Dr Michael Berks michael.berks@manchester.ac.uk
Lesson 1: The Basics: variables, scripts and functions

Why do I need to learn ‘it’?
Because Dr
Graham said so…

What does computer programming mean?
What is Matlab?
What is a computer program?
What is a programming language?
What is code?

What is a computer program?
Something you use to achieve some task on a computer…
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 Matlab lectures…

DATA
Image(s)
Lab results
Patient data
What is a computer program?
In medical imaging…
PROGRAM
Do something clever…
RESULT
Hopefully clinically useful!

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

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

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

x
You’re hungry and want x
Get mum to cook something good to eat…..
Go to a restaurant
Get a microwave meal x

Heating someone else’s food in the microwave
Ok if they’ve cooked exactly what you want
Vs
Cooking your own food
Can eat exactly as you like it
Using a computer program
Ok if it does exactly what you want
Vs
Writing your own computer program
Make it do exactly 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 my programs from scratch?
No! Just like in cooking, you don’t need make everything from raw ingredients, can use premade 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?
Excel
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).
Photoshop
+ +
Using other people’s code
+
Writing your own code
=
A really powerful tool for imaging research!

• To show you how to use Matlab
• 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 MSc
• To make some pretty pictures!

• Log on using your university ID
• Open a windows explorer window
– Click on ‘Documents’, then ‘MATLAB’
– Make a new folder TutorialSlides
• 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 your new TutorialSlides
• 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
• Start a new Matlab session

• Using the Matlab interface
• Some simple commands 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

• A fancy scientific calculator
– 2+3
– 2*3
– 2/3
– 2^3
– 2^0.5
– 2+3*6/2
– (2+3)*6/2
Any of the text in navy blue is code you can run in the command window. Try copy and pasting, then hitting return
• Try using ↑ and ↓
– Select earlier expressions and edit them

• 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

Shows you what variables are currently stored in memory

• 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);

• 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 from the Command
History
• Paste them into the blank document
• Save the document as ‘my_first_script.m’
• Type my_first_script (note the lack of ‘.m’) at the command line

• 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 lab book

• Scripts are useful…
• … but what if we want to re-compute y for different values of a and b?
• Create a new ‘script’, in the first line write
– function y = my_fun(a, b)
– y = (4*a^2 +3*b^3) / 5;
• Click save
– Note how my_fun.m is automatically selected as the filename

• Type y = my_fun(a, b); at the command line
• Clear the memory
• Try y = my_fun(4, 8);
• Note how y appears in the workspace, but a and b don’t
• Functions have their own memory space
• a and b are ‘arguments’ to the function
– They allow data to be moved into the function’s memory
• y is the function’s ‘output’
– This allows us to get data from the memory space

• Functions can be combined with other operators
(and themselves) in commands
– y1 = 2*my_fun(4, 8) + my_fun(3, 2) ;
• Functions can be called from other functions
– function y = my_fun2(a, b)
– y = my_fun(a,b) + my_fun(2*a, b/2);
• Matlab has 1000s of existing functions
• By combining these with your own functions you can get Matlab to do just about anything you want

• Matlab interprets each command it sees
• It recognises certain keywords, mathematical operators etc.
• When it sees something that isn’t a keyword it
1. Checks if it is a variable in the current memory space
2. Looks for a script or function in the Matlab path
3. If it can’t find either, returns an error

• Type ‘path’ at the command line
• This displays all the folders on your computer where
Matlab will ‘look’ for functions and scripts
• Use ‘File -> Set path’ to add new folders
• If 2 functions/scripts have the same name, Matlab uses the first one it finds on the path
– Avoid name clashes with existing functions
– Avoid mixing variable and function names

• Must start with a letter
• Followed by any number of letters, digits, or underscores.
• Matlab is 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

• Use scripts to generate results/output for specific tasks
– Assignments in your maths course
– Experiments in your project
– Give them a sensible name, and add comments at the start describing what they do
• Use functions for methods that can be reused across multiple tasks
– Organise them in sub-folders
• E.g. ‘stats’, ‘optimisation’, ‘image_processing’
• Remember, you can always rearrange the file structure
– As long as you remember to add any new folders to the path

• A little demonstration…
• If we can understand this concept now, it will make life a lot easier later…

• Type y = my_fun(a, b); at the command line
• Clear the memory
• Try y = my_fun(4, 8);
• Note how y appears in the workspace, but a and b don’t
• Functions have their own memory space
• a and b are ‘inputs’ to the function
– They allow data to be moved into the function’s memory
• y is the function’s ‘output’
– This allows us to get data from the memory space