Programming tutorial course

Dr Michael Berks
[email protected]

Lesson 1: Why learn to program? Python

vs Matlab;
The Basics: variables, scripts and functions
 Why do I
What is need to
Matlab? learn ‘it’?

What is Because the

course leader said

python? so…
 What is
Matlab/python?

What is a computer
program?
What does computer
programming mean?

What is a
programming
language?

What is code?
 What is a computer
program?
Something you use to achieve some task
on a computer (or phone, tablet etc)…

Word

Write a letter, essay, lab report etc…

Excel

Analyse results, produce graphs for your report

etc…

Angry Birds

Kill time when you’re sitting in boring programming

lectures…
 What is a computer
program?

In medical imaging…

DATA

PROGRAM RESULT
Image(s)

Lab results Hopefully

clinically useful!

Do something clever…
Patient data
 What is a computer
program?

In medical imaging…

DATA

PROGRAM RESULT

Predict whether
the patient has
Alzheimer’s
MR images of the brain Disease
Measure volume of
grey/white matter…
 What is a computer
program?

In medical imaging…

DATA

PROGRAM RESULT

Predict risk of
developing
breast cancer
Mammogram acquired
during routine screening Measure amount dense
+ patient data breast tissue…
 What is a computer
program?

In medical imaging…

DATA

PROGRAM RESULT

Tell doctor/drugs
company if the
drug is working
MRI liver tumours before
and after drug treatment Measure change in size
of tumour…
 What does computer
programming mean?
Writing your own computer programs...
… telling the computer to do exactly what
you want.

A way of translating human logic into What is a

commands a computer understands… programming
… like human languages, there a lots of language?
different languages (often similar to each
other), each with a specific set of rules
(syntax, grammar) to obey.

A chunk of commands in a specific

programming language…
What is ‘code’?
A program consists of bits of code put
together in a logical way …
… by using other people’s code, you can incorporate
bits of their program in your own (as long as you’re
using the same language!).
Now the big question….

Why do I need to learn

how to write my own
computer code?

Think of it like learning to

cook…..
 n ow! t, yo u can ’t afford it!

x
te r You’re stu d e n
nches

x
e in Ma
iv Go to a restaurant
You l

You’re hungry and want

something good to
Get parents to cook eat…..

x
Get a microwave meal

You’re a fussy ea
te r!
Heating someone else’s Using a computer
food in the microwave program
Ok if they’ve cooked Ok if it does exactly what
exactly what you want you want

Vs Vs

Writing your own

Cooking your own food
computer program
Can eat exactly as Make it do exactly
you like it what you want

Research is likely to be here

 How good a
cook/programmer do
I need to be?

Vs

Do I need to write all No! Just like in cooking, you don’t need
my programs from make everything from raw ingredients, can
scratch? use pre-made pasta, sauces, wine etc…

Remember you can use other people’s code to

include bits of their programs in yours …
… but you do need to know the basics to put those bits
together (how to chop an onion, when to add seasoning etc.)
 And finally….
What is Matlab?

Matlab is both a program and a programming language ...

… it has lots of tools you can just use to analyse data and
images. But you can also write code to extend it to do any
analysis you like (although unlike a ‘pure’ language, it will only
work if the Matlab program is installed on the computer).

Excel Photoshop
Using other Writing
+ + people’s
code
+ your own
code

= A really powerful tool for imaging research!

 But what about….
Python?

• General purpose
programming
language
• Packages provide
support for scientific
computing
• Open-source
 How does python differ from Matlab?
• It’s free
– No need for an expensive license*
– Widely used, both in academia and industry
– Often installed as part of OS
• No single development environment
– This can make it a little trickier get started
– But, also more flexible
– We’ll use Spyder on this course

*Currently free because of COVID, but usually you have to pay for Matlab!
 Course aims
• To show you how to use Matlab and/or python
• To introduce some basic programming ideas common
to all programming languages
• To give examples of some tasks in medical imaging
processing
• To provide code you can reuse later in your projects
• To make some pretty pictures!
I’m a bit confused…

Should I use Matlab…

..or Python?
For this course, consider Matlab and
python as interchangeable…
you can use either or both.

I will demonstrate mainly in Matlab,

but everything we do will be very
similar in both… just watch out for the
subtle differences!
 vs

If you see this I’m referring to If you see this I’m referring to
Matlab only differences in python
 First tasks
• Open Matlab (if you have it installed)
• Open Spyder (if you have it installed)
• Open a windows explorer window
– Go to the MSc folder you created for Professor’s Cootes,
maths course
– Make a new folder Programming
– Inside Programming, make new folders:
• Matlab
• Python
• Data
• TutorialSlides
 First tasks
• Open an internet explorer/Google chrome window
• Go to the following webpage:
– http://personalpages.manchester.ac.uk/staff/michael.berks
– Click on the Matlab Tutorial tab
– Bookmark this page for future weeks
• Save the week 1 powerpoint slides and tutorial exercise into
the TutorialSlides folder
– These will also be added to the ‘Course content’ section of blackboard

• Leave the window open (we’ll need it later)

• Open the ‘lesson 1’ powerpoint file you’ve just saved
– As I’m going through the slides, follow them on your computer
 Lesson Overview
• Using the Matlab/Spyder interface
• Doing maths in the Command Window
• Assigning variables and suppressing visual output
• Collecting sequences of commands: scripts
• An introduction to functions
• Basic programming tips: expressive variable names
and comments
Command window
 Command window
• A fancy scientific calculator
– 2+3 Any of the text in navy blue is code
you can run in the command
– 2*3 window. Try copy and pasting, then
– 2/3 hitting return
– 2^3
• Our first python difference! It’s 2**3 in python
– 2^0.5
– 2+3*6/2
– (2+3)*6/2
• Try using ↑ and ↓
– Select earlier expressions and edit them
In Spyder: console
 Assigning Variables
• Use ‘=‘ to assign variables
– Keeps data in memory to use again
–a=4
–b=3+6
– y = (4*a^2 +3*b^3) / 5
• Can also self-assign:
– b = b*2
• Check the work space
 Workspace

Shows you what variables are currently stored in memory

 Workspace

Shows you what variables are currently stored in memory

 Suppressing visual output
• Try a = rand(100)
• This creates a 100 x 100 matrix of random
numbers
• Use clc to clear the Command Window
• Try a = rand(100);
 Let's compute the number of
seconds in a year…
• Let's create some variables
– seconds_in_minute = 60
– minutes_in_hour = 60
– hours_in_day = 24
– days_in_year = 365
• Then compute:
– seconds_in_year = seconds_in_minute*
minutes_in_hour*hours_in_day*days_in_year
 Scripts
• Use clear to wipe the current memory
– Check that the workspace is now empty
• Click the ‘New script’ button (top left of main menu)
– Opens a blank page in the editor
• Copy the previous commands to compute the number of
seconds in a year from the Command History
• Paste them into the blank document
• Save the document as
– Matlab: programming_tutorial_lesson1_script.m
– Python: programming_tutorial_lesson1_script.py
Calling a script from the command-line
• Type: programming_tutorial_lesson1_script at
the command line
• Note the lack of ‘.m’
• Check your work-space
• We'll look at different ways of calling python
scripts in future lessons
 How many seconds in…
• 2 years?
• 10 years?
• N-years?
• Scripts are useful… but if we want to re-run
our script with different inputs, we should use
a function
 Matlab Functions
• In our script, type %%
• This creates a new cell – a part of a script that can be run separately
• Now at the BOTTOM of the script …
– function [seconds_in_n_years] = compute_seconds_in_years(n_years)
– seconds_in_minute = 60
– minutes_in_hour = 60
– hours_in_day = 24
– days_in_year = 365
– seconds_in_year = seconds_in_hour *hours_in_day*days_in_year
– seconds_in_n_years = n_years * seconds_in_year
– end
• Type another %% above the function, then
– compute_seconds_in_years(2)
 Python Functions
• Again type %%
• Now type …
– def compute_seconds_in_years(n_years)
seconds_in_minute = 60
minutes_in_hour = 60
hours_in_day = 24
days_in_year = 365
seconds_in_year = seconds_in_hour *hours_in_day*days_in_year
seconds_in_n_years = n_years * seconds_in_year
return seconds_in_n_years
• Run this cell, no output is generated but the function is now
available to use…
• Type another %%, and then:
– compute_seconds_in_years(10)
 vs

What differences did you spot

between the Matlab and python
functions?
 Inputs and output
• The variable n_years is an input to our function
• You will often see this described as an argument
• The variable seconds_in_n_years is the output of our
function
• We look next at using multiple inputs
• We can also have multiple outputs but will see those
in future lessons
 Exercises
• Lookup ‘Newton's law of universal gravitation’ (yes, you can use
wikipedia)
• In Matlab, use the command prompt to compute the force of
attraction between the moon and the earth
– You can assume
• Earth’s mass: 5.97x1024 kg
• Moon’s mass: 7.35x1022 kg
• Distance from earth to moon: 380,000km
• Gravitational constant: 6.674×10−11 N m2 kg−2
• Rewrite this as a function that takes as input, M1, M2 and r

• Use commas to separate multiple inputs to your function

• Can we write this in python?
Variable, script and function names
• Must start with a letter
• Followed by any number of letters, digits, or
underscores.
• Matlab and python are case sensitive
– A and a, my_fun and My_fun, etc are not the same name
• Certain keywords cannot be used
– if, for, end, etc
• Be expressive: try and use names that
– Describe what functions do
– Describe what variables are
 Scripts summary
• Scripts allow us to run sequences of commands
• All data is stored in the main workspace, as if we
typed the commands in the command window
• We can run parts of scripts by
– Selecting text and hitting F9
– Using %% to create ‘cells’

Even when ‘hacking around’ use scripts, date tagged

(e.g. work2013_02_11) to run commands
– That way you have a record of your work
– Think of them as your Matlab/Python lab book
 Functions summary
• Functions group commands so that we can run them
with different inputs
• We have looked at defining and calling functions
inside scripts
• Next week we will look at how we can call functions
from other places (hint: you've already done this!)
• Matlab and python have 1,000s of in-built functions,
by learning how to call those we can create really
powerful programs