Writing MATLAB Scripts

Overview

Teaching: 30 min
Exercises: 0 min

Questions

• How can I save and re-use my programs?

Objectives

• Write and save MATLAB scripts.

• Save MATLAB plots to disk.

So far, we’ve typed in commands one-by-one on the command line to get MATLAB to do things for us. But what if we want to repeat our analysis? Sure, it’s only a handful of commands, and typing them in shouldn’t take us more than a few minutes. But if we forget a step or make a mistake, we’ll waste time rewriting commands. Also, we’ll quickly find ourselves doing more complex analyses, and we’ll need our results to be more easily reproducible.

In addition to running MATLAB commands one-by-one on the command line, we can also write several commands in a script. A MATLAB script is just a text file with a .m extension. We’ve written commands to load data from a .csv file and displays some statistics about that data. Let’s put those commands in a script called analyze.m, which we’ll save in our current directory,matlab-novice-inflammation:

%---- Load data
patient_data = csvread('data/inflammation-01.csv');

%---- Print basic stats on screen
disp(['Analyzing "inflammation-01.csv": '])
disp(['Maximum inflammation: ', num2str(max(patient_data(:)))])
disp(['Minimum inflammation: ', num2str(min(patient_data(:)))])
disp(['Standard deviation: ', num2str(std(patient_data(:)))])

You can get MATLAB to run those commands by typing in the name of the script (without the .m) in the MATLAB command line:

analyze

Maximum inflammation: 20
Minimum inflammation: 0
Standard deviation: 4.6148

The MATLAB path

MATLAB knows about files in the current directory, but if we want to run a script saved in a different location, we need to make sure that this file is visible to MATLAB. We do this by adding directories to the MATLAB path. The path is a list of directories MATLAB will search through to locate files.

To add a directory to the MATLAB path, we go to the Home tab, click on Set Path, and then on Add with Subfolders.... We navigate to the directory and add it to the path to tell MATLAB where to look for our files. When you refer to a file (either code or data), MATLAB will search all the directories in the path to find it. Alternatively, for data files, we can provide the relative or absolute file path.

GNU Octave

Octave has only recently gained a MATLAB-like user interface. To change the path in any version of Octave, including command-line-only installations, use addpath('path/to/directory')

We’ve also written commands to create plots, so let’s include those in our script too, but this time we’ll save the figures to disk as image files using the print command. In order to maintain an organised project we’ll save the images in the results directory:

%---- Perform calculations
ave_day = mean(patient_data);
ave_patient = mean(patient_data,2);

%---- Plot figures
% Plot average inflammation per day
plot(ave_day)
title('Daily average inflammation')
xlabel('Day of trial')
ylabel('Inflammation')

% Save plot in 'results' folder as png image:
print('results/average','-dpng')

You might have noticed that we described what we want our code to do using the percent sign: %. This is another plus of writing scripts: you can comment your code to make it easier to understand when you come back to it after a while.

A comment can appear on any line, but be aware that the first line or block of comments in a script or function is used by MATLAB as the help text. When we use the help command, MATLAB returns the help text. The first help text line (known as the H1 line) typically includes the name of the program, and a brief description. The help command works in just the same way for our own programs as for built-in MATLAB functions. You should write help text for all of your own scripts and functions.

Let’s write an H1 line at the top of our script:

%ANALYZE   Print statistics for first patient.

We can then get help for our script by running

help analyze

Let’s extend our analyze script with commands to create and save plots. In order to maintain an organised project we’ll save the images in the results directory. We’ll also update the help text to reflect this.

%ANALYZE   Print statistics for first patient.
%          Save plots of statistics to disk.

patient_data = csvread('data/inflammation-01.csv');

disp(['Maximum inflammation: ', num2str(max(patient_data(:)))])
disp(['Minimum inflammation: ', num2str(min(patient_data(:)))])
disp(['Standard deviation: ', num2str(std(patient_data(:)))])

ave_day = mean(patient_data, 1);

subplot(1, 3, 1)
plot(ave_day)
title('Average')
ylabel('Inflammation')
xlabel('Day')

subplot(1, 3, 2)
plot(max(patient_data, [], 1))
title('Max')
ylabel('Inflammation')
xlabel('Day')

subplot(1, 3, 3)
plot(min(patient_data, [], 1))
title('Min')
ylabel('Inflammation')
xlabel('Day')

% Save plot in 'results' directory as png image.
print('results/patient_data-01','-dpng')

When saving plots to disk, it’s sometimes useful to turn off their visibility as MATLAB plots them. For example, we might not want to view (or spend time closing) the figures in MATLAB, and not displaying the figures could make the script run faster.

Let’s add a couple of lines of code to do this:

%ANALYZE   Print statistics for first patient.
%           Save plots of statistics to disk.

patient_data = csvread('data/inflammation-01.csv');

disp(['Maximum inflammation: ', num2str(max(patient_data(:)))])
disp(['Minimum inflammation: ', num2str(min(patient_data(:)))])
disp(['Standard deviation: ', num2str(std(patient_data(:)))])

ave_inflammation = mean(patient_data, 1);

figure('visible', 'off')

subplot(1, 3, 1)
plot(ave_inflammation)
title('Average')
ylabel('inflammation')
xlabel('Day')

subplot(1, 3, 2)
plot(max(patient_data, [], 1))
title('Max')
ylabel('Inflammation')
xlabel('Day')

subplot(1, 3, 3)
plot(min(patient_data, [], 1))
title('Min')
ylabel('Inflammation')
xlabel('Day')
subplot(1, 3, 1)

% Save plot in 'results' directory as png image.
print('results/patient_data-01','-dpng')

close()

If we call the figure function without any options, MATLAB will open up an empty figure window. Try this on the command line:

figure()

We can ask MATLAB to create an empty figure window without displaying it by setting its 'visible' property to 'off', like so:

figure('visible', 'off')

When we do this, we have to be careful to manually “close” the figure after we are doing plotting on it - the same as we would “close” an actual figure window if it were open:

close()

Key Points

• Save MATLAB code in files with a .m suffix.