Extending MATLAB
Write your own scripts and/or functions Scripts and functions are plain text files with
extension .m (m-files) To execute commands contained in m-files,
MATLAB needs to know where they are! store in working directory store in any directory, add to MATLAB's path
To check/change working directory pwd, cd, ls, dir menu bar current directory window
To check/modify path path addpath, rmpath, savepath File >> Set Path...
Reminders
Scripts
No input/output Operate on pre-defined workspace variables
and variables defined in script Variables created during script are saved in
workspace (side effects) Kind of like macros, relatively inflexible
→ good for executing repeated long/complicated sequences of commands on same data
How to execute a script
Save list of commands, variable definitions, etc in plain text file 'scriptEx.m'
Make sure 'scriptEx.m' is saved in wd, OR, its directory is added to path
type 'scriptEx' at command prompt (no quotes) Be aware of side effects
Functions
Basically, scripts that take input and create some output
Operate on input variables and variables defined in function
Variables created during function call only exist as long as function is running can be saved to workspace if defined as output
→ good for performing general tasks with optional parameters on different datasets
How to call your function (1)
Write it (we'll get to that), and save as plain text file 'functionEx.m'
Make sure 'functionEx.m' is saved in wd, OR, its directory is added to path
Let's assume your function has 2 input arguments, these could be input data or parameters to pass to function body
Examples ...
How to call your function (2)
Arg1 is data stored as workspace variable, Arg2 is file containing data, or could be a file to create for output
>> functionEx(x, 'filename.txt')
Arg1 is another function, Arg2 is scalar parameter
>> functionEx(@func, 1000) >> functionEx('func', 1000)
Defining your function
First line must contain the following 'function' command name(s) of output, if any name of function, should be same as name of m-file name(s) of input parameters/arguments
function output = userFunc(arg1, arg2)
function [ ] = userFunc(arg1, arg2, arg3)
function [out1, out2] = userFunc(arg1)
What about lines 2,3,4,...?
Function body can contain anything, as long as it's a valid MATLAB statement/command
Any text preceded by a % is not executed →
% this is a comment If function definition on line 1 is followed by
block of commented lines, comments will be printed as help file when user types
>> help userFunc
Programming basics
Loops for loop → perform command(s) for some
predetermined amount of times while loop → perform command(s) as long as some
condition is met If-then statements
if some condition is met → perform command(s) else and elseif
For loop While loop
for index = 1:n
do something
end
for i = 1:5
i
end
while condition
do something
end
j = 1;
while j <= 5
j
j = j+1;
end
For loops
Avoid hogging memory, use vector alternatives in MATLAB
vec = [2:2:10]
for i = 1:length(vec)
vec(i) = vec(i) + 10; end
vec =
12 14 16 18 20
vec = vec + 10
How to loop through a matrix
m = [1:4; 5:8; 9:12]; % create 3x4 matrix, values % 1:12 [rows cols] = size(m); % store # of rows and columns % in variablesfor rowstep = 1:rows % loop through rows for colstep = 1:cols % loop through columns rowstep % print current row colstep % print current column m(rowstep, colstep) % print value at current % position end % close column loopend % close row loop
Turn that script into a function...function [] = read_matrix(m)%% function [] = read_matrix(m)%% HELPFILE for trivial function 'read_matrix.m'%% 'm' is a matrix % elements of 'm' will be read starting with [1,1]% % at each step, indices and their corresponding value% will be printed to the screen % START CODE [rows cols] = size(m); % store # of rows and columns in variables for rowstep = 1:rows % loop through row numbers for colstep = 1:cols % loop through column numbers rowstep % print current row colstep % print current column m(rowstep, colstep) % print value at current position end % close column loopend % close row loop
If statements
if condition
do something
end
--------
if condition
do something
else
do something
end
val = m(3,2) if val < 5 val = 0; elseif val > 5 val = val * 10; else val = val^2;end
File handling
>>help iofun
>>help fileformats
load dlmread, dlmwrite xlsread, xlswrite urlread, urlwrite unzip, untar
More file handling, C style
fopen, fclose fgetl, fscanf, fseek, ftell
fid = fopen('mean.m'); % open file for reading while 1 % start loop, basically will loop % forever unless it is stopped line = fgetl(fid); % get next line in 'fid' if ~ischar(line) % if 'line' is empty break loop break end disp(line) % print the current lineend fclose(fid); % close file
Example: transition probabilities
Probabilistic sequence of events We have multiple examples of this sequence Given a particular event, how reliably can we
predict the next event (including the end)? Assume sequence is always same number of
events long Represent each event with a number
Ex. Sequence: 1 – 1 – 2 – 3 – 3 – 3 – 1 – 4 – 4 – 4
Basic idea
Represent each sequence as series of integers Collect a bunch of these sequences and put
them in a matrix where each row is one example of the sequence
We'll write code that will take the matrix and two of the events as arguments Code will return a probability: How often one event
follows the other
Some sequences2 3 4 6 71 2 3 4 61 2 3 4 61 2 3 4 61 2 3 4 61 2 3 4 61 2 3 2 31 2 3 4 61 2 3 4 61 2 3 4 61 2 4 6 71 2 3 4 61 2 3 4 62 1 4 6 71 2 3 4 61 2 3 4 61 2 3 4 61 2 3 4 51 2 3 4 62 3 4 6 7
Example: transition probabilities
Givens A matrix 'data' containing events/numbers, each
row is a sequence two events, 'leader' and 'follower'
Tasks Compute how often 'follower' immediately follows
'leader' Compute how often 'leader' ends the sequence, i.e.
is the last number in its row
Strategy
Loop through matrix, looking for 'leader' Check to see if it is at the end of the row
if yes, tally 1 Check to see if the next element is 'follower'
if yes, tally 1 Count total number of times 'leader' occurs Total up the tallies and divide each by the total
occurrences of 'leader'
Implement in a function
function [prob term_prob] = transProbEXAMPLE(filename,leader,follower)%% function [prob term_prob] = transProbEXAMPLE(filename,leader,follower)%% 'filename' is plain text file containing sequences stored in a matrix%% 'leader' and 'follower' are events/numbers of interest% % This function will compute transition probability from 'leader' to % 'follower'% i.e. how often 'leader' is immediately followed by 'follower'%% returns 'prob' - 'leader' -> 'follower' transition probability% 'term_prob' - probability that 'leader' is last element% in its row
read in data and define variables...
data = dlmread(filename); % pass info in 'filename' to variable 'data' % initialize empty counting vectorstrack_trans = []; % for tracking instances when 'leader' is % followed by 'follower' track_terms = []; % for tracking instances when 'leader' % terminates the line [data_row, data_col] = size(data); % save dimensions of 'data' % to use for looping
do the work...% loop over 'data' rowsfor row = 1:data_row % loop over 'data' columns for col = 1:data_col % look for instances of 'leader' if data(row, col) == leader % check if 'leader' terminates line if col == data_col % if yes, add 1 to counting vector track_terms = [track_terms 1]; % see if next element is 'follower' elseif data(row, col + 1) == follower % if yes, add 1 to counting vector track_trans = [track_trans 1]; end end endend
do the work...% loop over 'data' rowsfor row = 1:data_row % loop over 'data' columns for col = 1:data_col % look for instances of 'leader' if data(row, col) == leader % check if 'leader' terminates line if col == data_col % if yes, add 1 to counting vector track_terms = [track_terms 1]; % see if next element is 'follower' elseif data(row, col + 1) == follower % if yes, add 1 to counting vector track_trans = [track_trans 1]; end end endend
do the work...% loop over 'data' rowsfor row = 1:data_row % loop over 'data' columns for col = 1:data_col % look for instances of 'leader' if data(row, col) == leader % check if 'leader' terminates line if col == data_col % if yes, add 1 to counting vector track_terms = [track_terms 1]; % see if next element is 'follower' elseif data(row, col + 1) == follower % if yes, add 1 to counting vector track_trans = [track_trans 1]; end end endend
do the work...% loop over 'data' rowsfor row = 1:data_row % loop over 'data' columns for col = 1:data_col % look for instances of 'leader' if data(row, col) == leader % check if 'leader' terminates line if col == data_col % if yes, add 1 to counting vector track_terms = [track_terms 1]; % see if next element is 'follower' elseif data(row, col + 1) == follower % if yes, add 1 to counting vector track_trans = [track_trans 1]; end end endend
compute outputs...
% count total number of instances of 'leader'total_leader = length(find(data == leader)); % count number of times 'follower' followed 'leader' count_trans = sum(track_trans);
% count number of times 'leader' terminated lineterminations = sum(track_terms); % calculate probability that 'follower' follows 'leader'prob = count_trans/total_leader;
% calculate probability that 'leader' terminates lineterm_prob = terminations/total_leader;
compute outputs...
% count total number of instances of 'leader'total_leader = length(find(data == leader)); % count number of times 'follower' followed 'leader' count_trans = sum(track_trans);
% count number of times 'leader' terminated lineterminations = sum(track_terms); % calculate probability that 'follower' follows 'leader'prob = count_trans/total_leader;
% calculate probability that 'leader' terminates lineterm_prob = terminations/total_leader;
compute outputs...
% count total number of instances of 'leader'total_leader = length(find(data == leader)); % count number of times 'follower' followed 'leader' count_trans = sum(track_trans);
% count number of times 'leader' terminated lineterminations = sum(track_terms); % calculate probability that 'follower' follows 'leader'prob = count_trans/total_leader;
% calculate probability that 'leader' terminates lineterm_prob = terminations/total_leader;
Extra credit
Generalize this function to deal with sequences of variable length
Hint: more of a data representation problem than a coding problem can't have a matrix with rows of different lengths use 'NaN' to fill space, >>help isnan still want to know if 'leader' is last event in sequence
Only need a couple extra lines of code