MATLAB
A brief introduction
to programming
1) Background and
Getting Started
 Dartmouth College now has a site license
 http://caligari.dartmouth.edu/downloads/matlab
 Installs on Mac, Windows, or Linux
 Running in the BIL (Linux):
 Command “matlab” launches latest installed
version
 Currently, most machines default to MATLAB 8.3
(R2014a) or 8.0 (R2013b)
Launching MATLAB
[aic-bil-ibm1] % matlab &
(&: don’t wait for it to quit in this shell)
The MATLAB Path
The “path” is an ordered list of directories
used to match commands to files
>> path
>> addpath xyz
>> which abc
list the current path
add xyz to the path (for this
session only)
if abc is a command, give
file it runs from
2) MATLAB Data & Variables
Numbers in MATLAB are “floating point”
(not integer)
 Some image types are int or unsigned int
 For the most part, floats are fine for
anything numeric
Other basic data types are char
(characters), struct (data structure), and
cell (list element)
Basic Data Types
Most types can be turned into arrays:
 Numbers: vectors
 Chars: strings (or character arrays)
 Structs: struct arrays
 Cells: cell arrays
Arrays elements are accessed with “( )”
(cell arrays also use “{ }”)
Variables
Note that variable names are case
sensitive: A ≠ a
To see current variables in MATLAB:
>> whos
Examples
 Create a vector (number array):
>> a = [ 0 1 2 5 ]
(brackets)
 Create a string (char array):
>> b = 'my string’
(single quotes)
 Create a cell array:
>> c{1} = a
(allows mixing of
>> c{2} = b
various types)
OR: >> c = { [ 0 1 2 5 ], ‘my string’ }
3) Scripts and Functions
Scripts are MATLAB commands saved
into a file
 Exactly equivalent to typing in MATLAB
 All variables remain after execution
Functions are packaged scripts that
operate in their own environments
 Input in, output out
 Only designated output remains
Recommendations
Use scripts for quicker work
 Easier to debug, when small
 Can access all calculated values
Use functions for larger projects and
reusable code
 Less likely to cause trouble (multiple
definition of variables, interdependencies)
 “Cleaner” and more easily verified
How To…
 Create a script:
 Save commands in a file ending with ‘.m’
 Note: file must be in the path to execute!
 Create a function:
 as above, but start with a “function” line:
e.g.
or
or
function myfunc
function x = myfunc(y)
function [x1, x2] = myfunc(y1, y2, y3)
4) Help
Nearly all commands (all built-in, and
most others) have documentation
The help command:
>> help xyz
>> help
>> lookfor abc
help on command “xyz”
list of built-in functions
by category
search help by keyword
5) The Debugger
MATLAB’s debugger can suspend a
program while it is executing
Way to examine function contents before
they are cleared
Most frequent usage:
>> dbstop if error
>> dbquit
Go to debugger
on error
Quit debugger
More Debugger Commands
Other useful debugger commands:
>> dbup
Examine calling function
>> dbdown
Reverse a dbup
>> dbstop in xyz at 123 Stop in function
xyz at line 123
>> dbclear all
Undo current dbstops
Tip 1: Continuations
You can continue a line on the next line by
ending it with “…”
>> mylongvariable = {‘mylongstring1’, …
>> ‘mylongstring2’, ‘etc.’}
(this is particularly helpful in scripts and
functions)
Tip 2: Command Output
You can use “;” to suppress printing of a return
value
>> x = 5
x=
5
>> y = 3;
(the second assignment is made quietly)
Tip 3: Notes on ‘cd’
The ‘cd’ command is used to change
directories in MATLAB and in Linux…
but it works slightly differently
>> cd /home/fmri
% cd /home/fmri
(changes to directory in both)
>> cd
% cd
(prints current directory) (changes to home directory)
>> cd(‘/home/fmri’)
>> cd(myinputdir)
(also legal, and useful with string variables)
Tip 4: Shell Commands
You can use Linux commands in MATLAB
using “!”
>> ! rm -r mydir
>> ! cp /home/fmri/file1 .
(Note: the current directory is always
MATLAB’s current directory)
Tip (Trick?) 5: Bad Names
Beware of using variable names that “shadow”
functions
(sometimes MATLAB will alert you…)
>> end = 1
Error: Illegal use of reserved keyword "end".
(…but often it won’t)
>> spm = 5
>> spm
spm =
5
Tip 6: Clearing Variables
You can unassign variables with “clear”:
>> clear d*
(clear variables starting with “d”)
Clearing variables may prevent some
problems with scripts
>> clear all (clear all variables)
Tip 7: Saving a Session
 The ‘diary’ command can save everything
printed in the MATLAB window to a file:
>> diary myfile.txt
>> diary on
…
>> diary off
Programming Fundamentals
» Control - if-then, while loops, and for loops
» Expressions - operators and syntax
» Output – disp
If-Then Loop Structure
if expr
commands
elseif expr
commands
else
commands
end
% note: can use repeatedly
While Loop Structure
while expr
commands
end
% evaluated each time!
For Loop Structure
for var = values
commands
end
% often 1:N
% note: evaluated for
% each value
Expression Format
» Expressions are built using operators
» Common operators:
&& - logical AND
|| - logical OR (note: two vertical pipe symbols)
== - test of equality (note: = is assignment)
>, <, >=, <= - inequalities
~= and ~ - inequality and negation
() - parentheses can be used for grouping
Example
done = 0;
while ~done
x = myfunc;
if x < 0 || x > 10
done = 1;
end
end
The disp Command
» The simplest way to print a variable
» Note: non-string variables must be
converted to strings:
disp(num2str(x))
» Can also display other text:
disp(‘Finished:’)
disp([‘The value of x is ’ num2str(x)])
First Programming Task
» Try to create a small but non-trivial
program as an exercise
» Example:
» Ask the user to pick a date in some way
» Compare to today’s date and tell the user
how many days until that date comes, or
how many days ago it passed
Notes
» Months have different numbers of days… so
this seems non-trivial!
» MATLAB functions can help: for example, can
use date in MATLAB (it returns a string like
‘10-Apr-08’) and datenum
» How should we ask the user for a date?
» A calendar looks nice, but this is hard—it will
introduce days of the week, which we don’t
otherwise need
» The menu command can present a list of choices
(e.g., ask for a year, a month, and then a day)
Other Sample Learning Projects
» 1. Get historical population data for NH, VT,
and some other states from the Wikipedia,
save it to a file, and create code to read it into
MATLAB. Write a program that gives users
menu options to plot population growth graphs
and to use an extrapolation to predict what the
population might be in a future year.
» New commands to learn: fopen, fread, fclose,
plot, hold, legend, polyfit
Other Sample Learning Projects
» 2. Write a simple DICOM browser. The
program should be able to search for a given
DICOM file pattern and present a list of files to
select from. It should allow a user to see
particular fields (by calling Linux tools that can
read DICOM fields and parsing their output),
or print multiple fields in a tabular view.
» New commands to learn: system, listdlg,
strfind, strcmp, strrep, sprintf
Other Sample Learning Projects
» 3. Implement Mad Libs (Mad Lab version?).
Create a set of one or more template files that
have markers like %NOUN% to replace key
words. Read a random template into MATLAB,
then ask the user to input an appropriate set
of parts of speech, and display the result of
substituting these words for the markers.
» New commands to learn: fopen, fread, fclose,
strrep, rand, round, msgbox