level pictures

Each dot is now associated to an integer value, e.g. ranging from 0 to 255 for 8-bits codes, coding for a grey level
(smaller=darker). Each dot needs one byte.
How large is the file for an image 1024x768 pixels with 256 grey levels?
The following code displays an image:

from skimage import data

from skimage.color import rgb2gray

original = data.astronaut()
grayscale = rgb2gray(original)
plt.imshow(grayscale, cmap=plt.cm.gray)
plt.show()

This code runs a low pass (averaging) filter on it:

import scipy.ndimage
bl = scipy.ndimage.gaussian_filter(grayscale, 3)
plt.imshow(bl, cmap=plt.cm.gray)
plt.show()

Edge detector It is easy to implement an edge detector with a neural network. See https://courses.cit.cornell.edu/
bionb2220/UnderstandingLateralInhibition.html.
Using the ndimage.convolve function, apply the following filters to the image and diplay the results.

from skimage import data

from skimage.color import rgb2gray

original = data.astronaut()
grayscale = rgb2gray(original)

kernel1 = np.array([[-1, -1, -1],

[-1, 8, -1],
[-1, -1, -1]])

bl = scipy.ndimage.convolve(grayscale, kernel1)
plt.imshow(bl, cmap=plt.cm.gray)
plt.show()

kernel2 = np.array([[-1, -1, -1, -1, -1],

[-1, 1, 2, 1, -1],
[-1, 2, 4, 2, -1],
[-1, 1, 2, 1, -1],
[-1, -1, -1, -1, -1]])
bl=scipy.ndimage.convolve(grayscale, kernel2)
plt.imshow(bl, cmap=plt.cm.gray)
plt.show()

More manipulations are available at http://scipy-lectures.github.io/advanced/image_processing/.

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10.3.2 Colored bitmaps

Each dot is now associated to three bytes, representing the Red, Gree and Blue intensities (see http://www.colorpicker.
com/).
How large is the file for a 1024x768 RGB image?
Exercice: What are the RGB triplets for BLACK, WHITE, RED, YELLOW?

from skimage import data

plt.imshow(data.astronaut())
plt.show()

86 Chapter 10. Representations of numbers, text, images

 CHAPTER

ELEVEN

CREATING STIMULI

Contents

• Creating stimuli
– Static visual stimuli
∗ Displaying geometric shapes
∗ Troxler effect
∗ Kanizsa illusory contours
∗ Herman grid
∗ Extinction illusion
∗ Ebbinghaus-Titchener
∗ Fixation cross
∗ Hering illusion
∗ Random-dot stereograms
∗ Kitaoka visual illusions
∗ Stroop Effect
– Dynamic visual stimuli
∗ Illusory line-motion
∗ Flash-lag illusion
∗ Dynamic version of the Ebbinghaus-Titchener
∗ Lilac Chaser
– Creating and playing sounds
∗ Shepard tone
∗ Sound localisation from binaural dephasing
∗ Pulsation (Povel & Essen, 1985)
– More illusions

87
Programming for Cognitive and Brain Sciences

11.1 Static visual stimuli

To generate visual stimuli, we are going to rely on the Pygame74 module. You can check if it is installed on your system
by typing python on a command line and, at the >>> prompt, import pygame. If all is well, you should get the
following message:
>>> import pygame
pygame 2.0.1 (SDL 2.0.14, Python 3.8.5)
Hello from the pygame community. https://www.pygame.org/contribute.html

If, instead, you obtain a message ending in:

ModuleNotFoundError: No module named 'pygame'

you should check the instructions in Software Installation.

11.1.1 Displaying geometric shapes

Here is a Python script that opens a window and displays a square:

""" Display a square.

See https://sites.cs.ucsb.edu/~pconrad/cs5nm/topics/pygame/drawing/
"""

import pygame

# Colors are triplets containint RGB values

# (see <https://www.rapidtables.com/web/color/RGB_Color.html>
BLACK = (0, 0, 0)
WHITE = (255, 255, 255)
GRAY = (127, 127, 127)
RED = (255, 0, 0)
GREEN = (0, 255, 0)
BLUE = (0, 0, 255)

# Parameters of the Graphics Window

W, H = 500, 500 # Size of the graphic window
# Note that (0,0) is at the *upper* left hand corner of the screen.
center_x = W // 2
center_y = H // 2

pygame.init()

# Create the Graphic Window (designated by a variable `screen`)

screen = pygame.display.set_mode((W, H), pygame.DOUBLEBUF)
pygame.display.set_caption('square')

screen.fill(WHITE) # fill the window with white

# Draw a rectangle at the center of the window (in the backbuffer)

width, height = 200, 200 # dimensions of the rectangle in pixels
left_x = center_x - width // 2 # x coordinates of topleft corner
top_y = center_y - height // 2 # y coordinate of topleft corner
(continues on next page)
74 http://www.pygame.org

88 Chapter 11. Creating stimuli

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(continued from previous page)

pygame.draw.rect(screen, BLUE, (left_x, top_y, width, height))

pygame.display.flip() # display the backbuffer on the screen

# Note: this function is synonymous with `pygame.display.
,→ update()`

# Save the image into a file

pygame.image.save(screen, "square-blue.png")

# Wait until the window is closed

quit_button_pressed = False
while not quit_button_pressed:
pygame.time.wait(10)
for event in pygame.event.get():
if event.type == pygame.QUIT:
quit_button_pressed = True

pygame.quit()

Download (square.py) and run it by typing:

python square.py

Have a look at the code.

Exercise (*): make a copy of the script and modify the copy to
• change the color of the rectangle to RED
• change the size of the rectangle to 100 x 300
• comment the line pygame.display.flip() and run the script. You should realize that merely drawing something
to the display surface (screen) doesn’t cause it to appear on the screen – you need to call pygame.display.flip()
to move the surface from general memory to video memory. This will be useful when you want to make an
animation, that is, draw a sequences of images.
Have a look at:
• Pygame drawing basics75
• Pygame tutorial76
• Pygame’s on-line documentation77
It is of course possible to draw other shapes. Check out for example the two scripts: - circle.py and - triangle.py
Exercice (*): modify circle.py to draw two circles, one red and on blue, side-by-side

(solution in two_circles.py)
Exercise (*): Note that the circles above are filled with the color (actually, they are disks). Browse Pygame online
documentation78 to find how to color the circumference of the circle and keep its inner part white.
75 https://ryanstutorials.net/pygame-tutorial/pygame-shapes.php
76 https://pygame.readthedocs.io/
77 https://www.pygame.org/docs/
78 https://www.pygame.org/docs/

11.1. Static visual stimuli 89

Programming for Cognitive and Brain Sciences

Fig. 1: Two Circles

11.1.2 Troxler effect

Fixate your gaze at the center of the picture below for 30 seconds

What happened after a few seconds? This is the fill-in phenomenon (See https://en.wikipedia.org/wiki/Filling-in).
Exercise (*): Program the Troxler stimulus (hint: use https://www.google.com/search?q=color+picker to find the RGB
values for the disks)
For a solution, check out troxler.py

11.1.3 Kanizsa illusory contours

Created by Italian psychologist Gaetano Kanizsa in 1955, the Kanizsa Triangle is a classic example of illusory contours.
In the image below, a white equilateral triangle can be clearly perceived even though there are no explicit lines or enclosed
spaces to indicate such a triangle. (To find out more about this illusion, perform a Google search with the keywords
illusory contours.)

There exists many variants, e.g. the Kanizsa squares:

Exercice (**): Inspiring yourself from the code in square.py and circle.py, create a script that displays the (right)
Kanisza square .
A possible solution is proposed in kanizsa-square.py

90 Chapter 11. Creating stimuli

 Programming for Cognitive and Brain Sciences

Fig. 2: Troxler effect

Fig. 3: Kanizsa triangle

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Programming for Cognitive and Brain Sciences

Fig. 4: Kanizsa square

11.1.4 Herman grid

Fig. 5: Hermann Grid

Read about the Herman grid illusion79

Exercise (**) Using square.py as a starting point, write a program to display the grid.
Hints:
• use paper and pencil to draw the figure
79 https://en.wikipedia.org/wiki/Grid_illusion

92 Chapter 11. Creating stimuli

 Programming for Cognitive and Brain Sciences

• find out the formulas to compute the left top of the square in the ith row and jth column
• in your python script, use nested for loops over rows and columns to display each square one by one.
Check out grid.py.
Optional exercises:
• Play with the parameters ‘size of the squares’ and ‘space between the squares’ to see how they affect the illusion.
• Read https://stackabuse.com/command-line-arguments-in-python/ to learn how to read arguments on the com-
mand line use the sys.argv[] list from the sys module. Create a version of the grid script that can get the
number of columns, rows, the size of sides of squares, and the size of the space between squares. Play with those
parameters to see if you can make the illusion come and go. (see grid-args.py)
Remark: there exists two powerful modules to help parse arguments on the command line: argparse80 or docopt81

11.1.5 Extinction illusion

Fig. 6: McAnany-Levine extinction illusion (see McAnany, J. J. and Levine, M. W. (2004) The blanking phenomenon:
a novel form of visual disappearance. Vision Research, 44, 993-1001.)

Exercise: Program the McAnany-Levine extinction stimulus, that is, a grid of black squares with white circles at the
intersection.
Check out extinction.py
Remark: There exists variants of the extinction illusion:
• Niño’s Extinction illusion
• The Honeycomb illusion82 . You can read about it in Bertamini, Herzog, and Bruno (2016)83 . A Python script to
generate the stimulus is available on Bertamini’s web site84 but it requires installing the module PsychoPy85 which
can be challenging.
80 https://docs.python.org/3/howto/argparse.html
81 http://docopt.org/
82 https://www.youtube.com/watch?v=fDBYSFDXsuE
83 https://www.bertamini.org/lab/Publications/BertaminiHerzogBruno2016.pdf
84 https://www.programmingvisualillusionsforeveryone.online/scripts.html
85 http://www.psychopy.org

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Fig. 7: Niño’s Extinction illusion

11.1.6 Ebbinghaus-Titchener

Fig. 8: Ebbinghaus illusion

Read about the Ebbinghaus–Titchener stimulus86 .

Exercise (**): Using circle.py as a starting point, write a program to display a static stimulus (one central circle
surrounded by a number of circles).
Hint: A little bit of trigonometry87 helps:
86 http://www.abc-people.com/illusion/illusion-3.htm#axzz5SqeF15yC
87 https://en.wikipedia.org/wiki/Unit_circle

94 Chapter 11. Creating stimuli

 Programming for Cognitive and Brain Sciences

The coordinates of a location at and at distance R from the origin and an angle alpha from the left-right
line are:

x = R * cos(alpha)
y = R * sin(alpha)

Consult https://www.mathsisfun.com/polar-cartesian-coordinates.html if you need to convince yourself

about that.
Check out ebbinghaus.py

11.1.7 Fixation cross

Many visual experiments require participants to fixate a central fixation cross (in order to avoid eye movements).

Fig. 9: Fixation cross

Exercise (*): Using the function pygame.draw.line(), write a script that displays a cross at the center the screen.
(Solution at fixation-cross.py)

11.1.8 Hering illusion

Exercise (**): Program the stimulus . Then, check a solution at hering.py

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Programming for Cognitive and Brain Sciences

Fig. 10: Hering illusion

11.1.9 Random-dot stereograms

A random dot stereogram is a pair of images of random dots which, when viewed with the eyes focused on a point in
front of or behind the images, produces a sensation of depth To see how they can be generated, read the wikipedia entry
on random dot stereograms88 , to understand the phenomenon in details, read the one about Stereopsis89 .
Exercise (***) Write a script that generates random-dot stereograms (warning: this requires a bit of knowledge of
Numpy90 to represent the images as 2d arrays, and of slicing91 )
Check out random_dot_stereogram.py

11.1.10 Kitaoka visual illusions

Professor Akiyoshi Kitaoka has produced many fascinating visual illusions <http://www.ritsumei.ac.jp/~akitaoka/index-
e.html>. Notably:
Other notable stimuli are: the Rotary extinction illusion, Unstable square, Rotating snakes, Rotating rays, Primrose’s field,
Rollers, Slippage, Gaku ga gakugaku, Spa, Expanding cushions, Convection, The music, Seaweed, Joro-gumo, Packed
cherries, Earthquake, Wedding in Japan, Sausages, Raspberries, A curtain, Pyramids of donguri, Dongurakokko (The
donguri wave), Brownian motion, Waterways, A flow of the ecological flooring, Computer worms.
They are available on the following pages:
88 https://en.wikipedia.org/wiki/Random_dot_stereogram
89 https://en.wikipedia.org/wiki/Stereopsis
90 https://numpy.org/
91 https://www.w3schools.com/python/numpy_array_slicing.asp

96 Chapter 11. Creating stimuli

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Fig. 11: The Bulge

Fig. 12: The Dongururin

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Programming for Cognitive and Brain Sciences

http://www.ritsumei.ac.jp/~akitaoka/index-e.html http://www.psy.ritsumei.ac.jp/~akitaoka/o1saishe.html
http://www.psy.ritsumei.ac.jp/~akitaoka/kieru2e.html http://www.psy.ritsumei.ac.jp/~akitaoka/saishin2e.html
http://www.psy.ritsumei.ac.jp/~akitaoka/saishin3e.html http://www.psy.ritsumei.ac.jp/~akitaoka/saishin4e.html
Note: there are no exercise in this section. But, if you want to code some of the stimuli, feel free to do it, and please,
share your code with us!

11.1.11 Stroop Effect

In the Stroop Task, participants are presented with a cards on which words are written in various colors. The task is to
name as quickly as possible the colors of the printed words.

Fig. 13: Stroop card

It is difficult to name the color of a color word if they do not match. This phenomenon, known as the Stroop Effect92 ,
demonstrates the automaticity of reading. Write a python script to create 4x4 cards for the task, as image files, avoiding
repetitions of colors in neighboring cells.
You will need to read about how to generate images containing text, for example, in the tutorial How to display text with
pygame93
Then, check a solution at create_stroop_cards.py
92 https://en.wikipedia.org/wiki/Stroop_effect
93 https://nerdparadise.com/programming/pygame/part5

98 Chapter 11. Creating stimuli

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11.2 Dynamic visual stimuli

Animated movies are just a succession of still pictures. If the rate of presentation is fast enough, the brain creates an
illusion of continuity.
With pygame, programming an animation will follow the following temporal logic:
#draw picture1 in the backbuffer
#flip the backbuffer to screen

#draw picture2 in the backbuffer

#wait for some time
#flip the backbuffer to screen

#draw picture3 in the backbuffer

#wait for some time
#flip the backbuffer to screen

...

We take advantage of the double buffering mode (set by the option DOUBLEBUF in the call to pygame.display.
set_mode()) to draw the next image in memory while the current one is displayed on the screen. It is only when we
call pygame.display.flip() that the image in memory is displayed, replacing the current one on the screen.

11.2.1 Illusory line-motion

Illusory line motion (ILM) refers to a situation in which flashing a light at one end of a bar prior to the bar’s instantaneous
presentation results in the percept of motion.

Fig. 14: Illusory line-motion

Exercise (*): Program the stimulus, that is, first draw a square, wait for a few milliseconds using the function
pygame.time.wait(), then draw a rectangle overlapping with the initial square.
Check out visual-illusions/line-motion.py

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11.2.2 Flash-lag illusion

• Download visual-illusions/flash-lag.py and run it. Do not look at the code yet.
• Do you feel that the moving square’s x position coincides with the flashing square or not? If you want to read about
the Flash-lag illusion94 .
Exercise:
1. Create a movie of a square moving horizontally, back and forth. The principle is simple: you just need to create a
loop where you display a square at coordinates x, y ,wait a few milliseconds, then clear the screen, and increment or
decrement the x coordinate by a fixed amount. This strategy is explained in details at http://programarcadegames.
com/index.php?lang=en&chapter=introduction_to_animation
Check out out version visual-illusions/moving_square.py
2. Add the presentation of a flashing square then the moving square passes the middle line, to generate the flash-lag
illusion.
Now, you can look at the code in visual-illusions/flash-lag.py

11.2.3 Dynamic version of the Ebbinghaus-Titchener

• Watch this video95 .

• Program a version where the outer circles (inducers) grow and shrink in size.
• Check out visual-illusions/ebbinghaus-dynamic.py

11.2.4 Lilac Chaser

The Lilac Chaser96 is a dynamic version of the Troxler fill-in illusion.

Exercise (**): Program the Lilac Chaser stimulus, with 12 rose disks (you can use full disks without any blurring). Try
different colors.
For a possible solution, check out visual-illusions/lilac_chaser.py
(Optional exercise for advanced students: add blurring to the disks to make a stimulus similar to that of the wikipedia
page Lilac Chaser97 . Then, for a solution, check out visual-illusions/lilac_chaser_blurred.py)

11.3 Creating and playing sounds

Install the simpleaudio module:

pip install simpleaudio

Then run the quick check with ipython:

import simpleaudio.functionchecks as fc
fc.LeftRightCheck.run()

94 https://en.wikipedia.org/wiki/Flash_lag_illusion
95 https://www.youtube.com/watch?v=hRlWqfd5pn8
96 https://en.wikipedia.org/wiki/Lilac_chaser
97 https://en.wikipedia.org/wiki/Lilac_chaser

100 Chapter 11. Creating stimuli

 Programming for Cognitive and Brain Sciences

Check out simpleaudio’s tutorials98

The module sound_synth.py provides several functions to load, create, and play sounds.
Exercise (**) Using functions from the sound_synth module, write a script that loads the file cymbal.wav and plays it
10 times, at a rhythm of one per second. (Warning: a basic knowledge of numpy arrays is necessary to concatenate the
samples).
Check a solution at cycle.py

11.3.1 Shepard tone

Watch `this video <https://www.youtube.com/watch?v=LVWTQcZbLgY >`__ about Shepard tones.

Exercise (***): Program a Shepard tone.

11.3.2 Sound localisation from binaural dephasing

Exercise (**) Take the channel of a mono sound and create a stereo sound. Then dephase the two channels by various
delays, and listen to the results.
Hints: load the sound file into a one dimensional numpy array, make a copy of the array and shift it, assemble the two
arrays in a bidimensional array (matrix) and save it as a stereo file
If you know nothing about Numpy99 , you may find useful tutorials on the web, e.g. at https://github.com/paris-saclay-cds/
data-science-workshop-2019/blob/b370d46044719281932337ca4154e1b0b443ad97/Day_1_Scientific_Python/
numpys/numpy_intro.ipynb

11.3.3 Pulsation (Povel & Essen, 1985)

Exercise (***) Create rhythmic stimuli such as the ones described in Povel and Essen (1985) Perception of Temporal
Patterns100

11.4 More illusions

You can train your Python skills by programming some of the illusions at https://www.illusionsindex.org/

98 https://simpleaudio.readthedocs.io/en/latest/tutorial.html
99 https://numpy.org/
100 http://www.cogsci.ucsd.edu/~creel/COGS160/COGS160_files/PovelEssens85.pdf

11.4. More illusions 101

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102 Chapter 11. Creating stimuli

 CHAPTER

TWELVE

EXPERIMENTS

Contents

• Experiments
– Simple reaction times
– Decision times
– Numerical distance effect
– Lexical Decision
∗ Step 1: stimuli listed in constants
∗ Step 2: read stimuli from a csv file
∗ Select words in a lexical dabatase
∗ Automatising database searches with R and Python
∗ Generate nonwords
∗ Create a stimuli file
∗ Use sys.argv to pass the name of the file containing the list of stimuli
∗ Improving the pseudowords
∗ Data analysis
∗ Auditory Lexical Decision
∗ Finally
– Posner’s attentional cueing task
– Stroop Effect
– A general audio visual stimulus presentation script
– Sound-picture matching using a touchscreen
– More examples using Expyriment

103
Programming for Cognitive and Brain Sciences

12.1 Simple reaction times

Many psychology experiments measure reaction-times or decision-times.

The script simple-detection-visual-pygame.py is a simple detection experiment programmed with pygame.
The task is simple: the participant must press a key as quickly as possible when a cross appears at the center of the screen.
Download it and run it with:

python simple-detection-visual-pygame.py

The results are saved in reaction_times.csv which you can inspect with any text editor.
If you are an R afficionado, you can open it and type:

data = read.csv('reaction_times.csv')
summary(data)
attach(data)
plot(RT)
dev.new()
plot(RT ~ Wait)

Here are my results:

Fig. 1: Simple Reaction Times as a function of trial

Browse the code of simple-detection-visual-pygame.py

It is pretty technical! This is because Pygame101 is meant to program simple video games, not psychology experiments.
A more adequate library for this task is Expyriment102 (another one is Psychopy103 ).
From here, we are going to use it to generate experiments.
Make sure you have installed Expyriment104 :
101 http://www.pygame.org
102 http://www.expyriment.org
103 http://www.psychopy.org
104 http://www.expyriment.org

104 Chapter 12. Experiments

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Fig. 2: Relationship between wait time and reaction time

$ python
>>> import expyriment

If an error message moduleNotFoundError: No module named 'expyriment' appears, check Software

Installation.
Let us start by downloading simple-detection-visual-expyriment.py and run it with:

python simple-detection-visual-expyriment.py

Then, in the subfolder data, locate a file with a name starting with simple-detection... and the extension .xpd.
This is a text file containing the reactions times. To analyse them, download analyse_rt.py and run:

python analyse_rt.py data/simple-detection-visual-expyriment_*.xpd

Compare the codes of simple-detection-visual-expyriment.py and

simple-detection-visual-pygame.py. This should convince you that using expyriment will make
your life simpler if you need to program a psychology experiment.
The documentation of expyriment is available at http://docs.expyriment.org/. Have q a quick look at it, especially http:
//docs.expyriment.org/expyriment.stimuli.html
The basic principles of the expyriment module are introduced in https://docs.expyriment.org/Tutorial.html. I provide
a minimal template at expyriment_minimal_template.py that one can use to start writing a expyriment script.
Exercises:
1. Modify simple-detection-visual-expyriment.py to display a white disk instead of a cross.
2. Modify simple-detection-visual-expyriment.py to display a white disk on half of the trials and a
gray disk on the other half of the trials (thesis experimental conditions should be shuffled randomly). Then modify
it to display disks with four levels of gray. Thus you can assess the effect of luminosity on detection time. (see
xpy_simple_reaction_times/grey-levels.py for a solution using Expyriment’s design.Block
and design.Trial objects).
3. Modify simple-detection-visual-expyriment.py to play a short sound (click.wav) in lieu of
displaying a visual stimulus (hint: use stimuli.Audio()). Thus, you have created a simple audio detection
experiment.

12.1. Simple reaction times 105

Programming for Cognitive and Brain Sciences

4. Download and run simple-detection-audiovisual.py:

python simple-detection-audiovisual.py

There are three blocks of trials: a first one in which the target is always visual, a second one in which it is always a sound,
and a third one in which the stimulus is, randomly, visual or auditory. Are we slowed down in the latter condition? Use
analyse_audiovisual_rt.py to analyse the reaction times.
Exercice: add python code to simple-detection-audiovisual.py to display instructions at the start of the
experiment.

12.2 Decision times

In the previous example, the user just had to react to a stimulus. This involved a very simple type of decision (“is a target
present or not?”)
Other tasks involves taking a decision about some property of the stimulus.
Exercise: | - Modify simple-detection-visual-expyriment.py to display, rather than a cross, a random
integer between 0 and 9 (hint: Use stimuli.TextLine()). Now, the task is to decide if the figure is odd or even,
by pressing one of two keys.

Here is a solution: parity.py

Comparing the average decision time to the time to react to a simple cross provides a (rough) estimate of the time to
decide about the parity of a number. By the way, one can wonder what happens for multiple digits numbers: are we
influenced by the flanking digits?

- Add feedback; when the subjects presses the wrong key, play the sound wrong-answer.ogg.

Here is a solution: parity_feedback.py

12.3 Numerical distance effect

Exercise: Create a script to present, at each trial, a random number between 1 and 99, and ask the subject to decide wether
the presented number is smaller or larger than 55. Plot the reactions times as a function of the number.
Do you replicate the distance effect reported by Dehaene, S., Dupoux, E., & Mehler, J. (1990) in “Is numerical comparison
digital? Analogical and symbolic effects in two-digit number comparison.” Journal of Experimental Psychology: Human
Perception and Performance, 16, 626–641.?

106 Chapter 12. Experiments

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12.4 Lexical Decision

In a lexical decision experiment, a string of characters is flashed at the center of the screen and the participant has to
decide if it is a actual word or not, indicating his/her decision by pressing a left or right button. Reaction time is measured
from the word onset, providing an estimate of the speed of word recognition.
Let us program such a task.

12.4.1 Step 1: stimuli listed in constants

Modify the parity task script to display either a word or a pseudoword at each trial (in a random order).
For testing purposes, you can use the following variables:

words = ['bonjour', 'chien', 'président']

pseudos = ['lopadol', 'mirance', 'clapour' ]

A solution is proposed in lexdec_v1.py

12.4.2 Step 2: read stimuli from a csv file

Then modify the lexical decision script to read the stimuli from a comma-separated text file (stimuli.csv) with two columns.
Here is the content of stimuli.csv:

item,category
bonjour,W
chien,W
président,W
lopadol,P
mirance,P
clapour,P

(hint: To read a csv file, one can use pandas.read_csv())

A solution is proposed in lexdec_v2.py
Note: You can use a file comparator, e.g. meld105 , to compare the two versions:

meld lexdec_v1.py lexcdec_v2.py

12.4.3 Select words in a lexical dabatase

1. Go to http://www.lexique.org
Click on “Recherche en Ligne” and play with the interface:
• enter 5...5 in the nbletters field
• enter ^b.t$ in the field ortho field (see http://www.lexique.org/?page_id=101 for more examples of pat-
tern that can be used)
105 https://meldmerge.org/

12.4. Lexical Decision 107

Programming for Cognitive and Brain Sciences

2. how many words of grammatical category (cgram) ‘NOM’, and of length 5 (nblettres), of lexical frequency
(freqfilms2) comprised between 10 and 100 per millions are there in this database? (answer=367). Save these
words (i.e. the content of the field Words) into a words.csv file (you may have to clean manually, ie. remove
unwanted columns, using Excel or Libroffice Calc).

12.4.4 Automatising database searches with R and Python

To select words, rather than using the interface at http://www.lexique.org, one can write scripts in R or Python. This
promotes reproducible science.
1. Open https://github.com/chrplr/openlexicon/tree/master/documents/Interroger-Lexique-avec-R and follow the
instructions in the document interroger-lexique-avec-R.pdf
2. Read https://github.com/chrplr/openlexicon/tree/master/scripts#selecting-lexical-items-with-python
To select 100 five letters long nouns for our lexical decision, execute:

import pandas
lex = pandas.read_csv("http://www.lexique.org/databases/Lexique382/Lexique382.tsv",␣
,→sep='\t')

subset = lex.loc[(lex.nblettres == 5) & (lex.cgram == "NOM") & (lex.freqfilms2 > 10) &
,→ (lex.nombre == 's')]

samp = subset.sample(100)
samp2 = samp.rename(columns = {'ortho':'item'})
samp2.item.to_csv('words.csv', index=False)

This creates words.csv.

12.4.5 Generate nonwords

1. Write a function that returns a nonword (a string containing random characters)

def pseudo(length):
""" returns a nonword of length `length` """

Solution at create_nonwords.py
2. Use this function to create a list of 100 nonwords and save it in a file "pseudowords.csv" (one pseudoword
per line) (see https://www.pythontutorial.net/python-basics/python-write-text-file/)

12.4.6 Create a stimuli file

Merge words.csv and pseudowords.csv into a single stimuli2.csv file:

import pandas
w = pandas.read_csv('words.csv')
w['category'] = 'W'
p = pandas.read_csv('pseudowords.csv')
p['category'] = 'P'
allstims = pandas.concat([w, p])
allstims.to_csv('stimuli2.csv', index=False)

108 Chapter 12. Experiments

 Programming for Cognitive and Brain Sciences

12.4.7 Use sys.argv to pass the name of the file containing the list of stimuli

Modify lexdec_v2.py to be able to pass the name of the stimuli file as an argument on the command line:

python lexdec_v3.py stimuli2.csv

(hint: use sys.argv[]; see https://www.geeksforgeeks.org/how-to-use-sys-argv-in-python/)

Solution at lexdec_v3.py

12.4.8 Improving the pseudowords

1. Check out the pseudoword generator UniPseudo106

2. Generate a new list of pseudowords and add them to a new stimuli3.csv file

12.4.9 Data analysis

After running:

python lexdec_v3.py stimuli2.csv

the subject’s responses are stored in the subfolder data/ contains a file lexdec...xpd
You can download this xpd file as an example.
1. Use pandas.read_csv(..., comment='#') to read the responses into a pandas dataframe.
2. Compute the average reaction times for words and for pseudo-words.
3. Plot the distribution of reactions times using seaborn.boxplot()
4. Use scipy.stats.ttest_ind() to perform a Student t-test compairn gthe RTs of Words and Non-Words.
Check a solution analyze_RT.py

12.4.10 Auditory Lexical Decision

Transform lexdec_v1.py into an auditory lexical decision script using the sound files from the lexical decision folder
<../experiments/xpy_lexical_decision/>:

bonjour.wav
chien.wav
président.wav
clapour.wav
lopadol.wav
mirance.wav

Solution at lexdec_audio.py
106 http://www.lexique.org/?page_id=582

12.4. Lexical Decision 109

Programming for Cognitive and Brain Sciences

12.4.11 Finally

Check out an example of a “real” lexical decision experiment at https://chrplr.github.io/PCBS-LexicalDecision

12.5 Posner’s attentional cueing task

Exercise (**): Read about Posner’s attentional cueing task107 and program the experiment.
See a solution in Posner-attention/posner_task.py

12.6 Stroop Effect

The Stroop effect (Stroop, John Ridley (1935). “Studies of interference in serial verbal reactions”. Journal of Experimental
Psychology. 18 (6): 643–662. doi:10.1037/h0054651) may be the most well known psychology experiment. Naming
the color of the ink is difficult when there is a confict with the word itself. This is interpreted as a proof that reading is
automatic, i.e. cannot be inhibited.
In the previous chapter, we created Stroop cards with Pygame.

Stroop card
(see create_stroop_cards.py)
107 https://en.wikipedia.org/wiki/Posner_cueing_task

110 Chapter 12. Experiments

 Programming for Cognitive and Brain Sciences

Download stroop.zip. Extract the files and run:

python stroop_task.py

The times are in the subfolder data. Compute the average reading times as a function of the language (using R or
python).
Exercise: Program a Stroop task with a single colored word displayed at each trial. To record actual naming times, you
will need to record (!) the subject’s vocal response. A simple solution is to run a audio recording application while the
script is running. You script should play a brief sound each time you present a target. Then, with a audio editor (e.g.
Audacity108 ), you can locate the times of presentation of stimuli and the onsets of vocal responses. Check out the program
“CheckVocal” at https://github.com/0avasns/CheckVocal which does just that!

12.7 A general audio visual stimulus presentation script

In some experiments, we know in advance the precise timing of all stimuli (the program flow does not depend on external
events). A script that reads the timing of audiovisual stimuli in a csv file and presents them at the expected times is
available at https://www.github.com/chrplr/audiovis

12.8 Sound-picture matching using a touchscreen

The sentence-picture-matching.py script presents a sound, followed by a picture and waits for the participant
to press a button.
Exercise: Modify the previous script to present two pictures and use expyriment’s TouchScreenButtonBox to record the
subject’s response, using the example from expyriment/touchscreen_test/touchscreen-test.py

12.9 More examples using Expyriment

Besides the examples from this course, you can find more expyriment scripts at
• https://mbroedl.github.io/cognitive-tasks-for-expyriment/
• https://github.com/expyriment/expyriment-stash

108 https://www.audacityteam.org/

12.7. A general audio visual stimulus presentation script 111

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112 Chapter 12. Experiments

 CHAPTER

THIRTEEN

PROGRAMMING A LEXICAL DECISION TASK

In a lexical decision experiment, a string of characters is flashed at the center of the screen and the participant has to
decide if it is a actual word or not, indicating his/her decision by pressing a left or right button. Reaction time is measured
from the word onset, providing an estimate of the speed of word recognition.
Let us program such a task.

13.1 Step 1: stimuli in constants

Modify the parity task script to display either a word or a pseudoword at each trial (in a random order). the
task of the subject is to press ‘F’ when the displayed stimulus is a word, ‘J’ if it is a pseudowords.
For testing purposes, let us assume that:

words = ['bonjour', 'chien', 'président']

pseudos = ['lopadol', 'mirance', 'clapour' ]

Run the script and check the results in /data.

Compare your script with the solution proposed lexdec_v1.py

13.2 Step 2: read stimuli from a csv file

Modify the lexical decision script so that it reads the stimuli from a comma-separated text file (stimuli.csv) with two
columns. Here is the content of stimuli.csv:

item,category
bonjour,W
chien,W
président,W
lopadol,P
mirance,P
clapour,P

(hint: To read a csv file, you can use pandas.read_csv())

A solution is proposed in lexdec_v2.py
Note: You can use a file comparator, e.g. meld109 , to compare the two versions:
109 https://meldmerge.org/

113
Programming for Cognitive and Brain Sciences

meld lexdec_v1.py lexcdec_v2.py

Optional;

13.3 Select words in a lexical dabatase

1. Go to http://www.lexique.org
Click on “Recherche en Ligne” and play with the interface:
• enter 5...5 in the nbletters field
• enter ^b.t$ in the field Word field (see http://www.lexique.org/?page_id=101 for more examples of pat-
terns that can be used)
2. how many words of grammatical category (cgram) ‘NOM’, and of length 5 (nblettres), of lexical frequency
(freqfilms2) comprised between 10 and 100 per millions are there in this database? (answer=367). Save these
words (i.e. the content of the field Words) into a words.csv file (you may have to clean manually, ie. remove
unwanted columns, using Excel or Libroffice Calc).

13.4 Automatising database searches with R and Python

To select words, rather than using the interface at http://www.lexique.org, one can write scripts in R or Python. This
promotes reproducible science.
1. Open https://github.com/chrplr/openlexicon/tree/master/documents/Interroger-Lexique-avec-R and follow the
instructions in the document interroger-lexique-avec-R.pdf
2. Read https://github.com/chrplr/openlexicon/tree/master/scripts
To select 100 five letters long nouns for our lexical decision, execute:

import pandas
lex = pandas.read_csv("http://www.lexique.org/databases/Lexique382/Lexique382.tsv",␣
,→sep='\t')

subset = lex.loc[(lex.nblettres == 5) & (lex.cgram == "NOM") & (lex.freqfilms2 > 10) &
,→ (lex.nombre == 's')]

samp = subset.sample(100)
samp2 = samp.rename(columns = {'ortho':'item'})
samp2.item.to_csv('words.csv', index=False)

This creates words.csv.

13.5 Generate nonwords

1. Write a function that returns a nonword (a string containing random characters)

def pseudo(length):
""" returns a nonword of length `length` """

Solution at create_nonwords.py

114 Chapter 13. Programming a Lexical decision task

 Programming for Cognitive and Brain Sciences

2. Use this function to create a list of 100 nonwords and save it in a file "pseudowords.csv" (one pseudoword
per line) (see https://www.pythontutorial.net/python-basics/python-write-text-file/)

13.6 Create a stimuli file

Merge words.csv and pseudowords.csv into a single stimuli2.csv file:

import pandas
w = pandas.read_csv('words.csv')
w['category'] = 'W'
p = pandas.read_csv('pseudowords.csv')
p['category'] = 'P'
allstims = pandas.concat([w, p])
allstims.to_csv('stimuli2.csv', index=False)

13.7 Use sys.argv to pass the name of the file containing the list of
stimuli

Modify lexdec_v2.py to be able to pass the name of the stimuli file as an argument on the command line:

python lexdec_v3.py stimuli2.csv

(hint: use sys.argv[]; see https://www.geeksforgeeks.org/how-to-use-sys-argv-in-python/)

Solution at lexdec_v3.py

13.8 Improving the pseudowords

1. Check out the Unipseudo110 pseudoword generator.

2. Generate a new list of pseudowords and add them to a new stimuli3.csv file

13.9 Data analysis

After running:

python lexdec_v3.py stimuli2.csv

the subject’s responses are stored in the subfolder data/ contains a file lexdec...xpd
You can download this xpd file as an example.
1. Use pandas.read_csv(..., comment='#') to read the responses into a pandas dataframe.
2. Compute the average reaction times for words and for pseudo-words.
3. Plot the distribution of reactions times using seaborn.boxplot()
4. Use scipy.stats.ttest_ind() to perform a Student t-test compairn gthe RTs of Words and Non-Words.
110 http://www.lexique.org/shiny/unipseudo/

13.6. Create a stimuli file 115

Programming for Cognitive and Brain Sciences

Check a solution analyze_RT.py

13.10 Finally

Check out the example of a ‘real’ lexical decision experiment at https://chrplr.github.io/PCBS-LexicalDecision/)

116 Chapter 13. Programming a Lexical decision task

 CHAPTER

FOURTEEN

DATA ANALYSES

Contents

• Data Analyses
– Permutation tests
– Bootstrap
– Basic Data Analysis with R
– Comparing means using Easy ANOVA (Analysis of Variance)
– Frequency Analysis
• Lexical Statistics
– Zipf law
– Benford’s law
– Neuroimaging

14.1 Permutation tests

• Read about the principle of permutation tests111

• Implement a python script that uses a permutation test to compare two samples.
• Check out the solution I propose: permutation_test/permutation_test.py.

14.2 Bootstrap

• Implement the bootstrap112 to obtain confidence intervals on the means of a sample.

111 https://en.wikipedia.org/wiki/Permutation_test
112 https://en.wikipedia.org/wiki/Bootstrapping_(statistics)

117
Programming for Cognitive and Brain Sciences

14.3 Basic Data Analysis with R

See http://www.pallier.org/examples-of-basic-data-analyses-with-r.html#examples-of-basic-data-analyses-with-r

14.4 Comparing means using Easy ANOVA (Analysis of Variance)

See http://www.pallier.org/easy-anova-with-r.html#easy-anova-with-r

Note: Check out David Lakens’s github113 and, in particular, https://lakens.github.io/statistical_inferences/repository

14.5 Frequency Analysis

• See short-intro-fourier

113 https://github.com/Lakens

118 Chapter 14. Data Analyses

 CHAPTER

FIFTEEN

LEXICAL STATISTICS

15.1 Zipf law

• The script Zipf/word_count.py computes the distribution of frequencies of occurences in a list of words.
Use it to compute the distribution of word frequencies in Alice in Wonderland114 .
Note: To remove the punctuation, you can use the following function:

import string
def remove_punctuation(text):
punct = string.punctuation + chr(10)
return text.translate(str.maketrans(punct, " " * len(punct)))

• Zipf law states that the product rank X frequency is roughly constant. This ‘law’ was discovered by Estoup and
popularized by Zipf. See http://en.wikipedia.org/wiki/Zipf%27s_law. Create the Zipf plot for the text of Alice in
Wonderland showing, on the y axis, the log of the frequency and on the x axis the word rank (sorting words from
the most frequent to the least frequent).
• Display the relationship between word length and word frequencies from the data in lexical-decision/
lexique382-reduced.txt
• Generate random text (each letter from a-z being equiprobable, and the spacecharacter being 8 times more probable)
of 1 million characters. Compute the frequencies of each ‘pseudowords’ and plot the rank/frequency diagram.
• To know more about lexical frequencies:
– Read Harald Baayen (2001) Word Frequency Distributions Kluwer Academic Publishers.
– Read Michel, Jean-Baptiste, Yuan Kui Shen, Aviva P. Aiden, Adrian Veres, Matthew K. Gray, The Google
Books Team, Joseph P. Pickett, et al. 2010. “Quantitative Analysis of Culture Using Millions of Digitized
Books.” Science, December. https://doi.org/10.1126/science.1199644. (use scholar.google.com to find a
pdf copy). Check out google ngrams at https://books.google.com/ngrams. (Note that at the bottom of the
page, there is a message “Raw data is available for download here”).
114 http://www.umich.edu/~umfandsf/other/ebooks/alice30.txt

119
Programming for Cognitive and Brain Sciences

15.2 Benford’s law

Learn about Benford’s law115 . Write a Python script that displays the distribution of the most significant digit in a set of
numbers. Apply it to the variables in Benford-law/countries.xlsx.
A solution: Benford-law/Benford.py

15.3 Neuroimaging

• Check out nilearn116 and nistats117 and MNE-python118

• See stats-and-data-analyses/Example of a single subject-single run fMRI analysis with nistats.ipynb

115 https://brilliant.org/wiki/benfords-law/
116 http://nilearn.github.io/
117 https://nistats.github.io/
118 https://martinos.org/mne/stable/index.html

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SIXTEEN

ONLINE EXPERIMENTS

To program online experiments, you need to acquire basic knowledge of:

• HTML (Hyper Text Markup Language). The language that is used to write documents that can be displayed by
WEB browsers.
• CSS (Cascading style sheets). The language that describes the style of HTML elements.
• Javascript. The programming language spoken by the browsers.

16.1 HTML Basics

Browser display (including with jsPsych) relies on HTML, most often HTML5. Let us see how it works.
To go further The point of this lecture is to raise your understanding of HTML, CSS, JS & JsPsych enough
to code your own experiments. For those who may want to go further / better understand the magic at hand,
I will leave notes as the present one in the form of quotes. They are not necessary, but may answer questions
you may have.

16.1.1 HTML document structure overview

A HTML file contains:

• A declaration that you are using HTML5;
<!DOCTYPE html>
What happens if you remove it? - A note on browser compatibility Most browsers will not care
and behave similarly. However, you have no guarantee that it will do so: in fact, Internet Explorer
will just treat this as plain text! In the case of an online experiment, this means you may lose some
participants/data. Even worse, this means that you may have flawed data without realising it!
• A head where most webpage-level elements (e.g. title) are defined,

<head></head>

Tags in HTML Here, we write “head” between chevrons. This is known as a tag in HTML. Tags tell
information to your browser, here that this is the head of the document. Notice that we have two tags here,
one after another. Think of them as brackets: everything that we want to define in the head will be enclosed
between the tags. Accordingly, the first tag is called the opening tag and the other one the closing tag. Closing
tags specifically have an additional / slash at the start). Note that a few tags do not enclose content and only
use a single tag, with the slash / at the end (e.g. line breaks ).
• A body which will contain the main elements of the page, especially what will be displayed to the user.

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<body></body>

Our first document thus look like this, and is read as a blank page.
<!DOCTYPE html>
<head></head>
<body></body>

16.1.2 Setting up a title

You can use the <title> tag in the head of the document to set a title.
<head>
<title>My first page!</title>
</head>

16.2 Simple shapes

16.2.1 Square

Creating divs

Rectangles are very simple shapes to draw in HTML. Although there are a variety of way, we will start by using colored
‘divs’.
Divs Divs are precisely HTML element with a rectangle shape. They are most often used as generic con-
tainers, but this won’t interest us right now.
You may use the following body for your HTML code.
<body>
<div></div>
</body>

As you may notice, the page is still blank. Press f12 to understand why.
Inspector f12 opens your browser’s inspector, which allows you to see the HTML code of the web page you
are currently browsing.
Open the body tags and hover over the <div> element. It should show you the element on the webpage, and give you its
dimensions. Notice the issue? It is simply of width 0, so of course you won’t see it. TODO IMAGE

Setting size

Let’s specify a width for our <div>. To do so, will add specifications to our tag, so that the browser knows how to deal
with the element it marks. Here, we will use the style keyword to specify a style that forces a 200px width and a 200px
height.
The result is as follows:
<body>
<div style = "width: 200px; height: 200px"></div>
</body>

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Notice that the style specification has a precise syntax: keyword: value, with successive entries being separated by
semicolumns ;. The style won’t be applied if you omit semicolumns, or use equal sign instead of columns :! Similarly,
the value part must have a unit. Here we use pixels (px), but there are many others!
Setting size with style in HTML Here we use style to specify the width and height of the element. There are
other ways, with specific width and height tags. However, these specifications may behave unexpectedly
at times, which is why we will use style in this lecture.
Size units in HTML To set the size of an element, we have many useful units that can adapt to each screen.
Here we used pixels (px) which are the base unit of computer screens. Since pixel size may vary between
computers, we could also use centimeters (cm) to get a constant value. Conversely, we could want to adapt
our display to the size of the window, and use viewport height (vh) and width (vw). If we want more
specifically to adapt to a given container, we can use percents (%).

Setting background color

If you update the page, you’ll see that you in fact still don’t see the div. Check again with f12; it should highlight an actual
square this time. The reason why you don’t see it is that, by default, elements take the background color of their parent,
here <body>. So you are looking at a white square on a white background, which is a good reason not to see it!
To specify the color (actually background color of the square), you may use another specification in the style:

<body>
<div style = "...; background-color = "red""></div>
</body>

Names with spaces Names with spaces are always annoying when programming, since they should actually
be taken as a whole by the language. To prevent this, several alternatives exist (such as CamelCase or
snake_case), with each language having its usually prefered alternative. In HTML/CSS, we replace spaces
```` with dashes -.
Changing background color of the body Like with any other elements, you can change the style of the
body. Try setting it to gray with the background-color specification!

Centering

At this point, you should finally have a square ! However, it lies sad and alone in the corner of the screen. We’ll see more
on the placing of elements, but for now we will stick to simple solutions.
First, we can specify the position of the left corner on the square in the style. This works similar to setting the dimensions
of the square.

<div style = "...; top: 100px; left: 200px"></div>

Although we are moving the square, it is still not centered on the screen. It is pointless to use trial-and-error here, as it
won’t be centered anymore if you resize your browser window. To get a unit relative to the size of the window, we will
use viewport height (vh) and width (vw). 1vh correspond to 1% of the height of the window. 1vw is 1% of the width
of the window. Do not confuse both!
As such, we can (somewhat) center the square using the following style:

<div style = "...; top: 50vh; left: 50vw"></div>

Notice that we are still slightly off, since we actually centered the top left corner of the square. To correct this we will
apply a simple translation, of half the square dimensions.

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<div style = "...;

top: 50vh; left: 50vw;
transform: translate(-50%, -50%)"></div>

Percent unit The percent unit % refers to the dimension of the parent container. E.g., for our div within
the body, setting top and left to 50% would put our top left corner to the center of the body. Here, with
the call to translate, it becomes as if self centered, and the translation is thus of 50% of the square size.

ID

We can specify the id of an element using id = "my-id".

IDs are not necessary, but they come in handy for several reasons. The main reason for us now is to be able
to identify component in the inspector view. It also helps identification of the element by other elements,
which helps for applying a specific style (more later) or retrieving the element in JavaScript (more even later
, see next session).
And voilà, we have a neat centered square! The final code can be found here: [square.py (PLACEHOLDER)].

16.2.2 Circle

As said above, <div>s are rectangle elements, but they may also be slightly modified. As an example, their corners can
be rounded, a property which we will make use of to make circles. For that we will use a border-radius specification
within our style.

<div style = "...; border-radius = 50%"></div>

You may try and change the value of this border-radius, to better understand the behavior we’re making use of.
Notice how much we start definitely resorting to tricks here, which may (and will) be insufficient at some point. HTML
proposes alternatives that are more suited to drawing shapes, such as Scalable Vector Graphics (SVG).
In HTML, SVGs are elements like divs, but which are designed to contain shapes. Here we will use the <circle> shape
element. We will specify its properties (radius, center, color) with tags directly linked to the element.

<svg>
<circle cx="100" cy="100" r="100" fill="red"/>
</svg>

Notice that we are at the same level as style TODO Also notice that here we space things with spaces and
not semicolumns. some attributes are specific to <circle/>
What is going wrong here? Well, f12 can enlighten us here again. As you may see, the circle is cut by the border of the
container. In other words, our 150x300 pixels containers does not have the right shape to display the whole shape. We
thus have to specify the size of the container, with the usual style attribute.

<svg style = "height = 200px; width=200px">

<circle cx="100" cy="100" r="100" fill="red"/>
</svg>

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16.2.3 Triangle

A good reason to learn about SVGs is that you can’t draw triangles with divs (or rather, you will have an extremely
hard time doing so). With SVGs, doing so is much easier, as you can draw any polygon using the <polygon/> tag.
<polygon/> takes a specific attribute named points which takes a list of integers corresponding to the coordinates
of the polygon’s vertices. Integers in the list will be paired to create the x and y coordinates of each point.
You may separate integers with spaces ```` or commas , alike. In the code for an isoceles triangle below, I use a mix of
both: spaces separate x and y coordinates, while commas separates vertices.

<svg>
<polygon points="0 200, 200 200, 100 0" fill="red" />
</svg>

16.2.4 Style usage

In all the above examples, you probably reused the same value for the style attribute, over and over. HTML provides
a convenient way to deal with this by providing a style sheet. It may be defined in the head of the file as per the following
code (which defines an empty style).

<head>
<style>
<!-- Put the style here -->
</style>
</head>

Comments in HTML The <!-- and --> serve as opening and closing markers for comments in HTML.
This is made so that you’ll (hopefully) never need them for any other purpose, since HTML is designed to
display all kinds of texts.
We can now define our stylesheet. First, let us make all divs have a red background by default.

<style>
div {
background-color: red
}
</style>

This property can now be removed from the style of the <div> elements of the body. Try it!
We now want to deal with the centering elements. Since we don’t want to center everything, we’ll manually flag elements
that should be centered using the class attribute. To define a style for a class named my-class, we reuse the same
syntax as before, but replace the element name (div) with the class name my-class preceded by a dot .. The dot
indicates that this style applies to a class.
Cascading Style Sheets Style sheets can apply at several levels: to all elements of the document, to all
elements of a kind (e.g. divs), to all elements of a special class (defined with the class attribute), or
elements with a given id… These levels apply one after another, with most specific style sheets applying over
the more generic ones; they are, in a sense, cascading. This precisely gave this ‘style’ language its name:
Cascading Style Sheets, or CSS for short.
To apply this style to our divs, we have to specify that this class applies such as in the following example.

<body>
<div class = "centered">
</div>
</body>

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Multiple classes You may apply several classes to a single element, simply by listing them with a space in
between different classes: e.g. class = "centered circle" if you also happen to have a .circle
style.
Of course, redefining it at the beginning of each sheet can be very tedious, which is why style sheets are often defined in
their own .css file. Move everything we previously defined within <style> into a file named shapes.css. You
may now load the styl in your HTML file, using the following code in the <head> section.

<head>
<link rel="stylesheet" href ="./shapes.css">
</link>
</head>

Be careful, if you move the file from the current folder you will have to update the href attribute with the new path!

16.3 Combining shapes

You now have the basics to recreate the following illusion from previous lectures119 : - Two circles ([solution (PLACE-
HOLDER)]) - Troxler ([solution (PLACEHOLDER)]) - Kanisza square ([solution (PLACEHOLDER)])

16.3.1 A small note for Kanisza

If you did Kanisza (or peeked at the solution), you may have notice that we didn’t actually draw circle slices, but rather
hid the undesired parts of the circle with a square. This is because there is no simple way to do it with the tools we have
now.
The issue of the present design Since the result is visually satisfying, one may think it is not a big deal to
leave it as such. However, remember that the whole point of the Kanisza illusion is to trigger a form that
does not exist in the first place! You do not always control what happens on the screen, and as such this may
introduce some terrible noise in your data. As an example, since HTML elements are actually displayed one
after another, old computers might show the square with a delay that could be a comfounding factor to the
effect you want to show!
In the next section, we will learn how to draw these slices using canvas. These are some sort of ‘drawing boards’ that have
to be drawn upon using JavaScript.

16.4 Combining shapes with JS

16.4.1 Plugging JavaScript into HTML

You can plug a JavaScript script in HTML using the <script> tag. Note that everything within this tag will be inter-
preted as JavaScript.
For our first script, we will display a simple text on the console. To this end, we may use the line code console.
log(myText).

<body>
<script>
// All that is written here is JavaScript!
console.log("Bonjour le monde !");
(continues on next page)
119 https://pcbs.readthedocs.io/en/latest/stimulus-creation.html#static-visual-stimuli

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(continued from previous page)

</script>
</body>

TODO Here we use the method log from the object console. This relationship is embodied by the .
between the two.
Do not expect to see anything on your HTML page! The text is printed in the console, which you can access alongside
the inspector. This can be very useful for debugging!

16.4.2 Basic syntax of JavaScript

The following code shows you the basics of the JavaScript synta

let x = 0;
function printNumber(x){
console.log(x);
return -1;
}

console.log(x);
printNumber(x);
x = 1;
printNumber(x);
printNumber(0);
console.log(printNumber(x));

The semicolumn ; is facultative if you use line breaks.

Output:

0
0
1
0
1
-1

If you only get one 0 in the console, check that it is not because the two zeros were wrapped in the same line (a small 2
on the right).

Loops

This code prints integers from 0 to 5.

for (i = 0; i < 5; i++){

console.log(i);
}

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16.4.3 Modifying elements with innerHTML

document.body.innerHTML +=
"<div style = "background-color:red; height: 200px; width: 200px"></div>"

Multiline strings in JS It is done by adding a backslash \ continuation at the end of each line.

"This is \
a \
multiline string".

Be careful not to put any space after the continuation!

16.4.4 Modifying elements with pure JS

Create element with document.createElement("div") (you may use which ever type you prefer) Modify ele-
ment attributes (/ property): element.id = "my-id" Modify style: element.style.height = "200px"

16.4.5 Drawing on canvas.

16.5 Using JsPsych

JsPsych is a library that allows you to easily create experiments from premade plugins. First, download the library in
version 7.3.0 from the following link120 , create a subfolder jspsych-7.3.0 in your code folder and unzip jspsych.
zip there. The library’s code should be in ./jspsych-7.3.0/dist.

16.5.1 Loading JsPsych

The library itself consists in the jspsych.js JavaScript file, which we will load in our experiment. To load an external
script in HTML, one can simply use the src attribute of the <script> tag, with the path to the script file as a value.

<!DOCTYPE html>
<head>
<title>A simple jsPsych experiment</title>
</head>
<body>
<script src="./jspsych-7.3.0/dist/jspsych.js">
</script>
</body>

Here, you only loaded all the helper functions of JsPsych. You will now need to load create an instance of the plugin using
initJsPsych, which will handle all your JsPsych-related instructions.

<script src="./jspsych-7.3.0/dist/plugin-html-keyboard-response.js">
</script>

<script>
const jsPsych = initJsPsych();
</script>

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Constants Notice that here we use a const instead of a let or var declaration. This means that the value
of this variable can not be changed. This is convenient to prevent undesired bugs from redeclaring a variable.

16.5.2 Timeline and trials

As said in the introduction of the JsPsych lecture series, JsPsych revolves around successive trials forming what is called a
timeline. This timeline is implemented as an array containing all the trials. Arrays in JavaScript are defined using square
brackets []. We will first start with an empty timeline, which we’ll gradually fill.

let timeline = [];

Initializing non-empty arrays Arrays may be implemented with items already in them, by simply putting
the items within the square brackets [] and separating them with commas ,. As an example, if you al-
ready have two trials trial1 and trial2, you may create an array containing both (in this order) with
[trial1, trial2].
We now want to create trials to fill our timeline with. You can think of trials as a parametrized task, with the task being
effectively encoded as a JsPsych plugin.
For now, we will stick to simple decision tasks. Stimuli will be displayed from simple HTML code similar to what we
used previously. The dedicated plugin is (logically) called jsPsychHtmlKeyboardResponse.
We can thus instantiate a trial with this plugin, using an object structure. Long story short, an object structure is de-
fined using brackets {}; it holds properties, defined with name: value, and separated by commas ,. Below is the
instantiation of a jsPsychHtmlKeyboardResponse trial.

let trial = {
type: jsPsychHtmlKeyboardResponse,
};

Trailing commas You may notice I left a comma , after the type property, although I did not specify any
other property. This is not a typo: it is what we call a trailing comma. JavaScript licenses them as it makes
it easy to add new elements.
You may now add the trial to the timeline using the push method of arrays, which adds an element at the end of it.

timeline.push(trial);

In-place modifications TODO

And we can finally run the experiment with our 1-trial timeline, using the jsPsych instance we previously created.

jsPsych.run(timeline);

Your final code should look like this:

// We initialize JsPsych
const jsPsych = initJsPsych();

// We create an empty timeline

let timeline = [];

// We create a basic decision trial

let trial = {
type: jsPsychHtmlKeyboardResponse,
};

(continues on next page)

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(continued from previous page)

// We add this trial to the timeline
// /!\ Do not forget this essential step /!\
timeline.push(trial);

// We run the timeline with JsPsych

jsPsych.run(timeline);

You may now run it by opening your HTML page. Press a key and see what happens .
If nothing happens (and this should be the case!), just do as you should always do in this situation: open the console.
It should display you the following error message in red: “You must specify a value for the stimulus parameter in the
html-keyboard-response plugin.”. Such errors are fatal and prevent the script from proceeding any futher.
The issue here is that, although we did specify the type of our trial, we did not give it the necessary parameters for it to
run properly. As the message tells us, we actually didn’t specify what stimulus this decision task was about. In fact, the
plugin displays “unspecified” as the top of the page.
Let us first specify a simple text prompting to press any key as our stimulus. We can do it as follows.

let trial = {
type: jsPsychHtmlKeyboardResponse,
stimulus: "Bonjour! Please press any key."
}

Now, loading the page should prompt you with the text you entered. If you press any key, it disappears: the experiment
is actually finished.
We could also use jsPsychImageKeyboardResponse if we want to pre-generate our stimuli as im-
ages and display them directly. More precisions here121 .

16.5.3 Using the console interactively: accessing experiment data

Before going any further, let us test that the experiment worked as intended. If so, the data in our trial should have been
registered. You can access JsPsych’s saved data using jsPsych.data.get().
If we break down this line, here we access the property data of our jsPsych instance. But data actually
saves many metainfomations which are not of interest to us. Luckily; this data object has a convenient
function (or method) get() that allows us to precisely access test data.
Although you could use it in your script to access it at any given time, you can also use the console to access it whenever
you want. Try typing ``jsPsych.data.get() on the console.
It should print you something of the form Object { trials: (1) […] }, which you can unfold: trials
precisely contain the data about each trial. Right now, it should only contain one single trial, as an object with rt,
stimulus, and response properties.
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16.5.4 Response keys

In your trial’s data, response may contain any single key, since all are allowed by default. However, decision tasks will
require them to press one of two target keys. We can specify these targer keys using (yet another) parameter: choices.
As a value, we will pass it an array of valid keys in the forms of strings, here ‘f’ and ‘j’

let trial = {
type: jsPsychHtmlKeyboardResponse,
stimulus: "Bonjour! Please press any key.",
choices: ['f', 'j'].
}

16.5.5 Practice: color-detection task

You should now be able to program a simple experiments. Say we want to test if shapes interfere with color detection:
subjects will have to flag the color of successive shapes. They will have to press ‘f’ for red shapes and ‘j’ for blue shapes.
The design should be 3 shapes (rectangle, triangle, circle) by 2 colors (red and blue), with 6 trials in total. The order will
be fixed, and you are in charge of choosing it!
Beware of priming effects!
You can find a solution here.
Difference between viewport width (``vw``) and height (``vh``) and percents (``%``) If you used per-
cents, you may notice that the figures are slightly off.JsPsych uses a content wrapper, so % refers to it size.

16.5.6 Randomizing order

Of course, an experiment with trials in a fixed order is not interesting, because any effect we find may be restricted to this
specific order.
JsPsych provides use with a function to shuffle an array, i.e. order its element randomly: jsPsych.randomization.
shuffleNoRepeats. To randomize the timeline, use:

timeline = jsPsych.randomization.shuffleNoRepeats(timeline);

Here, we create a random array from the timeline. The ...NoRepeats part specifies that equal elements are not in
successive order. Since we only have a single occurrence of each trial, no item in our timeline is equal, and it thus does
not have any effect here.
However, it allows more to do more than prevent repetition of identical trials: we can also specifically define what it means
to be equal. To do so, we simply pass an additional argument: a function that returns whether two trials are equals. Here,
we want to define equal trials as those which have the same shape.
First, let’s add a shape property to our trial object. If you coded cleanly, creating a trial should be done using parame-
ters (in a for loop or even better a function) including a shape variable. Adding it to the trial should thus be fairly
straightforward.

trial = {
...
color: color;
}

Additional properties to the trial In JsPsych, a trial is a javascript object that uses some mandatory and/or
optional properties. It will only ever look up those, but that doesn’t mean you can not add other properties.

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You may check with the console that properties added this way will not be added in the data! The next session will develop
how to do it.
In the mean time, we can now define our equality function:

timeline = jsPsych.randomization.shuffleNoRepeat(timeline,
function(trial1, trial2){return trial1.shape == trial2.shape});

Factorial design We used here a 3 by 2 factorial design, which was simple enough to gen-
erate with a for loop. For more complicated factorial design, you may want to look up
the `jsPsych.randomization.factorial function <https://www.jspsych.org/7.0/reference/
jspsych-randomization/#jspsychrandomizationfactorial>`__.

16.5.7 Adding data to be saved

Although we could theoretically retrieve the color and property from the HTML string, it would be rather uneasy. We
can rather save directly color and shape values in our data, using the data property of our trial. data will be an
object that contains, as properties, everything we might want to plug into our data.

let trial = {
...
data: {color: "red", shape: "blue"},
}

As a small exercise: how can we update our equality test function?

16.5.8 Saving answer

If you go through the trials and try to analyse your data, you may notice that response only contains the pressed keys,
and not the color responded by the participant. While you could theoretically reconstruct it during your data analysis, this
approach is error-prone (in particular when you randomly assign responses keys).
Random response keys It is advised to randomly assign response keys to your participants, since
there are some known interactions between response side and task performance (see, e.g., the SNARC
effect122 ). To implement such a random choice, you may want to have a look at the `Math.
random function <https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/
Math/random>`__ from native JavaScript.
However, since the response is not known a priori, there is not much you can do as you create the trial (but you should
register response side for safekeeping!). JsPsych provides us with a neat workaround with the on_finish property of
trials. on_finish has to be a function that takes the trial’s data as an argument; it is not expected to return anything.
We can thus use on finish to modify the response encoded in our data:

let trial = {
...,
on_finish: function(data){
// We first save the response key in a more adequate variable
data.responseKey = data.response;

// We then save the actual responded color as the response

if(data.responseKey == "f"){
data.response = "red";
} else {
(continues on next page)
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(continued from previous page)

data.response = "blue";
}
}
};

Ternary operators The if-else construction here is rather cumbersome. Most languages (including
JavaScript) offer a ternary operator ?: that allow to replace it: condition ? a : b is a when
condition is true, and b otherwise. Try it!
This design is however very error-prone: if the [F] key is not litteraly encoded as the character "f" (or whichever you
use here), it may assign the wrong color to the response key! You also have to adapt everything each time you want to
change the keys or the color.
We’ll only focus on the first issue of key encoding here, since you should be able to have a code that is more robust to
keys/color changes on your own. JsPsych provides us with a way to compare the encoding of a key to a representation
such as "f": jsPsych.pluginAPI.compareKeys.

let trial = {
...,
on_finish: function(data){
// We first save the response key in a more adequate variable
data.responseKey = data.response;

// We then save the actual responded color as the response

if(jsPsych.pluginAPI.compareKeys(data.responseKey, "f")){
data.response = "red";
} else {
data.response = "blue";
}
}
};

16.5.9 Audio feedback

Here are two .wav sounds: correct.wav and incorrect.wav.We want to play them at the end of the trial to give audio
feedback to our participants.
To play audio in JavaScript, you first have to create Audio objects containing the audio file you want to play.

let audio = new Audio(pathToFile);

You can now play the audio using the play function of this audio object:

audio.play()

As small exercise, you should now be able to play a valid auditory feedback at the end of every trial. Hint below!
Hint

You should use the `on_finish` property we saw above!

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Programming for Cognitive and Brain Sciences

16.5.10 Saving the data

The experiment is almost ready! What we want to do now is to save our data. It can be saved locally (on the machine that
took the experiment), or, more interestingly, on a distant server.
In this course, we will only use local save, which is still useful for debugging and/or piloting. Our data object possesses
a localSave method that precisely saves the experiment’s data as a .csv file:

jsPsych.data.get().localSave('csv', "data.csv");

Where (i.e. when) to should this instruction be executed? At the end of the experiment! Similarly to trials, our JsPsych
instance can be created with an additional on_finish method. Note that unlike for trials, this one does not take a
data argument.

let jsPsych = initJsPsych({

on_finish: function(){
jsPsych.data.get().localSave('csv', "data.csv");
}
})

You may be surprised that we make a reference to the variable jsPsych within its actual creation. This is
possible because JavaScript will not evaluate functions before actually calling them. In other words, when
on_finish is called at the end of the trial, the function will then (and only then) look at whatever variable
labeled jsPsych it can find. By then, we will have created the variable already and so it will work. I
personally dislike this design which is error-prone (what if some code changes the value of jsPsych?);
however, this is what is officially used in JsPsych’s documentation123 . One protection I can propose is to
make jsPsych a constant with the const keyword. In JS like in most languages, constants have a name
in capital letters and spaces ```` are replaced by underscores _: JS_PSYCH.
Of course, youwant to go further than just storing the data on the participant’s computer. We want to retrieve it on our
laboratory server! Since the code will be very tributary of how said server is set up, you should see details with your lab’s
referent (where can you store the code, what protections…). You may find some documentation here124

16.5.11 Random ID

You may notice that we haven’t done anything about participant IDs. Assigning each participant a random ID is of course
mandatory in psychology experiments. JsPsych provides use with a convenient way to generate random IDs of a given
length: jsPsych.randomization.randomID.
We can create a 10-character long ID for our participant with the following line. We use a constant here because it should
never be modified.

const ID = jsPsych.randomization.randomID(10);

We can now add this ID info to all our trials. To this end, you can modify each trial individually using the data property
as above. Another way is to add a common property to the whole data, as describe in the documentation125 .
As a final note, you will most likely want to use this ID for the data file you save at the end of the experiment: if all
participants’ files have the same name, they will overwrite one another!

jsPsych.data.get().localSave('csv', "data-"+ID+".csv");

123 https://www.jspsych.org/7.0/overview/data/
124 https://www.jspsych.org/7.0/overview/data/#storing-data-permanently-as-a-file
125 https://www.jspsych.org/7.0/overview/data/#adding-data-to-all-trials

134 Chapter 16. Online experiments

 Programming for Cognitive and Brain Sciences

String formatting To get a cleaner script, you may use string formatting to plugging code output into a
string. Formatted string use this quote ``and have codes marked between brackets, the
opening bracket being preceded by a dollar sign$. An exemple:Bonjour! My
name is ${my_name}!`.

16.5.12 Final code

You can find a solution for the final code here. Make sure to try out to code it first! Practice makes perfect.
I did not do it in this example, but you should leave an end message to your participants, thanking them for their time. You
can create a jsPsychHtmlKeyboardResponse trial with no possible response by giving the choices property
the "NO_KEYS" value.

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136 Chapter 16. Online experiments

 CHAPTER

SEVENTEEN

REGULAR EXPRESSIONS

17.1 Tutorial

1. Watch the following introduction video to see how useful regular expressions can be.
Use of regular expressions to extract and transform information from text.
Watch on youtube126
2. Read the first two sections in Chapter 7 of Al Sweigart’s book “Automate the boring stuff”, page 161 to 166.
This will show you how regular expressions can be used in Python.
The book is available on Schoology127
3. Do all the lessons of the interactive tutorial at regexone.com128
This will teach you, through practice, the syntax of regular expressions.
4. Continue onto the practice problems at regexone.com129
To practice putting regular expressions to use in real-world problems.

17.2 Example in Cognitive Science research

Regular expressions have many applications, especially in natural language processing. Check out, for example, the
chapter Regular Expressions, Text Normalization, Edit Distance130 from Dan Jurasfky and Alex Martin’s book Speech
and Language Processing131 .
Regular expressions were used to locate syllable boundaries in the phonetic representation of words by Pallier (1999).
Syllabation des représentations phonétiques de brulex et de lexique.132 (see https://github.com/chrplr/openlexicon/tree/
master/scripts/french-syllabation for scripts and more).
126 https://youtu.be/xseViAOrKvM
127 https://app.schoology.com/course/4637783206/materials/gp/4653909275
128 https://regexone.com/
129 https://regexone.com/
130 https://web.stanford.edu/~jurafsky/slp3/2.pdf
131 https://web.stanford.edu/~jurafsky/slp3/
132 https://www.pallier.org/papers/syllabation.pdf

137
Programming for Cognitive and Brain Sciences

17.3 More on the Theory

A regular regression describes a formal language. A formal language is a set of strings over a finite alphabet. For example,
the set L = { an bn | n > 0} is a formal language.
A formal language is often defined by means of a formal grammar: a start symbol and a set of production rules that,
when applied, generate all the strings of the language but no more. For example, the grammar with start symbol ‘S’ and
production rules S -> aSb, S -> ab generates L.
The problem of matching or recognizing a language is to decide whether a given strings belongs to the language (as
when deciding whether a string matches a regular expression). Depending on the language, this can be more or less
difficult to solve. For example, L cannot be recognized by a finite-state automaton, but can be recognized by a type of
automaton equipped with a stack (known as a pushdown automaton). One such automaton would push onto its stack each
‘a’ encountered starting from the beginning of the string, then pop one ‘a’ from the stack for each ‘b’ encountered, and
would decide that the string matches iff the stack is empty when reaching the end of the string.
Chomsky’s hierarchy establishes a direct correspondance between certain classes of languages or grammars and certain
types of machines/automata that can recognize them. See the wikipedia article133

Fig. 1: Chomsky’s hierarchy (copied from wikipedia)

Regular expressions are a class of languages that can be recognized very efficiently while still being expressive
enough for many applications, which is why they are such a practical tool for everyday practice. (Note: The “regular
expressions” provided in modern computer software are a bit more expressive than the narrower “regular language” class
as defined in theory, because they include additional mechanisms such as lookahead).
To learn more about theory, check out this reference book (chapter 3 for regular expressions and automata):
Alfred V. Aho, Ravi Sethi & Jeffrey D. Ullman. “Compilers: principles, techniques, & Tools”. Addison-
Wesley, 1986.

133 https://en.wikipedia.org/wiki/Chomsky_hierarchy#The_hierarchy

138 Chapter 17. Regular Expressions

 CHAPTER

EIGHTEEN

SIMULATIONS

Contents

• Simulations
– Monte Carlo Estimation
– Fractals
– Formal systems
∗ MU Puzzle
∗ Cellular Automata
∗ Natural Language Parsing
– Artificial Neural networks
∗ Hopfield network
∗ Perceptron
∗ Backpropagation
∗ Using tensorflow and keras to build neural nets

18.1 Monte Carlo Estimation

• Read about Monte Carlo estimation of PI134

• Write a script that estimates the number ‘pi’ using this method.
• Compare it to my solution: simulations/estimate_PI_by_MonteCarlo.py)
134 https://academo.org/demos/estimating-pi-monte-carlo/

139
Programming for Cognitive and Brain Sciences

18.2 Fractals

Fractals135 are figures that are self-similar at several scales.

• Write a script that displays the Koch snowflake136
Hints:
– use the turtle module
– use recursion
My solution: koch0.py

18.3 Formal systems

18.3.1 MU Puzzle

A famous seminal book in Cognitive Science is Gödel Escher Bach: An Eternal Golden by Douglas Hofstadter. Its main
topic is recursion and self-reference (see also I am strange loop by the same author).
According to Hofstadter, the formal system that underlies all mental activity transcends the system that supports it. If
life can grow out of the formal chemical substrate of the cell, if consciousness can emerge out of a formal system of
firing neurons, then so too will computers attain human intelligence. Gödel, Escher, Bach is a wonderful exploration of
fascinating ideas at the heart of cognitive science: meaning, reduction, recursion, and much more (from https://medium.
com/@alibedirhan.d/mu-puzzle-f651ef3957c5)
The book is filled with puzzles, including Hofstadter’s famous MU puzzle. The MU puzzle involves a simple formal
system called MIU.
A starting string, MI, is given. Four rules for changing the string of characters into a new one are provided (see below).
A each step, the current string can be transformed into a new string by the application of one of the four rules. Note that
rules are one-way! In case there are several applicable rules, there is nothing that will dictate which rule you should use,
it’s up to you! Here are the rules:
1. If you possess a string whose last letter is I, you can add on a U at the end. For example MIUI can be rewritten
MIUII. This rule can be written xI -> xIU where x represents any string
2. Suppose you have Mx. Then you may rewrite it Mxx. For example, from MIU, you may get MIUIU (x = IU
therefore; Mxx = MIUIU; From MUM, you may get MUMUM, From MU, you may get MUU, …
3. If III occurs in one of the strings, you may make a new string with U in place of III. For example,
From UMIIIMU, you could make UMUMU; From MIIII, you could make MIU (also MUI). From IIMII,
you can’t get anywhere using this rule because the three I’s have to be consecutive.
4. If UU occurs inside one of your strings, you can drop it. From UUU, you get U. From MUUUIII, get MUIII.
The Mu Puzzle asks whether starting from the string MI, there exists a derivation, that is a sequence of aplications of the
rules, that can yield the string MU.
Exercice: Write a Python script that explores the set of strings generated by this formal system: study the length of the
string produced after ‘n’ steps (run this process several times and compute an histogram).
Then you may read :
• https://en.wikipedia.org/wiki/MU_puzzle
135 https://en.wikipedia.org/wiki/Fractal
136 https://en.wikipedia.org/wiki/Koch_snowflake

140 Chapter 18. Simulations

 Programming for Cognitive and Brain Sciences

• Ernest Nagel and James Newman’s book Gödel’s Theorem137 (translated into French : Le théorème de Gödel138 )

18.3.2 Cellular Automata

Learn about Conway’s Game of Life139 . Watch this140 and that141 videos.
• Implement an Elementary cellular automaton142 . The aim is to reproduce the graphics shown at the bottom on the
previous page. you can take inspiration from the excellent Think Complexity143 by Allen B. Downey. My solution
is at cellular-automata/1d-ca.py.
• Implement the Game of Life in 2D.
• Going futher: If you enjoy Cellular Automata, you can read Stephen Wolfram’s A New Kind of Science144 . A
more general book about Complexity is Melanie Mitchell’s Complexity: a guided tour.

18.3.3 Natural Language Parsing

Parsing refers to building the syntactic structure of a sentence from the linear sequence of words that compose it.
• Read Chapter 12 (Constituency Grammars) and 13 (Constituency Parsing) of Dan Jurafsky and James H. Martin’s
Speech and Language Processing145
• Explore the various parsing algorithms146 using the Natural Language Toolkit147 .

18.4 Artificial Neural networks

18.4.1 Hopfield network

Read https://towardsdatascience.com/hopfield-networks-are-useless-heres-why-you-should-learn-them-f0930ebeadcd
and do not look at the jupyter notebook implementation provided by the author. Try to program a hopefield network and
teach irt a few patterns. Only then, check the author’s solution.
To go further you can read:
• Ramsauer, Hubert, Bernhard Schäfl, Johannes Lehner, Philipp Seidl, Michael Widrich, Thomas Adler, Lukas
Gruber, et al. 2020. “Hopfield Networks Is All You Need.” ArXiv:2008.02217 [Cs, Stat], December.
http://arxiv.org/abs/2008.02217.
137 http://calculemus.org/cafe-aleph/raclog-arch/nagel-newman.pdf
138 https://www.eyrolles.com/Sciences/Livre/le-theoreme-de-godel-9782020327787/
139 https://en.wikipedia.org/wiki/Conway%27s_Game_of_Life
140 https://www.youtube.com/watch?v=S-W0NX97DB0
141 https://www.youtube.com/watch?v=C2vgICfQawE
142 https://en.wikipedia.org/wiki/Elementary_cellular_automaton
143 http://greenteapress.com/wp/think-complexity-2e/
144 https://en.wikipedia.org/wiki/A_New_Kind_of_Science
145 https://web.stanford.edu/~jurafsky/slp3/
146 http://www.nltk.org/book/ch08.html
147 https://www.nltk.org/

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Programming for Cognitive and Brain Sciences

18.4.2 Perceptron

1. Read about the Percepton at https://medium.com/@thomascountz/perceptrons-in-neural-networks-dc41f3e4c1b9

2. Implement a Perceptron in Python
For a solution, check : https://blog.dbrgn.ch/2013/3/26/perceptrons-in-python/

18.4.3 Backpropagation

To understand the basics of artificial neural networks, I recommend that you first read https://victorzhou.com/
blog/intro-to-neural-networks/ and then watch the four excellent videos at https://www.youtube.com/playlist?list=
PLZHQObOWTQDNU6R1_67000Dx_ZCJB-3pi . The last two of them focus on the backpropagation algorithm that
allows one to train network to learn mappings.
Next, you can read and try to understand this implementation148 of the backpropagation algorithm.
Then, see a modern and efficient implementation of neural networks: https://pytorch.org/tutorials/beginner/deep_
learning_nlp_tutorial.html
More readings:
• The Unreasonable Effectiveness of Recurrent Neural Networks149 on Andrej Karpathy’s blog.
• understanding LSTM Networks150
• Pattern recognition and machine learning151 by Christopher M. Bishop

18.4.4 Using tensorflow and keras to build neural nets

The following book is a gentle introduction: https://www.goodreads.com/book/show/

53483757-ai-and-machine-learning-for-coders

148 https://visualstudiomagazine.com/articles/2017/06/01/back-propagation.aspx
149 http://karpathy.github.io/2015/05/21/rnn-effectiveness/
150 http://colah.github.io/posts/2015-08-Understanding-LSTMs/
151 https://www.springer.com/fr/book/9780387310732

142 Chapter 18. Simulations

 CHAPTER

NINETEEN

HOPFIELD NETWORKS

Hopfield networks are a type of artificial neural network that can implement an associative memory.
A Hopfield network can be wired to memorize certain states: when given an incomplete or corrupted version of one of
the memorized state, it will restore the original state. Demo152 .

19.1 Model

19.1.1 Structure

• A Hopfield network consists of N neurons, each of which can have two states, +1 or -1. The state of the whole
network can be written as a binary vector of size N. We will use a 1-dimensional array to code that state, e.g.
state = np.array([+1, -1, -1, -1]).
• The weights of the connections between the neurons can be written as a matrix of size N×N. We will use a 2-
dimensional array to code that matrix, e.g. weight = np.array([[0, -1, -2, +1], [-1, 0, +3,
-1], [-2, +3, 0, -1], [+1, -1, -1, 0]]).
152 https://www.youtube.com/watch?v=HOxSKBxUVpg

143
Programming for Cognitive and Brain Sciences

• In Hopfield networks, the connections are symmetric and there are no self-recurrent connections. Thus, the weight
matrix is symmetric (weight[i, j] == weight[j, i]) and its diagonal is zero (weight[i, i] ==
0).

19.1.2 Updating

• The state of a neuron is updated according to the sign of the input it receives in the following way:
• Here we will use the synchronous update rule, where all of the neurons are updated at the same time from one time
step to the next.

19.1.3 Exercise 1.

• Write a function to compute the next state of a Hopfield network given the previous state and the weight matrix.
Tip: You can use a matrix multiplication153 (to do it in NumPy, see here154 ).
• Write a function to compute the final state reached by a network given an initial state and its weight matrix. This
will either be a stable state, starting from which the next state remains the same, or the state after a max. number
of iterations that you will set in case no stable state is reached.
• Test your function with the below initial state and weight matrix. The final state should be [+1, -1, -1, +1].
Is it a stable state?

initial_state = np.array([+1, -1, -1, -1])

weight = np.array([
[0, -1, -1, +1],
[-1, 0, +1, -1],
[-1, +1, 0, -1],
[+1, -1, -1, 0]])

A solution: hopfield_1.py155 .

19.2 Computing the weight matrix

19.2.1 To memorize a single state

Suppose you want to memorize the state [s1, s2, s3, s4]. To do so, you will set the matrix to:

weight = np.array([
[0 , s1*s2, s1*s3, s1*s4],
[s2*s1, 0 , s2*s3, s3*s4],
[s3*s1, s3*s2, 0 , s3*s4],
[s4*s1, s4*s2, s4*s3, 0 ]])

153 https://en.wikipedia.org/wiki/Matrix_multiplication
154 https://numpy.org/doc/stable/user/quickstart.html#basic-operations
155 https://github.com/chrplr/PCBS/blob/master/simulations/hopfield/hopfield_1.py

144 Chapter 19. Hopfield Networks

 Programming for Cognitive and Brain Sciences

19.2.2 Exercise 2a.

• Try it using your own example state. Replace the values in the above weight matrix with the values of the state you
want to memorize, then test that it is stable state using the function you wrote earlier.
• Also try an initial state that is a corrupted version of the memorized state where one neuron has been flipped. Is
the state effectively restored?

19.2.3 To memorize multiple states

Now, suppose that you want to memorize multiple states. To do so, you simply need to sum the weight matrices corre-
sponding to each state according to the previous formula.

19.2.4 Exercise 2b.

• Write a function to compute the weight matrix from a set of states.

• If you have time: Implement this function using the outer product (if you haven’t done so already). It gives a neat
and efficient way to perform this computation.
Tip: Formally, the individual weight matrix to memorize one state is the outer product of this state with itself. The
wikipedia page156 tells you how to compute this outer product with a matrix multiplication. You can then think of
how to extend this operation for multiple states such that it gives you the sum of the outer products of individual
states.
• Test your function with two memorized states of size 4. Verify that they are stable states, and that you can recover
them starting from a corrupted state with one neuron flipped.
A solution: hopfield_2.py157 .

19.3 Encoding images

• Let’s make all of this more visual and fun! We will encode 5×5 binary images into states. To define these images,
we will use strings such as this one:

"""
11111
1....
11111
....1
11111
"""

156 https://en.wikipedia.org/wiki/Outer_product
157 https://github.com/chrplr/PCBS/blob/master/simulations/hopfield/hopfield_2.py

19.3. Encoding images 145

Programming for Cognitive and Brain Sciences

19.3.1 Exercise 3.

• Write a function to convert such a string into 2d matrix which represents the image. Test your function and display
the image using matplotlib.pyplot.imshow().
• Write a function to convert such a 2d image matrix into a 1d state vector that can be encoded by a Hopfield network,
and another function to convert the state into a 2d image. Here is a tip158 . Test your functions.
A solution: hopfield_3.py159 .

19.4 Simulations

19.4.1 Exercise 4

• Make a network to memorize the following images160 .

• For each of the following initial states161 , compute the final state that the network reaches and plot the 2d images
corresponding to the initial state and the final state side-by-side.
• What do you observe? Does the network successfully restore the memorized images? Does it always converge to
one of these images? Are there any unexpected behaviors?
A solution: hopfield_4.py162 .

19.4.2 Exercise 5

• Now make another network to memorize the following images163

• Test the network with those same states as initial states.
• What do you observe?
A solution: hopfield_5.py164 .

19.5 Discussion

What do you think are the strengths and weaknesses of such networks as a model of the brain?

158 https://numpy.org/doc/stable/reference/generated/numpy.reshape.html?highlight=reshape#numpy.reshape
159 https://github.com/chrplr/PCBS/blob/master/simulations/hopfield/hopfield_3.py
160 https://github.com/chrplr/PCBS/blob/master/simulations/hopfield/str_pattern_defs.py
161 https://github.com/chrplr/PCBS/blob/master/simulations/hopfield/str_initial_state_defs.py
162 https://github.com/chrplr/PCBS/blob/master/simulations/hopfield/hopfield_4.py
163 https://github.com/chrplr/PCBS/blob/master/simulations/hopfield/str_pattern_defs_2.py
164 https://github.com/chrplr/PCBS/blob/master/simulations/hopfield/hopfield_5.py

146 Chapter 19. Hopfield Networks

 CHAPTER

TWENTY

WEB SCRAPING

(activity developed by Ewan Dunbar165 )

• !!Read this first!!
• Overview
• Web scraping
– General instructions and a partly-worked example exercise
∗ Notes on idiomatic Python
∗ Notes on Python style conventions
∗ Notes on how to do this project
∗ Notes on opening files
∗ Notes on testing your code
∗ Hint
∗ Unicode
– Exercise 1: Command line arguments
∗ Recommended approach
– Exercise 2: Processing HTML
∗ Structure
∗ Reminder
∗ Documentation strings
∗ Docstrings versus inline comments
∗ What functions should do
∗ Note
∗ Scope
– Exercise 3: Accessing web pages
∗ BE CAREFUL
∗ This is a bigger task
– Exercise 4: Refactoring your code
165 http://individual.utoronto.ca/ewan_dunbar/

147
Programming for Cognitive and Brain Sciences

∗ Importing functions
∗ Scripts and modules
∗ Testing your code
– Exercise 5: Crawling websites
– Exercise 6: Cleaning up text
– Exercise 7: Transition probabilities
– Exercise 8: Generating text from a bigram language model
• Resources

!!Read this first!!

This is an optional project aimed at those who have a fair bit of experience programming and want to learn
quickly how to do some useful things in Python, and/or feel like they know how to mess around with code
but don’t quite feel like “programmers,” or would just like to become better programmers. You may not feel
like a programmer when you are done either, but, if you follow the instructions you will certainly feel much
more like a programmer. In that spirit, it is very much a “self-guided tour.” You will get instructions on
what to do, but you will need to make heavy use of online resources to figure out how to do these things.
This project consists of a series of exercises. It is incremental. You need to start at the beginning, because
each part relies on the previous, but you can stop at any point.
This project will not be marked. But, if you take this project on, we would like to:
• See you finish it by the end of the course
• Check in on you each week
• Spend a small amount of time at the end of the course going over your project to give qualitative
comments
We will also of course help you by answering any questions you may have by email or in person. For this
reason, if you are going to do this project, we ask that you sign up: send an e-mail to both Info 2 instructors
(Christophe Pallier and Ewan Dunbar) saying that you’re going to do the project (not to the Google Group).
Keeping in touch will also help us to fix any potential bugs in the project instructions as quickly as possible.
You are encouraged, but not required, to find a partner, and work on this project in pairs. If you choose to do
this, it is up to you to divide the labour. It is recommended that you use the opportunity to read each other’s
code carefully, check it over, and discuss it.
In either case, again, if you are going to do this project, we ask that you sign up: please send an e-mail
to us saying that you’re going to do the project (not to the Google Group). If you are going to work in
pairs, one email (cc’ed to both partners), will suffice.

148 Chapter 20. Web Scraping

 Programming for Cognitive and Brain Sciences

Overview

This project will introduce you to a programming task that will be useful if you do projects with language:
harvesting textual data from the web and cleaning it up. The last exercise will also get you thinking about
what you can do with textual data.
On the way, you will be required to learn certain key Python skills which are far more generally applicable,
including:
• Using the Python documentation
• Reading from a file
• Writing to a file
• Downloading web pages
• Command line arguments
• Common Python idioms
• Imports
• Basic text processing
Thus, perhaps the more pertinent goal of this project is to give a self-guided tour of Python to those who
have programmed before in other languages, and/or to give those who have programmed before, either in
Python or not, a good sense for some basic good programming practices, including:
• Style and variable naming
• Documentation
• Use of functions
• Organizing your code
• Attacking complex problems by sub-dividing them
The point of the last is to help you build up the skills to create working code. The point of the first four is
to prevent you from creating code that is “write-only”: code which works, but which cannot be revisited or
modified (or maybe even finished) by you or anyone else, because it cannot be read or understood. The larger
goal of these last four is to remind you that computer source code is exclusively for human beings, not for
computers; compiled computer machine code (which you may never touch) is for computers. Source code
is a way for you to sort out a human-comprehensible explanation of what the machine code to solve your
problem should do, save it, share it with other human beings who would like to understand it too, and use it
again in the future for other purposes (it is, incidentally, also the easiest way to generate machine code, but
it is not the only way). The instructions for this project will give you some very general guidance on how to
do these five things.
The instructions for this project will not give you much guidance on how to integrate two other essential
programming practices into your work, the use of unit tests and the use of the interactive debugger,
because the above is already a lot, but, if you’d like a bit more practice, you may also find this to be a
good exercise in developing these practices. You can find useful information on unit tests and the interactive
debugger below under Resources.
By the end of the project, your instructions will become less detailed. You will have to make more and more
design and style decisions for yourself. To guide you, should try and find as many examples of good Python
code as possible. This page is a good resource.166
166 http://docs.python-guide.org/en/latest/writing/reading/

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Web scraping

You may often want to download a large set of web pages, or specific content from those web pages, from an
entire web site or set of web sites. A program which does this is called a web crawler. A web crawler that
looks for very specific information and tries to extract it automatically is called a web scraper. Web scrap-
ing is sometimes used by companies to collect up-to-date information on prices or other quickly-changing
information, and may not be well looked upon by the target sites, for various reasons, but mainly that any
web crawler has the potential to create a huge amount of traffic and overload the site. However, if done in a
respectful way, web crawlers can be very useful, and, indeed, are essential to your daily life: Google relies
on a massive web crawler to find new or updated web pages, so that it can then index them so that you can
find them when you search.
Your job is to write Python code that automatically downloads a portion of Wikipedia. It is not strictly nec-
essary to crawl Wikipedia, because the entire contents are freely available to download in large compressed
files. If you want to work with Wikipedia in the future, it is recommended that you make use of thse files
instead of crawling. However, Wikipedia permits light crawling of articles, and, as Wikipedia is a very useful
collection of natural language texts, it serves as a useful example.

General instructions and a partly-worked example exercise

This is a warmup exercise that is mostly done for you. This section is intended to establish some coding
conventions that you should use in this project.
All of your code should run on the command line (rather than from inside a Python notebook or iPython).
If you’re not familiar with how to run Python scripts programs from the command line, read this document
first167 (if your path is set up correctly on Windows, which it already should be, then you should not need
to type the full path name to the Python interpreter, python.exe, contrary to what is suggested in the
document).
You should create a folder just for this project.
Go in your browser to the English Wikipedia page for the stipple-throated antwren.168 Copy and paste all of
the text from this page and save it as a text file in your project folder. Let’s start by writing a Python program
that reads this file and prints it to the screen.

Notes on idiomatic Python

In each programming language, there are conventions for writing programs or for doing certain programming
tasks in a particular way that are generally adhered to, or at least very easily understood, by the community, but
may not be obvious a priori (programming language “idioms”). Programmers in that language adhere to these
conventions mainly because doing so helps make programs in that language easier to read and understand
(for you, not just for others), and also sometimes because they may be useful ways to avoid errors.
The idiomatic Python way to write a program that runs on the command line is to structure your file like this:

# Imports, definition of functions, ...

if __name__ == "__main__":
# The code that runs when the program is launched...

coming at the end of the file. The reason for this convention is explained on this Stack Overflow question.169
You should adhere to this convention for the rest of this project.
167 http://pythoncentral.io/execute-python-script-file-shell/
168 https://en.wikipedia.org/wiki/Stipple-throated_antwren
169 http://stackoverflow.com/questions/419163/what-does-if-name-main-do

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For example, in this exercise - which doesn’t really require you to write any new functions, but which might
require you to import the sys module, depending on how you solve it - you might get a short script that
looks something like this:

import sys

if __name__ == "__main__":
# All your code...

You can get more tips on writing idiomatic Python at this site.170

Notes on Python style conventions

Similar to idioms (but more to do with low-level things like formatting) is “style.” This includes naming
variables and constants, the number of spaces with which you indent, how many spaces you put around
parentheses, and so on. When working on large collaborative projects you will almost always be asked to
adhere to a set of style guidelines (and if you are working in a pair, you should do that here too). At the very
least, you need to be consistent internally. Many text editors have a “Format” function which can apply many
of your personal style conventions automatically, and most will do automatic indentation and allow you to
set the number of spaces.
In Python, the standard, and highly recommended, style guidelines are called PEP 8, and are accessible
here171 .
The specification for this exercise asks you to read one file. The simplest way to do this (and there-
fore the ideal way, following the Zen of Python172 ) is to hard-code the filename as a constant (a vari-
able that doesn’t change). In Python, unlike in other languages, constants have no special status - they
are variables like any other, and it is up to you not to change them. The style convention for showing
that something is a constant (nearly universally adhered to in all programming languages) is to put them in
ALL_CAPS_SEPARATED_BY_UNDERSCORES. Thus, your program will look something like this:

# Imports if necessary

if __name__ == "__main__":
INPUT_FILE = "stipple_throated_antwren.txt"
# Code to read and print the contents of that file...

Notes on how to do this project

This project is a self-guided tour. That means that the Python documentation173 and Stack Exchange174 are
your new best friends - well, right after Google175 .
Here, for example, is the sub-page from the Python tutorial on modules and imports.176
170 http://python.net/~goodger/projects/pycon/2007/idiomatic/handout.html
171 https://www.python.org/dev/peps/pep-0008/
172 http://python.net/~goodger/projects/pycon/2007/idiomatic/handout.html#the-zen-of-python-1
173 https://docs.python.org/2/
174 http://stackoverflow.com/questions/tagged/python
175 https://www.google.fr/?q=google+is+your+friend
176 https://docs.python.org/2/tutorial/modules.html

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Notes on opening files

There are many ways to open a file and you may find various pieces of advice, but there is an idiom. The
idiom has changed over the years, so we point out the idiomatic way to do this today, which is using with,
as described here.177 This page will give you almost the whole solution to this exercise (but not quite).

Notes on testing your code

You should always verify that your code is correct (i.e., that it gives the right answer on some important cases
for which you know the right answer).
In this case, the way to do that is to put the output of your program in a new file and then compare that one
with the original file. You can do this by redirecting the output that is printed to the screen into a text file,
such as output.txt (see instructions here178 for Unix-type systems, a subset of which should also work
on Windows179 ).
On Unix-type systems (such as Linux and OS X), as well as Windows 10 (if you follow these instructions180 ),
you can then compare the two files byte-by-byte using the diff program. If you don’t have access to diff,
there are many tools online for comparing two files.
The best practice is to have a program that automatically runs tests on your code, so that when you change
it, you know that it’s still doing what it used to do correctly. An important tool for doing this is to write
unit tests for each of your functions. As discussed above, developing the habit of unit testing is beyond the
scope of this project. However, it is a good idea, and if you wish to start now, you can start by reading this
document about unit testing in Python.181

Hint

Yes, the output should be exactly the same. If there are extra spaces or blank lines in your output, even at
the end of the file, get it so that your script’s output matches exactly before moving on.

Unicode

Sooner or later, you will run into error messages that mention Unicode, which have to do with special (non-
ASCII) characters. These errors are awful. Fixing problems with Unicode was a major motivation behind
Python 3. We, however, are using Python 2. As soon as you start getting these errors, see the Unicode
section under Resources below, and learn how to work them out as quickly as you can.
177 http://stackoverflow.com/questions/11555468/how-should-i-read-a-file-line-by-line-in-python
178 http://sc.tamu.edu/help/general/unix/redirection.html
179 https://www.microsoft.com/resources/documentation/windows/xp/all/proddocs/en-us/redirection.mspx?mfr=true
180 http://www.howtogeek.com/249966/how-to-install-and-use-the-linux-bash-shell-on-windows-10/
181 http://pymbook.readthedocs.io/en/latest/testing.html

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Exercise 1: Command line arguments

Finish the example exercise if you haven’t already, and save it as exercise_warmup.py. Make a copy
called exercise_1.py and modify it so that it reads the input filename as the first and only command-
line argument rather than storing it as a constant, and gives an appropriate error if no arguments are given.
Continue to save the rest of the exercises as separate scripts (for example, with the next exercise in a new file
called exercise_2.py).

Recommended approach

After a bit of Googling, you will be able to work out the basics of how command-line arguments work in
Python (you’ll know you’ve arrived when you start playing around with something called sys.argv). You
may also discover modules called getopt and argparse, which are more general solutions for reading
command-line arguments. It is very rarely a good idea to use a general solution when there is a simple one
unless you really need it, but argparse is so useful that there is no reason not to use it all the time. Learn
to use argparse. It will serve you well for the rest of the project, and for the rest of your career, to keep
a template handy for all your new Python scripts that might look very roughly like this:

import sys
import argparse

if __name__ == "__main__":
parser = argparse.ArgumentParser()
# ... Set up argparse ...
args = parser.parse_args(sys.argv[1:])
# ... Rest of your program starts here ...

Exercise 2: Processing HTML

In a web browser, save the raw HTML of the Wikipedia article on the stipple-throated antwren (rather than
just copying and pasting the text). Write a function called extract_wikipedia_contents that takes
HTML source and returns just the text of the article. Your script should take a single command-line argument
which is the name of the HTML file, call this function on the contents of the HTML file, and print the text of
the article to the screen (to be more precise, to standard output182 ). It’s up to you to determine what exactly
“the text of the article” means, except that it shouldn’t contain HTML codes or JavaScript, and it should
correspond, basically, to the English text that a human being would read if they went to read the Wikipedia
article. It doesn’t need to be the exact text that you copied and pasted above (and in fact, it probably shouldn’t,
because that likely contained Wikipedia navigation links which aren’t part of the article text).

Structure

This is where the idiomatic Python script structure starts to become non-trivial. Put your function defini-
tion(s) above if __name__ == "__main__", not inside it. This will make your script look something
like this:

# ... Imports ...

def extract_wikipedia_contents():
# ... Docstring ...
# ...
(continues on next page)
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(continued from previous page)

if __name__ == "__main__":
# ... Get command line arguments, read file ...
article_contents = extract_wikipedia_contents(article_html_source)
# ... Print article contents ...

Reminder

Your function should apply to the contents of the HTML file, not to the filename, and it should return the
text, not print it.

Documentation strings

All of your functions must be documented with block comments called documentation strings, or simply doc-
strings. The purpose of a docstring is to explain what the arguments to your function are, what it returns, as
well as a very concise, one-phrase summary of what it does, with perhaps a short paragraph elaborating some
relevant details. To get you started, here is a partial docstring for the extract_wikipedia_contents.
(Notice that html_source is the name of the argument to the function.)

"""Extract the text of a Wikipedia article from HTML

Here, it would be useful to describe a bit more about how you've chosen to
format the text that you're returning, and what exactly you mean by the
"article text."

Args:
html_source (str): HTML source of a Wikipedia article

Returns:
str: The text of the Wikipedia article
"""

A good practice (one which you have to force yourself to do, but which will help you write your programs
faster) is to write your docstrings before you write your functions. They force you to state exactly what
you intend the function to do. If you have that sorted out, writing the function becomes much easier. (For
example, now it should be absolutely clear that the input and output to this function are supposed to be
strings, and not lists or anything else.)
In the Resources below, you will find guidelines for writing docstrings in Python. Be consistent in your style
and remember that you’re communicating with the rest of the world.

Docstrings versus inline comments

Docstrings are not the same as inline comments. Inline comments (comments interspersed in your code)
should be used sparingly, and only where necessary, unlike docstrings. Inline comments explain the logic
of your code, if it isn’t obvious. They should not be used to explain what variable or function names mean,
or to explain enigmatic constants or clever ways to do things in only one line. The way to clarify unclear
variable names or mysterious constants is not to use unclear variable names or mysterious constants. The
way to clarify the clever thing you did is to never do clever things. Source code is a human-comprehensible
explanation of how some machine code works. You have the power to make fun puzzles for the reader, but
you shouldn’t.

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Here is a good summary of appropriate uses of inline comments183 .

What functions should do

Another useful result of writing your docstrings before you write your functions is that you will find out
whether or not your function is trying to do too much. A general rule is that if you can’t state precisely in a
few words what your function does, it’s probably trying to do too much.

Note

You may, of course, write as many functions as you want for this exercise, as long as you write ex-
tract_wikipedia_contents.

Scope

The goal of this exercise is not to learn to parse HTML. That’s a pain. Doing it well demands a whole course
of its own. Find a Python module that parses the HTML for you, then get the text out. Find the simplest one
possible.

Exercise 3: Accessing web pages

Write a modified version of your previous script which accesses Wikipedia online. It will still take a single,
text input file, specified on the command line, but that file will now contain a list of URLs to Wikipedia
articles, each on one line. The script will download each of these pages, and then print the contents of all
of them to standard output, in sequence. No clear separation between articles is necessary, nor do they
need to be in any particular order. You should be able to find Python modules that will download the
HTML contents of web pages for you and return them as a string, so you should be able to re-use your
extract_wikipedia_contents function (copy and paste it into your new script).

BE CAREFUL

You are writing a script that accesses web pages. People who build websites make web pages for people, not
for scripts. You should not push your luck, or you may be blocked from accessing the website. Wikipedia is
fine with you using scripts to access it, as long as you respect some rules:
• Don’t go too fast. Put a short delay (one second at least) between requests for pages.
• Make sure that your script reads and respects the robots.txt file. Specifically, that file (which is
just a text file), specifies what URLs you are allowed to access and what files you are not. Don’t access
any URLs you’re not allowed to.
• Respect Wikipedia’s policy on User-Agents184 .
183 https://blog.codinghorror.com/code-tells-you-how-comments-tell-you-why/
184 https://meta.wikimedia.org/wiki/User-Agent_policy

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This is a bigger task

This exercise is more complex. It may take some time, and it should take more than one function to accom-
plish. You need to read the robots.txt file, retrieve the contents of each of the URLs (being sure to
filter appropriately to respect robots.txt), and then apply extract_wikipedia_contents. You
need to make quite a few design decisions, and you need to document them in your docstrings. (Where do
you apply extract_wikipedia_contents? Where do you filter the URLs? Where do you read the
robots.txt? Where do you pause between requests?) Furthermore, before you do any of that, you need
to do some digging to figure out just how to do each of those things. (How do you access web pages? Where
is the robots.txt file? What happens if there’s a problem accessing a web page?)

Exercise 4: Refactoring your code

Your code from Exercise 3 has two logical components, corresponding to Exercise 2 (cleaning up Wikipedia
page HTML) and a new part corresponding to Exercise 3 (accessing websites). Up to now, you’ve been told to
write separate scripts, one for each exercise, and you were told to copy and paste your function from Exercise
2 into your Exercise 3 script. In this exercise, you will learn how to share Python code across different files
in the same directory, each of which collects together a set of useful, related functions.
Make a copy of your Exercise 2 script called wikipedia.py, and a copy of your Exercise 3 script called
web.py. In your exercise_4.py script, you will treat those scripts as modules, and import the functions
that you need from them. Your Exercise 4 script should behave exactly like your original Exercise 3 script
from the outside (that is, this is an exercise in refactoring your code185 ). However, you should ensure that
all the functions in your new web.py script should work for any website, not just Wikipedia. You may
simplify your interpretation of complex robots.txt files, so long as you err on the side of caution (never
do anything that you’re not allowed to do).

Importing functions

There are two conventional ways of importing functions (from your own code or from other modules) that
are recommended. One is to import the individual functions you need, as follows:

from wikipedia import extract_wikipedia_contents

Another is to import the entire file/module as a separate namespace186 .

import wikipedia

This requires that you then make explicit reference to the file/module that you imported when calling functions
from it:

article_contents = wikipedia.extract_wikipedia_contents(article_html_source)

This can get quite verbose, so there is a way of abbreviating the names of the files/modules you import (or,
rather, of changing the names of the associated namespaces):

import wikipedia as wp

# ...

article_contents = wp.extract_wikipedia_contents(article_html_source)

185 https://en.wikipedia.org/wiki/Code_refactoring
186 https://bytebaker.com/2008/07/30/python-namespaces/

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There is one method that is often cautioned against, because it may fill up your namespace unexpectedly with
function or variable names that you do not need and do not want, and that is this:

from wikipedia import *

In this case, it probably won’t do anything different (unless you defined additional functions in wikipedia.
py). But the above alternatives represent more predictable and understandable code.

Scripts and modules

You have just learned to import functions not from external modules, but from your own code! You may
be wondering how this is possible. It is possible because a Python module is simply any Python script that
defines functions, variables, or anything else (see here187 ). Yet the files you’ve written weren’t originally
intended for that. They were intended to be used as scripts to be run on the command line. This is not a bug
- it is a feature. There’s no need to work against it by removing the if __name__ == "__main__":
section of your newly created wikipedia.py and web.py files. This section of your code now serves as
an example of a standard way to use the functions you’ve defined.

Testing your code

Your Exercise 4 script should behave exactly like your original Exercise 3 script, and you should ensure that
all the functions in your new web.py script should work for any website, not just Wikipedia (including
respecting the robots.txt file, under whatever conservative interpretation you have decided to take). As
always, you should test your code and ensure that this is true. Now that you know how to import functions,
it is all the easier to start unit testing, i.e., writing your tests as separate functions that you put into a separate
testing script.

Exercise 5: Crawling websites

Instead of reading a list of URLs from a file, you will now crawl Wikipedia, starting from one article (or
perhaps a set of articles) and following links from those articles to find more articles to download. The article
or set of articles should be specified as titles (not as URLs) and you should also specify which language’s
Wikipedia contains the target article. You should decide whether it makes more sense to start from one
article or from more than one, and how to pass the article titles and the language in to your program. Your
crawler will download a maximum of 100 articles by following the first article link contained in each article.
(Your job is not to crawl all of Wikipedia - that will take forever and it may get you blocked - and you should
not need to build a tree of any kind.)
Instead of writing to standard output, you should now write the text of each article to a separate text file.
Each text file should have a filename that uniquely identifies that article in that language (it needn’t be the
title and language directly, but it could be).
As in Exercise 4, structure your code using modules and imports. You are free to create as many new
module files as you feel are appropriate, and add new functions to your old modules. Modules can import
code from other modules if necessary, but try and organize them so that they don’t, so that they can be used
independently of each other, as much as possible. Don’t reinvent the wheel. If you can reuse your old code,
do so. As always, document and test everything.
187 https://docs.python.org/2/tutorial/modules.html

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Exercise 6: Cleaning up text

Exercise 6 will be intended to work on the basis of the output of Exercise 5. Your new script will take as
command line arguments an output directory, and a list of file names (corresponding to individual Wikipedia
articles). For each file name, you will save a new version of that file in the specified output directory, which
has been cleaned up so as to have:
• One sentence per line
• The words in each sentence separated from each other by exactly one space
• Case (upper-case/lower-case) should be removed (normalize to either upper or lower case)
Choose to define “sentence” and “word” in some convenient (not necessarily careful) way. Decide how to
organize your new code, and document and test it.

Exercise 7: Transition probabilities

Write a script that takes a collection of text formatted as in the output of Exercise 6, specified on the com-
mand line as a set of corpus files and estimates, over the whole corpus (i.e., all the files, taken together),
the transition probability between words. That is, the probability of observing word :presentation:`B\
:math:`B``B right after word :presentation:`A\ :math:`A``A in the corpus. For example, in the following
three sentences -

The fox jumped

The dog kicked the fox
A fox jumped

• an easy transition probability to estimate is the probability of dog given the. There are three instances
of the, and one of them is followed by dog, so a reasonable estimate of the transition probability of dog
following the would be 1/3. The word here is “estimate” because your corpus is only a finite sample, and
simply counting would lead to some surprising results. For example, the transition probability of dog
following a would come out as zero. Look up and implement back-off and smoothing, and implement
simple versions of these. You will also need to calculate the probability of starting or finishing a sentence
with a particular word.
A useful resource for understanding these concepts is Jurafsky and Martin’s textbook188 , and in particular
Chapter 4 on n-grams.
Do not rely on NLTK or any external module for this.
Print the transition probabilities to a text file, in a format of your choosing. Decide how to organize your new
code, and document and test it.

Exercise 8: Generating text from a bigram language model

Write a script that takes the output of Exercise 7 and generates random text that follows the transition prob-
abilities.
188 http://stp.lingfil.uu.se/~santinim/ml/2014/JurafskyMartinSpeechAndLanguageProcessing2ed_draft%202007.pdf

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Resources

Idioms and style

• On the ``if __name__ == “__main__”:`
convention <http://stackoverflow.com/questions/419163/what-does-if-name-main-do>`__
• `On writing idiomatic
Python <http://python.net/~goodger/projects/pycon/2007/idiomatic/handout.html>`__
• `PEP 8 style
guidelines <https://www.python.org/dev/peps/pep-0008/>`__.
• The ``with` idiom for opening
files <http://stackoverflow.com/questions/11555468/how-should-i-read-a-file-line-by-line-in-python>`__
Docstrings and comments - Wikipedia on Python docstrings189 - Google Python docstring style190 - PEP 257 docstring
guidelines191 - What inline comments are for192
Command line arguments - `argparse <https://docs.python.org/3/library/argparse.html>`__
Useful facts - Standard input, output, and error193 - Namespaces194 - Python modules195
Examples Example Python code196
Unicode - Stack Overflow explanation of Unicode print problems197 - More on Unicode print problems198 - A more
technical list of Unicode frustrations in Python199 - Reading Unicode200 - Python Unicode HOWTO201
Unit testing - Unit testing and the ``unittest` module <http://pymbook.readthedocs.io/en/latest/testing.html>`__
Python debugger - pdb202
NLP textbook - Jurafsky and Martin draft203

189 https://en.wikipedia.org/wiki/Docstring#Python
190 http://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html
191 https://www.python.org/dev/peps/pep-0257/
192 https://blog.codinghorror.com/code-tells-you-how-comments-tell-you-why/
193 http://www.diveintopython.net/scripts_and_streams/stdin_stdout_stderr.html
194 https://bytebaker.com/2008/07/30/python-namespaces/
195 https://docs.python.org/2/tutorial/modules.html
196 http://docs.python-guide.org/en/latest/writing/reading/
197 http://stackoverflow.com/questions/4545661/unicodedecodeerror-when-redirecting-to-file
198 https://wiki.python.org/moin/PrintFails
199 https://pythonhosted.org/kitchen/unicode-frustrations.html
200 http://www.evanjones.ca/python-utf8.html
201 https://docs.python.org/2/howto/unicode.html
202 https://docs.python.org/2/library/pdb.html
203 http://stp.lingfil.uu.se/~santinim/ml/2014/JurafskyMartinSpeechAndLanguageProcessing2ed_draft%202007.pdf

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 CHAPTER

TWENTYONE

TOOLS TO DO REPRODUCIBLE SCIENCE

You should strive to make your experiments, simulations and data analyses reproducible, that is, anyone should be able to
check what you did, and reproduce it. You should be able to understand what you did, even years later.
This means that you should:
• keep track of exactly how you selected your materials (not only the end result)
• keep track of the precise recipes for the data analyses
This is very difficult to achieve! Here are some possible strategies:
1. keep a detailed lab notebook (few people manage to do it properly)
2. write computer scripts that automate the processing pipelines.
3. give up, hope you have not made mistakes, and will not need to check or rerun the experiment.
Although 3 is still the most widespread strategy among scientists, I cannot recommend it!

21.1 Two tools: literate programming and version control

Literate programming mixes code and text to produce a human readable document. It goes way beyond simply docu-
menting one’s code with comments. For example:
• Rmarkdown:
– comparing two treatments with R204 (source: https://github.com/chrplr/PCBS/blob/master/data-analysis/
comparing-two-means-dependent-groups.Rmd)
– see more at https://github.com/chrplr/statistics_with_R
– http://chrplr.github.io/PCBS/databases/lexique/interroger-lexique-avec-R.nb.html
• jupyter notebook:
– tutorial on Fourier analysis205
– tutorial on fMRI data analysis206
– see more at https://github.com/jupyter/jupyter/wiki/A-gallery-of-interesting-Jupyter-Notebooks
Remarks:
1. There are problems with tools such as Excel, E-Prime, …
• they are impossible to check thoroughly.
204 http:/chrplr.github.io/PCBS//data-analysis/comparing-two-means-dependent-groups.html
205 http:/chrplr.github.io/PCBS//data-analysis/short-intro-fourier.html
206 http:/chrplr.github.io/PCBS//data-analysis/Example+of+a+single+subject-single+run+fMRI+analysis+with+nistats.html

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• the files are saved in binary format (not human readable)

• the compatibility is not assured between successive versions.
2. In literate programming tools, text is often written in the markup language Markdown. You should definitely learn
it! (see https://www.markdownguide.org/getting-started). It is good enough to produce scientific reports (LaTeX
not needed!).
Version control systems (e.g. git, svn, mercurial,…) are useful for two reasons:
1. They allow you keep track of the complete history of a project. While your scripts or documents improve, it keeps
cached copies of the previous versions. This is much, much better than M using a numbering scheme and multiple
copies of the same file or directory (myfile001.doc, myfiles002.doc…).
2. They facilitate collaborating on projects (documents and programs) with other people.
• Bad: use email’s attachments to exchange successive versions of a file.
• Good: collaborate on a project by using a shared git repository
To go further;
• “Software Carpentry” : a site dedicated to teaching basic computing skills to researchers. See https://
software-carpentry.org/lessons
• INRIA’s MOOC: “Recherche reproductible: principes méthodologiques pour une science transparente”207
• Simon Tatham’s “How to Report Bugs Effectively”208

21.2 Lesson 101: how to compare files or directories

The most basic task is to compare two files. Your text editor may already have such a function built in — for example, in
Emacs, it is accessible through the command ediff or the menu Tools/Compare).
You can also compare two files on the command-line with the command diff:

diff file1 file2

But I recommend another command, meld (which can be downloaded from http://meldmerge.org), as it has a more
user-friendly output:

meld file1 file2

On Mac, meld can be difficult to install, you can rather use opendiff or filemerge (See https://eclecticlight.co/
2018/04/14/comparing-files-filemerge-opendiff-and-bbedit/).
These tools also work on directories. To quickly check if there is any difference between two directories:

diff -r -q dir1 dir2

or:

meld dir1 dir2

Note: If you compare text files that contain natural language, I recommend wdiff which ignores changes in whitespaces
(line breaks, etc.). For latex files, latexdiff produces a formatted output that clearly shows the textual differences.
207 https://learninglab.inria.fr/mooc-recherche-reproductible-principes-methodologiques-pour-une-science-transparente/
208 https://www.chiark.greenend.org.uk/~sgtatham/bugs.html

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21.3 Introducing git

A version control system keeps track of the history of changes to a project, allows one to explore ideas by maintaining
several parallel versions of the code.
In these lectures, we use Git. Although Git is a complex beast, you will only need to know a few commands (git
clone, git pull, git init, git add, git status, git commit and git push)

21.3.1 Creating a local repository

A local repository is simply a folder where you have ran the command git init:

mkdir project
cd project
git init
Initialized empty Git repository in /home/pallier/cours/Python/version_control/git-
,→test/.git/

Often, you will work on a local copy of a remote repository, imported either from another directory or from the Internet
using git clone:

git clone https://github.com/chrplr/pyepl_examples

Note: If, when you create a repository you already know that you want to share it on the internet, I recommend to first
create a repository on http://github.com or http://bitbucket.org, and then clone it on your local hard drive. In this way,
the internet location will be automatically added to the list of remote repositories under the name origin.
Importanly, with git, you can still do version control locally, and only transfer your changes to the remote repository
whenever you want, or never, because git is a decentralized version control system and all repositories are equal.

21.3.2 Adding files to the local repository

While working on the projectdirectory, you can tag files to track using the git add command:

echo 'essai1' > readme.txt # create a file "readme.txt"; you can also use an editor␣
,→like atom

git add readme.txt

To check which files are currently being tracked (or staged in git’s terminology), use the command `git status``:

git status
# On branch master
#
# Initial commit
#
# Changes to be committed:
# (use "git rm --cached <file>..." to unstage)
#
# new file: readme.txt
#

Note that you can add entire directories, for example:

git add .

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It is possible to prevent certain files to be tracked (see https://help.github.com/articles/ignoring-files)209 ).

21.3.3 Creating a commit (a.k.a. committing)

Once you are satisfied with the files in your working directory, you can take a snapshot, that is make a permanent copy
of all the tracked files. This operation is also called commiting your changes:
git commit -m 'my first attempt'
[master (root-commit) a7a3a47] First commit
1 file changed, 1 insertion(+)
create mode 100644 readme.txt

This saves a snapshot (or commit) of the staged files in the hidden directory .git at the root of your project. Unless you
delete this directory, this version of your files is saved there forever and will always be accessible.
Note: Before commiting, it is always useful to check which files are tracked and which are not, with git status.

21.3.4 Modifying the project

Let us now modify the file readme.txt in the working directory:

echo 'line2' >> readme.txt

The command git status allows us to check the state of the files in the working directory:
git status
# On branch master
# Changes not staged for commit:
# (use "git add <file>..." to update what will be committed)
# (use "git checkout -- <file>..." to discard changes in working directory)
#
# modified: readme.txt
#
no changes added to commit (use "git add" and/or "git commit -a")

git add readme.txt

git status
# On branch master
# Changes to be committed:
# (use "git reset HEAD <file>..." to unstage)
#
# modified: readme.txt
#

Let us create a new file, `readme2.txt``:

echo 'trial2' >readme2.txt
ls
readme2.txt readme.txt
git status
# On branch master
# Changes to be committed:
# (use "git reset HEAD <file>..." to unstage)
(continues on next page)
209 https://help.github.com/articles/ignoring-files

164 Chapter 21. Tools to do Reproducible Science

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(continued from previous page)

#
# modified: readme.txt
#
# Untracked files:
# (use "git add <file>..." to include in what will be committed)
#
# readme2.txt

We now add readme2.txt to the repository:

git add readme2.txt

git commit
[master a7e25a1] First revision; added readme2.txt
2 files changed, 2 insertions(+), 1 deletion(-)
create mode 100644 readme2.txt

Let us consult the history of the project:

git log
commit a7e25a158ce52a75c62381420f7dc375de631b1b
Author: Christophe Pallier <[email protected]>
Date: Mon Aug 27 10:49:54 2012 +0200

First revision; added readme2.txt

commit a7a3a47edfae9d7c720356b691000a81ded73906
Author: Christophe Pallier <[email protected]>
Date: Mon Aug 27 10:47:32 2012 +0200

First commit

git status
# On branch master
nothing to commit (working directory clean)

21.3.5 Renaming a file

To rename a tracked file, you should use git mv rather then just `mv``:

git mv file.ori file.new

21.3.6 Recovering a file deleted by accident

Let us delete readme2.txt “by accident”:

rm readme2.txt # oops
ls
readme.txt
git status
# On branch master
# Changes not staged for commit:
(continues on next page)

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(continued from previous page)

# (use "git add/rm <file>..." to update what will be committed)
# (use "git checkout -- <file>..." to discard changes in working directory)
#
# deleted: readme2.txt
#
no changes added to commit (use "git add" and/or "git commit -a")

To recover it:

git checkout -- readme2.txt

ls
readme2.txt readme.txt
cat readme2.txt
trial2

21.3.7 Checking for changes

Let us now modify readme2.txt and then compare the file in the current directory from the ones in the last commit:

echo 'line2 of 2' > readme2.txt

git diff
diff --git a/readme2.txt b/readme2.txt
index 33d1e15..e361691 100644
--- a/readme2.txt
+++ b/readme2.txt
@@ -1 +1 @@
-trial2
+line2 of 2
git status
# On branch master
# Changes not staged for commit:
# (use "git add <file>..." to update what will be committed)
# (use "git checkout -- <file>..." to discard changes in working directory)
#
# modified: readme2.txt
#
no changes added to commit (use "git add" and/or "git commit -a")

You prefer meld, you can use

git difftool -t meld

Compare the working version of a f ile with the one in the last commit ———————————————————
————

git diff HEAD

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21.3.8 Inspecting the history of the project

git log

For a graphical view of the history of the project:

gitk

21.3.9 Branches

One interest of git is that it is possible to create several branches to make independent developments and merge them
later.
To create a new branch:

git checkout -b [new_branch_name]

To list all branches:

git branch -a

To switch to an existing branch:

git checkout [branch_name]

To compare two branches

git difftool -d branch1..branch2

To compare a specific file:

git difftool branch1..branch2 -- filename

To merge a branch to the master branch:

git checkout master

git merge [branch_name]

21.4 Working with remotes

To add a remote repository

git remote add -f nameforremote path/to/repo_b.git

git remote update

To list the remotes

git remote -v

To compare the current branch with one in a remote

git diff master remotes/b/master

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To see branches on remotes

git branch -r

(To see local branches: git branch -l, all branches, git branch -a)

21.4.1 Downloading the most recent changes from the distant repository

If you imported your repository from the internet with git clone, you can import the recent changes with:

git fetch
git merge

21.4.2 Comparing the local working direcoty with a remote

If you want to compare the current working directory with the distant remote origin/master.

git fetch origin master

git diff --summary FETCH_HEAD
git diff --stat FETCH_HEAD

21.4.3 Pushing your changes to the distant repository

You can send your modified repository (after commiting) to the original remote internet repository:

git push

21.4.4 Handling very large files (e.g. data)

git-annex allows you to leave large files in some of the repositories and keep only links in others.
See https://writequit.org/articles/getting-started-with-git-annex.html and https://git-annex.branchable.com/
walkthrough/

21.4.5 Resources to learn more about Git

To learn more about git, check out:

• Openclassrooms’ MOOC Manage your code with Git and Github210
• https://product.hubspot.com/blog/git-and-github-tutorial-for-beginners
• https://git-scm.com/book/en/v2/Getting-Started-Git-Basics
• The Git Book211
• My own git cheat page212
• https://backlogtool.com/git-guide/en/
210 https://openclassrooms.com/en/courses/5671626-manage-your-code-project-with-git-github
211 https://git-scm.com/book/en/v2
212 http://www.pallier.org/version-control-at-your-fingertips-a-quick-start-with-git.html#version-control-at-your-fingertips-a-quick-start-with-git

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• https://www.atlassian.com/git/tutorials
To understand the inner workings of git, the following documents are useful:
• The Git Parable213
• Git from the bottom up214
Finally, the comprehensive documentation is the Git Book215

213 http://tom.preston-werner.com/2009/05/19/the-git-parable.html
214 https://jwiegley.github.io/git-from-the-bottom-up/
215 https://git-scm.com/book/en/v2

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170 Chapter 21. Tools to do Reproducible Science

 CHAPTER

TWENTYTWO

RESOURCES TO LEARN GIT

To understand why you need to learn git, see Tools to do Reproducible Science
• Openclassrooms’ MOOC Manage your code with Git and Github216
• https://product.hubspot.com/blog/git-and-github-tutorial-for-beginners
• https://git-scm.com/book/en/v2/Getting-Started-Git-Basics
• The Git Book217
• My own git cheat page218

216 https://openclassrooms.com/en/courses/5671626-manage-your-code-project-with-git-github
217 https://git-scm.com/book/en/v2
218 http://www.pallier.org/version-control-at-your-fingertips-a-quick-start-with-git.html#version-control-at-your-fingertips-a-quick-start-with-git

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172 Chapter 22. Resources to learn Git

 CHAPTER

TWENTYTHREE

HOW TO SOLVE PROBLEMS

“An expert is a man who has made all the mistakes which can be made, in a narrow field.” – Niels Bohr

Contents

• How to solve problems

– How to think like a programmer: lessons in problem solving
∗ Understand
∗ Plan
∗ Divide
∗ Stuck?
∗ Practice
∗ Conclusion
– How to report bugs effectively
– How to solve it by Polya
– Computer Science Distilled

23.1 How to think like a programmer: lessons in problem solving

The following sections are copied from https://medium.freecodecamp.org/how-to-think-like-a-programmer-lessons-in-problem-solving-d1

by Richard Reis.
So, what should you do when you encounter a new problem?
Here are the steps:

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23.1.1 Understand

Know exactly what is being asked. Most hard problems are hard because you don’t understand them (hence why this is
the first step).
How to know when you understand a problem? When you can explain it in plain English.
Do you remember being stuck on a problem, you start explaining it, and you instantly see holes in the logic you didn’t see
before?
Most programmers know this feeling.
This is why you should write down your problem, doodle a diagram, or tell someone else about it (or thing… some people
use a rubber duck).
“If you can’t explain something in simple terms, you don’t understand it.” –Richard Feynman

23.1.2 Plan

Don’t dive right into solving without a plan (and somehow hope you can muddle your way through). Plan your solution!
Nothing can help you if you can’t write down the exact steps.
In programming, this means don’t start hacking straight away. Give your brain time to analyze the problem and process
the information.
To get a good plan, answer this question:
“Given input X, what are the steps necessary to return output Y?”
Sidenote: Programmers have a great tool to help them with this… Comments!

23.1.3 Divide

Pay attention. This is the most important step of all.

Do not try to solve one big problem. You will cry.
Instead, break it into sub-problems. These sub-problems are much easier to solve.
Then, solve each sub-problem one by one. Begin with the simplest. Simplest means you know the answer (or are closer
to that answer).
After that, simplest means this sub-problem being solved doesn’t depend on others being solved.
Once you solved every sub-problem, connect the dots.
Connecting all your “sub-solutions” will give you the solution to the original problem. Congratulations!
This technique is a cornerstone of problem-solving. Remember it (read this step again, if you must).
“If I could teach every beginning programmer one problem-solving skill, it would be the ‘reduce the problem
technique.’
For example, suppose you’re a new programmer and you’re asked to write a program that reads ten num-
bers and figures out which number is the third highest. For a brand-new programmer, that can be a tough
assignment, even though it only requires basic programming syntax.
If you’re stuck, you should reduce the problem to something simpler. Instead of the third-highest number,
what about finding the highest overall? Still too tough? What about finding the largest of just three numbers?
Or the larger of two?

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Reduce the problem to the point where you know how to solve it and write the solution. Then expand the
problem slightly and rewrite the solution to match, and keep going until you are back where you started.”
–V. Anton Spraul

23.1.4 Stuck?

By now, you’re probably sitting there thinking “Hey Richard… That’s cool and all, but what if I’m stuck and can’t even
solve a sub-problem??”
First off, take a deep breath. Second, that’s fair.
Don’t worry though, friend. This happens to everyone!
The difference is the best programmers/problem-solvers are more curious about bugs/errors than irritated.
In fact, here are three things to try when facing a whammy:
Debug: Go step by step through your solution trying to find where you went wrong. Programmers call this debugging (in
fact, this is all a debugger does).
“The art of debugging is figuring out what you really told your program to do rather than what you thought
you told it to do.”” –Andrew Singer
Reassess: Take a step back. Look at the problem from another perspective. Is there anything that can be abstracted to a
more general approach?
“Sometimes we get so lost in the details of a problem that we overlook general principles that would solve
the problem at a more general level. […]
The classic example of this, of course, is the summation of a long list of consecutive integers, 1 + 2 + 3 + …
+ n, which a very young Gauss quickly recognized was simply n(n+1)/2, thus avoiding the effort of having
to do the addition.” –C. Jordan Ball
Sidenote: Another way of reassessing is starting anew. Delete everything and begin again with fresh eyes. I’m serious.
You’ll be dumbfounded at how effective this is.
Research: Ahh, good ol’ Google. You read that right. No matter what problem you have, someone has probably solved
it. Find that person/ solution. In fact, do this even if you solved the problem! (You can learn a lot from other people’s
solutions).
Caveat: Don’t look for a solution to the big problem. Only look for solutions to sub-problems. Why? Because unless you
struggle (even a little bit), you won’t learn anything. If you don’t learn anything, you wasted your time.

23.1.5 Practice

Don’t expect to be great after just one week. If you want to be a good problem-solver, solve a lot of problems!
Practice. Practice. Practice. It’ll only be a matter of time before you recognize that “this problem could easily be solved
with .”
How to practice? There are options out the wazoo!
Chess puzzles, math problems, Sudoku, Go, Monopoly, video-games, cryptokitties, bla… bla… bla….
In fact, a common pattern amongst successful people is their habit of practicing “micro problem-solving.” For example,
Peter Thiel plays chess, and Elon Musk plays video-games.
Fast-forward to today. Elon [Musk], Reid [Hoffman], Mark Zuckerberg and many others say that games have been
foundational to their success in building their companies.”–Mary Meeker (2017 internet trends report)
Does this mean you should just play video-games? Not at all.

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But what are video-games all about? That’s right, problem-solving!

So, what you should do is find an outlet to practice. Something that allows you to solve many micro-problems (ideally,
something you enjoy).
For example, I enjoy coding challenges. Every day, I try to solve at least one challenge (usually on Coderbyte).
Like I said, all problems share similar patterns.

23.1.6 Conclusion

That’s all folks!

Now, you know better what it means to “think like a programmer.”
You also know that problem-solving is an incredible skill to cultivate (the meta-skill).
As if that wasn’t enough, notice how you also know what to do to practice your problem-solving skills!
Phew… Pretty cool right?
Finally, I wish you encounter many problems.
You read that right. At least now you know how to solve them! (also, you’ll learn that with every solution, you improve).
“Just when you think you’ve successfully navigated one obstacle, another emerges. But that’s what keeps life
interesting.[…]
Life is a process of breaking through these impediments–a series of fortified lines that we must break through.
Each time, you’ll learn something.
Each time, you’ll develop strength, wisdom, and perspective.
Each time, a little more of the competition falls away. Until all that is left is you: the best version of you.”
– Ryan Holiday (The Obstacle is the Way)
Now, go solve some problems!
And best of luck!

23.2 How to report bugs effectively

A crucial skill is to be able to report problems so that other people can actually help you. Also by formulating a precise
question, chances are that you will see the solution by yourself.
On this topic, read How to Report Bugs Effectively219
219 https://www.chiark.greenend.org.uk/~sgtatham/bugs.html

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23.3 How to solve it by Polya

A classic book giving advice on how to solve problem: How to solve it220 by George Polya.
You can get the gist of it at https://en.wikipedia.org/wiki/How_to_Solve_It

23.4 Computer Science Distilled

A relevant book: Computer Science Distilled: Learn the Art of Solving Computational Problems221

220 https://math.hawaii.edu/home/pdf/putnam/PolyaHowToSolveIt.pdf
221 https://www.amazon.com/dp/0997316020/ref=sspa_dk_detail_4?psc=1

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 CHAPTER

TWENTYFOUR

WRITING CLEAN CODE

Contents

• Writing clean code

– Names
– Functions
– Successive refinement
– General
– Comments
– Testing

Most of these recommendations are copied verbatim from the book Clean Code222 by Robert C. Martin.

24.1 Names

• A function name should describes what the function does. Don’t be afraid to make a name long. A long descriptive
name is better than a short enigmatic name. A long descriptive name is better than a long descriptive comment.
• Don’t be afraid to spend time choosing a name. Indeed, you should try several different names and read the code
with each in place.
• Be consistent in your names. Use the same phrases, nouns, and verbs in the function or variables names.

24.2 Functions

• The first rule of functions is that they should be small. The second rule of functions is that they should be smaller
than that. Between 1 and 10 lines is usually good.
• A function must do one thing, and do it well. This is because we want each function to be transparently obvious.
For example, passing a boolean into a function is a truly terrible practice. It loudly proclaims that this function does
more than one thing: It does one thing if the flag is true and another if the flag is false!
• A function should have no side effects. If it does, your function promises to do one thing, but it also does other
hidden things. Sometimes it will make unexpected changes to the variables passed as parameters or to system
222 https://www.goodreads.com/book/show/3735293-clean-code

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globals. In either case they are devious and damaging mistruths that often result in strange temporal couplings and
order dependencies.
• Functions should either do something or answer something, but not both. Either your function should change the
state of an object, or it should return some information about that object. Doing both often leads to confusion.

24.3 Successive refinement

• Writing software is like any other kind of writing. When you write a paper or an article, you get your thoughts down
first, then you massage it until it reads well. The first draft might be clumsy and disorganized, so you wordsmith it
and restructure it and refine it until it reads the way you want it to read.
• In R. Martin’s words:
“When I write functions, they come out long and complicated. They have lots of indenting and nested loops.
They have long argument lists. The names are arbitrary, and there is duplicated code. But I also have a suite
of unit tests that cover every one of those clumsy lines of code.
So then I massage and refine that code, splitting out functions, changing names, eliminating duplication.
In the end, I wind up with functions that follow the rules I’ve laid down. I don’t write them that way to start.
I don’t think anyone could.”

24.4 General

• We want the code to read like a top-down narrative. Each function must tell a story. And each function should led
you to the next in a compelling order.
• Don’t Repeat Yourself. Duplicating the same code at, say four locations in your program, is a problem because
it bloats the code and will require four-fold modification should the algorithm ever have to change. It is also a
four-fold opportunity for an error of omission. Structured programming and Object-oriented programming were
invented in part as strategies to avoid duplication.

24.5 Comments

• Comments are, at best, a necessary evil. If our programming languages were expressive enough, we would not need
comments very much—perhaps not at all.
• Comments should say things that the code cannot say for itself.
• A comment worth writing is worth writing well. If you are going to write a comment, take the time to make sure
it is the best comment you can write. Choose your words carefully. Use correct grammar and punctuation. Don’t
ramble. Don’t state the obvious. Be brief.
• Learn about docstrings in Python223
• Learn about automatic generation of documentation with sphinx and readthedocs at https://www.pythonforthelab.
com/blog/documenting-with-sphinx-and-readthedocs/
223 https://www.datacamp.com/community/tutorials/docstrings-python

180 Chapter 24. Writing clean code

 Programming for Cognitive and Brain Sciences

24.6 Testing

It is an excellent idea to write tests that check your that your modules and function keep working as they should. It can be
as simple as having scripts that just run your code on some examples and check that it does not crash after an upgrade,
or following a unit testing methodology (see Getting Started With Testing in Python224 )

224 https://realpython.com/python-testing/

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182 Chapter 24. Writing clean code

 CHAPTER

TWENTYFIVE

BUILDING ABSTRACTIONS WITH RECURSIVE FUNCTIONS AND

HIGHER-ORDER FUNCTIONS

In programming, we control the intellectual complexity of our programs by building abstractions that hide details
when appropriate. You already know of one such means to build abstractions in Python: the ability to define your own
functions. This allows you to chunk compound operations as conceptual units, give them a name and manipulate them. In
this module, you will explore two other means to build abstractions with functions: recursive functions and higher-order
functions.

25.1 Recursive functions

1. Watch the introduction video and read the following summary paragraph.
Summary. Recursive definitions allow us to describe many complex concepts in a simple and elegant way. Likewise,
recursive functions in Python allow us to define methods for solving problems in a simple and elegant way. When doing
so, we think in terms of base cases, for which there is an immediate solution, and recursive cases, for which we can define
the solution to our problem in terms of solutions to smaller versions of the same problem. Once the solution has been
defined in such a way, translating it into Python code is a snap. This frees us from without having to worry about a whole
series of questions that would arise if we were to solve the problem iteratively (how to traverse sub-problems, how to
keep track of intermediate results, what the iteration variable is, what the stop conditions are…). In other words, we have
abstracted the solution from the nitty-gritty details of control flow, memory, etc.
2. Read section 16.1 to 16.6 of the interactive book thinkcspy at: https://runestone.academy/runestone/books/
published/thinkcspy/IntroRecursion/toctree.html
Sections 16.5. and 16.6 use the turtle graphics module which you may not be familiar with, but you should still be
able to grasp the code easily. You can skip them if you want, but visualization is a powerful way to learn about recursion.
3. Do some of the following practice exercises.
You can move to the next section whenever you feel ready to learn more, but make sure to do at least two exercises (like
any other programming concepts/techniques, recursive functions cannot be understood without practice).
Time to complete. [*]: short, [**]: medium, [***]: long.
Exercise 1. [*] Write a recursive function to reverse a list. (Hint: to concatenate two lists, use the ‘+’ operator).
Exercise 2. [*] Write a recursive function to reverse a list.
Exercise 3. [**] Write a script that displays the Koch snowflake (see on wikipedia225 ) using a recursive function. You
can use the turtle graphics module to draw on screen (as shown in section 16.5 of thinkcspy226 ).
A solution: link to code227 .
225 https://en.wikipedia.org/wiki/Koch_snowflake
226 https://runestone.academy/runestone/books/published/thinkcspy/IntroRecursion/intro-VisualizingRecursion.html
227 https://github.com/chrplr/PCBS/blob/9a9ebc54b5a03c4e58311cb0d0bd20ea12d0ec02/games/koch.py

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Exercise 4. [**] Write a script that returns the pathnames of all the files ending in .txt contained inside a directory (at
any depth of the hierarchy). You will need to use os.listdir() and os.path.isdir().
Exercise 5. [**] Write a recursive function to generate all permutations of a list of values. (This could be useful, e.g., to
do a permutation test for statistical analyses.)
Exercise 6. [***] Write a recursive function to evaluate an arithmetic expression given in Polish notation (i.e. prefix
notation, see on wikipedia228 )
Exercise 7. [***] Produce strings from the MIU formal grammar and investigate the MU puzzle. See detailed explana-
tions on the MU Puzzle.
Side remark: in some cases, recursive functions can take a prohibitive amount of time and/or memory. This happens when
the same computations are performed many times. This issue can be addressed using memoization. If you are curious,
you can read the article Memoization in Python229

25.2 Higher-order functions

1. Watch the introduction video.

2. Read section 1.6 Higher-Order Functions of the online textbook at: https://wizardforcel.gitbooks.io/
sicp-in-python/content/6.html
This textbook is an adaptation for Python of the textbook cited at the bottom of the page. (Author’s note: I haven’t
checked out the rest of this adaptation. I recommend to read the original book if you want to learn more.)
Stop and think: In the section of the book you have read, the functions summation and iter_improve were
implemented iteratively, using a while statement. Can you think of how to implement them recursively?
3. Do some of the following practice exercises.
Time to complete. [*]: short, [**]: medium, [***]: long.
Exercise 1. [*] Write a product function to compute the product of the values of a function at points over a given
range (the function should be an argument of product). Then, define a function to compute the factorial in terms
of product. Finally, use product to compute an approximation to pi using the Wallis product formula (see on
wikipedia230 ).
Exercise 2. [**] The summation function (from the textbook section you read) and the product function (de-
fined above) can be defined as special cases of an even more general reduce function which has two more arguments:
binary_operator (which specifies what operation should be applied to reduce all the values to a single one) and
neutral_element (which specifies what base value should be used when the range is empty). Write such a reduce
function, and then define summation and product functions in terms of reduce. Make sure to test your functions.
Exercise 3. [**] Write a function that finds a fixed point of a function (see on wikipedia231 ) starting from an initial
guess value, which could be defined as: find_fixed_point(f, initial_value, error_margin). The
returned value, x, should be such that abs(f(x) - x) < error_margin. Then, define a function to calculate
the square root of a positive number, using the property that the square root of x is a fixed point for the function y -> 1/2
(y + x/y). Make sure to test your square root function.
Exercise 4. [**] Write a function to numerically compute any statistic of an arbitrary random variable. The statistic and
the random variable should both be functions which are given as argument.
(Hints. A statistic can be defined as a function of a collection of samples, e.g. sample mean, sample variance. A random
variable can be defined as a function that, when it is called, generates one sample.)
228 https://en.wikipedia.org/wiki/Polish_notation
229 https://towardsdatascience.com/memoization-in-python-57c0a738179a
230 https://en.wikipedia.org/wiki/Wallis_product
231 https://en.wikipedia.org/wiki/Fixed_point_(mathematics)

184 Chapter 25. Building abstractions with recursive functions and higher-order functions
 Programming for Cognitive and Brain Sciences

25.3 Reference

This module was inspired by: Abelson, Harold, and Gerald Jay Sussman. Structure and interpretation of computer pro-
grams. The MIT Press, 1996.
It is an excellent computer science textbook. If you are curious, go check it out, it is freely available online as pdf232 and
as a web document233 .

232 https://web.mit.edu/alexmv/6.037/sicp.pdf
233 https://mitpress.mit.edu/sites/default/files/sicp/full-text/book/book.html

25.3. Reference 185

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186 Chapter 25. Building abstractions with recursive functions and higher-order functions
 CHAPTER

TWENTYSIX

SENDING TTL TRIGGERS

Many pieces of equipment synchronize by exchanging triggers (0/1 bits) on a TTL interface234 .
A TTL signal is defined as “low” when it is between 0 V and 0.8 V with respect to the ground terminal, and “high” when
it is between 2 V and VCC (5 V).
For example, you may need to send a trigger to an EEG or MEG recording machine, or wait for a MRI scanner signaling
that it is starting to acquire brain images.
To send or read TTL signals with your computer, you need some extra hardware (unless you have a Raspberry Pi which
has a GPIO port).

26.1 Parallel Port

A parallel port has become a rarity these days. It provides a number of Digital (TTL) Input/Ouput lines. The `ParallelPort
object in Expryiment <https://docs.expyriment.org/expyriment.io.ParallelPort.html>__ makes it extremely easy to access
them.
For example, to swith on and off every second the data lines of the first parallel port:

from time import sleep

from expyriment.io import ParallelPort

pp = ParallelPort('/dev/parport0')

while True:
pp.set_data(255)
sleep(1)
pp.set_data(0)
sleep(1)

Or to detect any change on any input pin of the parallel ports:

from expyriment import io

pports = [io.ParallelPort('/dev/' + pp)

for pp in io.ParallelPort.get_available_ports()]

prev_state = []
while True:
state = str([bin(p.poll()) for p in pports])
if state != prev_state:
(continues on next page)
234 https://en.wikipedia.org/wiki/Transistor%E2%80%93transistor_logic

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Programming for Cognitive and Brain Sciences

(continued from previous page)

print(state)
prev_state = state

(under Linux, you may need to run http://www.vdwalle.com/Norte/ppdiag.txt to set the adequate permissions)

26.2 DLP-IO8-G

The DLP-IO8-G235 is a USB-TTL device that provides 8 digital lines on which you can read or write. Plugged in USB
port, it is seen by the computer as a serial device. Thus, to communicate with it, you simply need to open the relevant
serial port and then write to or read from it.

Under Linux, the dlp-OI8-G driver is already present in the kernel. Once plugged, to determine the serial port it is attached
to, type the command dmesg in a Terminal. You should get something like:

[ 5128.109725] usbcore: registered new interface driver usbserial_generic

[ 5128.109730] usbserial: USB Serial support registered for generic
[ 5128.112142] usbcore: registered new interface driver ftdi_sio
[ 5128.112148] usbserial: USB Serial support registered for FTDI USB Serial Device
[ 5128.112175] ftdi_sio 1-1:1.0: FTDI USB Serial Device converter detected
[ 5128.112190] usb 1-1: Detected FT232RL
[ 5128.113130] usb 1-1: FTDI USB Serial Device converter now attached to ttyUSB0

The last line tells you that the device is at /dev/ttyUSB0.

235 http://www.ftdichip.com/Support/Documents/DataSheets/DLP/dlp-io8-ds-v15.pdf

188 Chapter 26. Sending TTL triggers

 Programming for Cognitive and Brain Sciences

26.3 Python

To use the device under Python, you need the pyserial module236

26.3.1 sending triggers

from serial import Serial

dlp = Serial(port='/dev/ttyUSB0', baudrate=115200) # open serial port

dlp.write(b'QWERTYUI') # set all lines to '0'

dlp.write(b'12345678') # set all lines to '1'

#! /usr/bin/env python3

""" Generate a square wave on pin1 of DLP-IO8-G """

from time import perf_counter

from serial import Serial

dlp = Serial(port='/dev/ttyUSB0', baudrate=115200) # open serial port

# byte codes to control line 1:
ON1 = b'1'
OFF1 = b'Q'

# number of periods
NPERIODS = 1000

# Timing of the square wave

TIME_HIGH = 0.010 # 10ms pulse
TIME_LOW = 0.090 # send every 100ms
PERIOD = TIME_HIGH + TIME_LOW

onset_times = [ (PERIOD * i) for i in range(NPERIODS) ]

i = 0
while i < NPERIODS:
if i == 0:
t0 = perf_counter()

# wait until the start of the next period

while perf_counter() - t0 < onset_times[i]:
None

dlp.write(ON1)

# busy wait for 'TIME_HIGH' seconds. This should be more accurate than time.
,→ sleep(TIME_HIGH)
t1 = perf_counter()
while perf_counter() - t1 < (TIME_HIGH):
None

dlp.write(OFF1)
(continues on next page)
236 https://pyserial.readthedocs.io/en/latest/shortintro.html

26.3. Python 189

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(continued from previous page)

i = i + 1
print(f"\r{i:4d}", end='')

time.sleep(TIME_LOW)
print()
print(f'{NPERIODS} periods of {PERIOD} seconds')
print('Total time-elapsed: ' + str(perf_counter() -t0))
dlp.close() # close the port

Here is the result on an oscilloscope:

26.4 Reading an input line

import time
import serial
import numpy as np
import matplotlib.pyplot as plt

dlp = serial.Serial(port='/dev/ttyUSB0', baudrate=115200) # open serial port

print(dlp.name) # check which port was really used
dlp.write(b'`') # switch to ascii mode

N = 1000
o = np.zeros(N) # will store timestamps when the input line is HIGH

i = 0
while i < N:
dlp.write(b'A') # request to read
(continues on next page)

190 Chapter 26. Sending TTL triggers

 Programming for Cognitive and Brain Sciences

(continued from previous page)

x = dlp.read(3).decode('utf-8')
if x[0] == '1': # the line is HIGH
o[i] = time.perf_counter()
i += 1

plt.hist(np.diff(o) * 1000.0) # plot the deltas between timestamps

26.4.1 Latencies and reliability to measure a time interval

TODO

26.5 Arduino

If you do not have a DLP-IO8-G, another approach is to use an Arduino237 and program it to send a signal to your PC
when it received a trigger. The Leonardo version238 is recommended as it can be seen as an HID device and it is trivial to
program it to send a key press to your computer upon receving a trigger. Thus, you stimulation program just has to wait
for a keypress and does not even need to open a serial port.

26.6 Raspberry Pi

You can use gpizero239 or RPi.GPIO240

The RPi.GPIO web page warns that “this module is unsuitable for real-time or timing critical applications. This is because
you can not predict when Python will be busy garbage collecting. It also runs under the Linux kernel which is not suitable
for real time applications - it is multitasking O/S and another process may be given priority over the CPU, causing jitter
in your program. If you are after true real-time performance and predictability, buy yourself an Arduino”
This is true, but nevertheless the Raspberry PI may be sufficient for an application that does not overloard the PC and just
need to read or send some sparse triggers. The only way to know is to check for latencies using an external equipment.

237 https://www.arduino.cc
238 https://www.arduino.cc/en/Main/Arduino_BoardLeonardo
239 https://gpiozero.readthedocs.io/en/stable/
240 https://pypi.org/project/RPi.GPIO/

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192 Chapter 26. Sending TTL triggers

 CHAPTER

TWENTYSEVEN

COGMASTER LECTURES

Ateliers de Programmation pour les (Neuro)Sciences Cognitives / Programming for Cognitive and Brain Sciences
This year (2023-2024) the lecture is split in two:
1. PROG101 Introduction to Programming with Python (first semester)
This series of lectures targets students with little or no prior knowledge of programming. It will introduce the
fundamentals concepts of coding : variables, expressions, functions, control structures, input/ouput. The course
will make use of https://pythontutor.com/
2. PCBS Programming Experiments for Cognitive and Brain Sciences (second semester)
The purpose of this module is to train students to program cognitive psychology experiments. During the first
7 lectures, the course starts with an introduction and is follwoed by hands-on exercises. In the second part of the
semester, Each student chooses an experiment to implement. The project’s development should be public on github.
Instructors
• Henri van den Driessche <[email protected]> (PROG101)
• Christophe Pallier <[email protected]> (PROG201)
• Maxime Cauté <[email protected]> (PROG201)
Moodle
https://moodle.u-paris.fr/course/view.php?id=7378
Slides
http://github.com/chrplr/PCBS/tree/master/slides

27.1 Course description

27.1.1 Objectives

The purpose of the PCBS course is to make students able to write clean code in order to solve the tasks that are typically
encountered in cognitive or neurosciences (data manipulation and analysis, creation of stimuli, programming of real-time
experiments, simulations…). The first half (6 weeks) of the course consists of lectures with hands-on exercises, then,
during the last 6 weeks, students have to realize a project publicly available on http://github.com

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Programming for Cognitive and Brain Sciences

27.1.2 Learning outcomes

On successful completion of this course, students should be able to write readable, well- documented, Python programs,
and use system such as git that promote reproducible science.

27.1.3 Pedagogy, class organization and homework

The first classes are lectures with hands-on exercices. The remaining classes, I and the teaching assistant are present for
individual support to help the students accomplish their project. I also give weekly assignments to be done before the next
lecture.

27.1.4 Assessment

The projects will be graded on a 20 points scale. The main criterion is clarity (see Projects for more details).

27.1.5 Textbook and readings

All the materials are available on the course’s web site at http://github.com/chrplr/PCBS.

27.1.6 Course policies

Laptops: Students must bring there own laptop (preferably fully charged!) with the specified software preinstalled (see
https://pcbs.readthedocs.io/en/latest/software-installation.html)
Participation: You are strongly encouraged to participate in lectures and on the discord discussion forum. The more
advanced students are expected to help the beginners.

27.2 Prerequisites

They should acquainted with basic programming concepts: instructions, variables, tests (if..then..else), loops (while and
for).
Students are expected to know how to open a terminal and navigate in the file system241 and to know how to view and
edit text files with a text editor such as Sublime Text242 .

27.3 Projects

The project should try to replicate an experiment related to cognitive (neuro-) science.
An example of the kind of things that we expect is provided at http://chrplr.github.io/PCBS-LexicalDecision
• All documents (scripts, stimuli, documentation, data files) related to the project should be on a github.com reposi-
tory with a name starts with PCBS- followed by a label that gives an idea of what the project is about.
• The main page of the repository (README.md) should :
– describe the aim of the project (explain the experiment or the simulation
241 http://linuxcommand.org/lc3_lts0020.php
242 https://www.sublimetext.com

194 Chapter 27. Cogmaster Lectures

 Programming for Cognitive and Brain Sciences

– explain how to install and run the experiment on one’s computer (which command line, which options if
any).
– if the project involves analyses, the README.md should point to a documents (html, pdf, not Word!!!)
containing the report.
• It is highly recommended to use the ‘Pages’ system of github to generate a nice looking page (see https://docs.github.
com/en/github/working-with-github-pages/configuring-a-publishing-source-for-your-github-pages-site ).
• It should be possible to clone your repository and execute your code without modifying anything. This implies that
you should absolutely avoid absolute pathnames. Also your code must be portable and run on MacOS, Windows
and Linux.
• Send us a link to your github project as soon as possible so that we can check your progress.
• The readability of the code, and of the main page are of the main criteria of evaluation.
• Do not be overambitious: a well written project that does a simple thing but well will receive a better score than
one that has an unreadble code that does complicated things.
• You can work in binomes to read, check and criticize each other code regularily. it is very useful to have someone
else check that the documentation and code that you write is readable.
• use the discord channel to ask questions
• At the end of the README.md file, you must include a section detailling:
– your previous coding experience
– what you have learned since then, by following the lecture, coding the project or working by yourself
– what you missed in this course.

27.3. Projects 195

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196 Chapter 27. Cogmaster Lectures

 CHAPTER

TWENTYEIGHT

PROJECTS

The project should try to replicate an experiment or some simulations related to cognitive (neuro-) science.
An example of the kind of things that we expect is provided at http://chrplr.github.io/PCBS-LexicalDecision
• All documents (scripts, stimuli, documentation, data files) related to the project should be on a github.com reposi-
tory with a name starts with PCBS- followed by a label that gives an idea of what the project is about.
• The main page of the repository (README.md) should :
– describe the aim of the project (explain the experiment or the simulation
– explain how to install and run the experiment on one’s computer (which command line, which options if
any).
– if the project involves analyses, the README.md should point to a documents (html, pdf, not Word!!!)
containing the report.
• It is highly recommended to use the ‘Pages’ system of github to generate a nice looking page (see https://docs.github.
com/en/github/working-with-github-pages/configuring-a-publishing-source-for-your-github-pages-site ).
• It should be possible to clone your repository and execute your code without modifying anything. This implies that
you should absolutely avoid absolute pathnames. Also your code must be portable and run on MacOS, Windows
and Linux.
• Send us a link to your github project as soon as possible so that we can check your progress.
• The readability of the code, and of the main page are of the main criteria of evaluation.
• Do not be overambitious: a well written project that does a simple thing but well will receive a better score than
one that has an unreadble code that does complicated things.
• You can work in binomes to read, check and criticize each other code regularily. it is very useful to have someone
else check that the documentation and code that you write is readable.
• use the slack forum https://cogmaster-pcbs.slack.com/ to ask questions
• At the end of the README.md file, you must include a section detailling:
– your previous coding experience
– what you have learned since then, by following the lecture, coding the project or working by yourself
– what you missed in this course.
—
I have uploaded some experimental papers on the Schoology web size (in Materials: papers-for-projects.zip) that can be
used as the basis of your project.

197
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198 Chapter 28. Projects

 CHAPTER

TWENTYNINE

RESOURCES

29.1 Learning Python3

• Check Python in a Nutshell for a quick tour of Python.

• Books:
– Automate the boring stuff with Python243 (highly recommended!)
– Apprendre à Programmer avec Python3244
– Think Python245
• MOOCs:
– Udemy’s Python programming for absolute beginners246
– Code Academy’s Learn Python module247
– Openclassrooms’ Apprendre à programmer en Python248
– Python 3 : des fondamentaux aux concepts avancés du langage249

29.2 Programming skills

• Software Carpentry250 provides nice lessons about writing software for science and do reproducible science.
243 https://automatetheboringstuff.com/
244 https://inforef.be/swi/python.htm
245 http://greenteapress.com/thinkpython2/
246 https://www.udemy.com/python-programming-for-absolute-beginners/
247 https://www.codecademy.com/learn/learn-python
248 https://openclassrooms.com/fr/courses/235344-apprenez-a-programmer-en-python
249 https://www.fun-mooc.fr/en/cours/python-3-des-fondamentaux-aux-concepts-avances-du-langage/
250 https://software-carpentry.org/lessons/

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Programming for Cognitive and Brain Sciences

29.2.1 Resources to learn the command shell

• The Linux Command Line251 by Williams Shotts.

• Openclassrooms MOOC252
Remarks:
• Under Windows, if you have installed Git for Windows253 , you have access to Git bash which provides a terminal
with the bash shell and emulates many Unix commands.
• Under Windows 10, Microsoft has recently made available the “Windows Subsystem for Linux”, which provides
a virtual Linux system running inside Windows. (See https://itsfoss.com/install-bash-on-windows/, and https:
//itsfoss.com/windows-linux-kernel-wsl-2/).
• Under MacOSX, when you open a terminal, you may be interacting withthe bash shell or the zsh shell (to know
which, type echo $SHELL).

29.2.2 Resources to learn Git

To understand why you need to learn git, see Tools to do Reproducible Science
• Openclassrooms’ MOOC Manage your code with Git and Github254
• https://product.hubspot.com/blog/git-and-github-tutorial-for-beginners
• https://git-scm.com/book/en/v2/Getting-Started-Git-Basics
• The Git Book255
• My own git cheat page256

29.3 Books relevant to Cognitive and Brain Sciences Programming

• Programming Visual Illusions for Everyone257 by Marco Bertamini:

• Neural Data Science: A Primer with MATLAB and Python by von Erik Lee Nylen and Pascal Wallisch
• Matlab for Brain and Cognitive Scientists and Analyzing neural time series data by Mike X Cohen
• Python in Neuroscience258
• Modeling Psychophysical Data in R by Kenneth Knoblauch & Laurence T. Maloney
251 http://linuxcommand.org/tlcl.php
252 https://openclassrooms.com/courses/reprenez-le-controle-a-l-aide-de-linux
253 https://git-scm.com/download/win
254 https://openclassrooms.com/en/courses/5671626-manage-your-code-project-with-git-github
255 https://git-scm.com/book/en/v2
256 http://www.pallier.org/version-control-at-your-fingertips-a-quick-start-with-git.html#version-control-at-your-fingertips-a-quick-start-with-git
257 https://www.programmingvisualillusionsforeveryone.online/
258 https://www.frontiersin.org/research-topics/8/python-in-neuroscience

200 Chapter 29. Resources

 Programming for Cognitive and Brain Sciences

29.4 Stimulus/Experiment generation modules

• http://www.expyriment.org (See Get started with Expyriment259

• http://psychopy.org (See Programming with PsychoPy260 )
• http://psychtoolbox.org/ (See Psychtoolbox demos261 )
• https://www.jspsych.org/ (See intro at https://blog.s-m.ac/using-jspsych/)
• https://dialoguetoolkit.github.io/chattool/

29.5 Data analyses, Statistics in Python

• Modules: numpy, scipy, pandas, seaborn, statsmodel, sklearn

– Data manipulation:
∗ http://pandas.pydata.org/pandas-docs/stable/tutorials.html
– Plotting:
∗ http://matplotlib.org/users/pyplot_tutorial.html
∗ https://seaborn.pydata.org/tutorial.html
• Scipy Lecture Notes: http://www.scipy-lectures.org/
• Think Stats by Allen B. Downey: http://greenteapress.com/thinkstats2/
• Python Data Science Handbook by Jake VanderPlas: https://jakevdp.github.io/PythonDataScienceHandbook
• Introduction to Data Science in Python: notebook from a 2 day workshop organized by the Paris-Saclay Center for
Data Science: https://github.com/paris-saclay-cds/data-science-workshop-2019
• Machine Learning with scikit-learn” MOOC: https://www.fun-mooc.fr/en/courses/
machine-learning-python-scikit-learn/ (on github: https://inria.github.io/scikit-learn-mooc/)

29.6 Simulations

• Think Complexity262 by Allen B. Downey

• The Brian spiking neural network simulator263
• Deep Learning for Natural Language Processing with Pytorch264

259 https://docs.expyriment.org/Tutorial.html
260 https://www.socsci.ru.nl/wilberth/nocms/psychopy/print.php
261 http://peterscarfe.com/ptbtutorials.html
262 http://greenteapress.com/wp/think-complexity-2e/
263 http://briansimulator.org/
264 https://pytorch.org/tutorials/beginner/deep_learning_nlp_tutorial.html

29.4. Stimulus/Experiment generation modules 201