Programming and Scientific Computing in Python

✍ Scribed by J.M. Hoekstra, J. Ellerbroek

• Publisher: TU Delft
• Year: 2022
• Tongue: English
• Leaves: 222
• Edition: 6.0
• Category: Library

✦ Synopsis

The first version of this reader was developed for, and during the pilot of, the Programming course in
the first year of the BSc program Aerospace Engineering at the Delft University of Technology in 2012.
Originally it was written for Python 2 and then converted to Python 3.
The goal of the Python programming course is to enable the student to:
• write a program for scientific computing
• develop models
• analyse behaviour of the models, for instance using plots
• visualise models by animating graphics
The course assumes some mathematical skills, but no programming experience whatsoever.
This document is provided as a reference for the elaboration of the assignments. The reader is encouraged to read through the relevant chapters applicable to a particular problem. For later reference,
many tables, as well as some appendices with quick reference guides, have been included. These
encompass the most often used functions and methods. For a complete overview, there is the excellent documentation as provided with Python in the IDLE Help menu, as well as the downloadable and
on-line documentation for the Python modules NumPy, SciPy, Matplotlib and Pygame.
Also, the set-up of the present course is to show the appeal of programming. Having this powerful tool
at hand allows the reader to use the computer as a ‘mathematical slave’. And by making models, one
basically has the universe in a sandbox at one’s disposal: Any complex problem can be programmed
and displayed, from molecular behaviour to the motion in a complex gravity field in space.
An important ingredient at the beginning of the course is the ability to solve mathematical puzzles and
numerical problems. Also the very easy to use graphics module Pygame module has been included in
this reader. This allows, next to the simulation of a physical problem, a real-time visualization and some
control (mouse and keyboard) for the user, which also adds some fun for the beginning and struggling
programmer in the form of visual feedback.
Next to the mathematical puzzles, challenges (like Project Euler and the Python challenge) and simulations and games, there is a programming contest included in the last module of the course for which
there is a prize for the winners. Often students surprise me with their skills and creativity in such a
contest by submitting impressive simulations and games.
Also check out the accompanying videos: Search for “AE1205” on Youtube.
Many thanks to the students and teaching assistants, whose questions, input and feedback formed the
foundation for this reader.

✦ Table of Contents

Getting started
What is programming?
What is Python?
Installing Python
Windows
macOS
Linux
Explanation of the installed modules
Configuring the IDLE editor
Working environments: IDLE, PyCharm, Spyder, and others
Documentation
Sneak preview: Try the Python language yourself
Variables and the assignment statement
Finding your way around: many ways in which you can get help
Method 1: Using help("text") or interactive help()
Method 2: Python documentation in Help Pull-down menu
Method 3: Get help from the huge Python community
Variable assignment and types
Assignment and implicit type declaration
Short-hand when using original value with an operator
Number operations in Python
Float: variable type for floating point values
Int: variable type for round numbers like counter or index)
Complex numbers
String operations
Booleans and logical expressions
The list type: an ordered collection of items
What are lists?
Indexing and slicing, list functions and delete
Quick creation of lists with repeating values
List methods
Some useful built-in functions
Python syntax: Statements
Assignment
The print statement
Using print
Formatting your output
The input function
Checking conditions: the if-statement
Iteration using a for-loop
Additional tools for for-loops: itertools
Iteration using a while-loop
Controlling a loop: break and continue
Making your code reusable and readable
Extending Python: Using modules
The import statement
Importing from a module
Renaming imports within the import statement
Math functions in Python: the math module
Overview of functions and constants in the math module
The random module
Exploring other modules
Defining your own functions and modules
Defining a function: The def statement
Accepting arguments in your function
Providing default values
Passing arguments by order or by name
Returning data from your function
Variable names: Arguments and return variables
Returning a result by updating an argument
Managing a project: defining your own modules
File input/output and string handling
Opening and closing files
Easy opening and closing: the with statement
Reading data from the file object
Iteratively reading data
If you need more control
A full example: Reading a formatted file
Writing to files
Useful string methods
Matplotlib: Data visualisation in Python
The basics: plotting a 2D XY-graph
Multiple plots and setting their scaling: subplot and axis
Interactive plots
3D and contour plots
Plotting on a map
Overview of essential pyplot functions
Numerical integration
Euler's method
Adding dimensions and the atan2 function
NumPy and SciPy: Scientific programming with arrays and matrices
Arrays
Creating NumPy arrays
Indexing and slicing NumPy arrays
Logical expressions using arrays
Speeding it up: Vectorising your code with NumPy
Matrix operations: Linear algebra with NumPy
Genfromtxt: Easy data-file reading using NumPy
SciPy: a toolbox for scientists and engineers
SciPy example: Polynomial fit on noisy data
Tuples, dictionaries, and sets
Tuples
Sets
Dictionaries
Pygame: Animation, visualisation and controls
The basics: importing and initialising
Setting up the Pygame window
Surfaces and Rectangles
Bitmaps and images
Drawing shapes and lines
When your drawing is ready: flipping the display
Timing and the game loop
Method 1: Fixed time-step
Method 2: Variable time-step
The termination condition of the game loop
Processing inputs: Keyboard, mouse, and other events
Overview of basic Pygame functions
Creating your own types: Object-Oriented Programming
Implementing operator behaviour for your type
Graphical User Interface building in Python
TkInter
PyQt
wxPython
PyGtk
Reading and writing data files: beyond the basics
Tabular data: CSV files
Doing it yourself
Doing it with a library
Tabular data: Excel spreadsheets
Openpyxl: Reading and writing directly to XLSX Excel files
Xlrd and xlwt: Reading and writing the old .xls format
Reading and writing Excel files with Pandas
Hierarchical data: JSON files
Hierarchical data: XML files
Binary data: MATLAB mat files
Binary data: PDF files
Binary data: Any binary file
Exception handling in Python
Creating self-contained bundles of your program using PyInstaller
Making an executable of your program
Example Mazeman game
Adding additional files to make your program run
Making a setup installer for your program
Version Control
Basic concepts of version control
Repository, working copy
Revision, commit, check-out
Comparing source code
Distributed vs centralised VCS
Branches and merging
Overview of Git commands
Overview of Subversion commands
Beyond the course: Exploring applications of Python
Alternatives for Pygame for (2D) visualisation
TkInter Canvas (included in Python)
Arcade
Alternatives for 3D visualisation
Visual Python: easy 3D graphics
Panda3D
OpenGL
Animating your graphics: Physics
Creating graphics
GIMP and its Python console
Blender
Interfacing with hardware
The Raspberry Pi
MicroPython
Examples
Logicals and loops: Bubblesort
Answers to exercises
Jupyter: the interactive Python notebook
Programming and Scientific Computing in Python - Cheat sheet
Getting started
Variable assignment and types
Python syntax: Statements
Making your code reusable and readable
Extending Python: using modules
Defining your own functions and modules
File IO and string handling
Matplotlib: Data visualisation in Python
Numerical integration
NumPy and SciPy: Scientific programming with arrays and matrices
Tuples, dictionaries, and sets
Pygame: Animation, visualisation and controls