Overview
Teaching: 30 min
Exercises: 0 minQuestions
How can I save and re-use my programs?
Objectives
Write and save Octave scripts.
Save Octave plots to disk.
So far, we’ve typed in commands one-by-one on the command line to get Octave 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 Octave commands one-by-one on the
command line, we can
also write several commands in a script. A Octave 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:
% script analyze.m
patient_data = csvread('data/inflammation-01.csv');
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(:)))]);
Before we can use it, we need to make sure that this file is
visible to Octave. Octave doesn’t know about all the files on your
computer, but it keeps an eye on several directories.
The most convenient of these directories is generally the
“working directory”, or “current directory”. To find out the
working directory, use the pwd (print working directory) command:
pwd
Once you have a script saved in a location that Octave knows about,
you can get Octave to run those commands by typing in the name
of the script (without the .m) in the Octave command line:
analyze
Maximum inflammation: 20
Minimum inflammation: 0
Standard deviation: 4.6148
We’ve also written commands to create plots:
ave_inflammation = mean(patient_data, 1);
plot(ave_inflammation);
ylabel('average')
Octave let’s us save those as images on disk:
% save plot to disk as png image:
print ('average','-dpng')
You might have noticed that we described what we want
our code to do using the %-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.
Let’s extend our analyze script with commands to
create and save plots:
% script analyze.m
patient_data = csvread('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);
subplot(1, 3, 1);
plot(ave_inflammation);
ylabel('average')
subplot(1, 3, 2);
plot(max(patient_data, [], 1));
ylabel('max')
subplot(1, 3, 3);
plot(min(patient_data, [], 1));
ylabel('min')
% save plot to disk as png image:
print ('patient_data-01','-dpng')
When saving plots to disk, it’s a good idea to turn off their visibility as MATLAB plots them. Let’s add a couple of lines of code to do this:
% script analyze.m
patient_data = csvread('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);
ylabel('average')
subplot(1, 3, 2);
plot(max(patient_data, [], 1));
ylabel('max')
subplot(1, 3, 3);
plot(min(patient_data, [], 1));
ylabel('min')
% save plot to disk as png image:
print ('patient_data-01','-dpng')
close()
If we call the figure function without any options,
Octave will open up an empty figure window.
Try this on the command line:
figure()
We can ask Octave 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 Octave code in files with a
.msuffix.