How can I call a script within a for loop, looping over multiple files?

Hi all, I know this information must be out there somewhere but I'm just not seeing what I need or maybe I'm just not understanding what I'm reading since I'm not very MATLAB literate. Anyway, thank you for your help in advance.

I'm trying to put together a script containing a for loop, in which I can call another script and apply that second script to a number of files. The files are organized by participant ID and by visit number so in my loop script (loop.m), I have included variable identifiers:

ID = {'1','2','3'};
Visit = {'1','2'};

These IDs correspond to the IDs referenced in the script that I'm calling and have the same name as in the script that I'm calling. Once I've specified those variables, I start my for loop:

for nSubject = 1:length(ID)
    for nVisit = 1:length(Visit)
        result = scriptname(nSubject,nVisit));
    end
end

Within the second script, here referred to as scriptname.m, the first few lines take that information and then start working with it:

function task1 = scriptname(ID,Visit)
filename = append('ECG_',ID,'_',Visit,'.txt');
filelocation = fullfile('path\',ID,'\',Visit);
cd(filelocation)

etc.

What I'm running into is that when I run loop.m, I get errors.

Error using append (line 62)
Input must be a string array, character vector, or cell array of character vectors.
Error in scriptname (line 8)
filename = append('ECG_',ID,'_',Visit,'.txt');
Error in loop (line 22)
result = scriptname(nSubject,nVisit);

I think I have a few problems:

1. It looks like ID and possibly also Visit aren't creating correctly - when I run that part of the script, the resulting cells includes all the participant IDs in the origin file, even if I haven't specified those IDs.
2. I'm probably calling the script incorrectly in the for loop. I know that scriptname.m works just fine when I specify ID and Visit alone and then just run scriptname.m - so it sounds to me like loop.m is the problem, not necessarily scriptname.m.

Any suggestions for me? THANK YOU

[Matt J]

Note that you are confusing the terminology "script" with "functions",

https://www.mathworks.com/help/matlab/matlab_prog/create-functions-in-files.html

[Stephen23]

Note that the point of FULLFILE is that it correctly handles the filepath delimiter, so this:

fullfile('path\',ID,'\',Visit);

should be replaced with this:

fullfile('path',ID,Visit);

Also note that using CD programmatically is slow and rarely (i.e. almost never) required. It is certainly not required to import/export from data files, because all MATLAB functions accept absolute/relative filepaths. Rather than slow and difficult-to-debug CD you should just generate a suitable filename (with absolute/relative filepath).

And as Matt J pointed out, you are calling a function, not a script. The differences are quite significant:

https://www.mathworks.com/help/matlab/matlab_prog/scripts-and-functions.html

[Caitlin Ridgewell]

Thank you both, Stephen and Matt. Your comments were very helpful and I learned a few things! I definitely need to work on the efficiency of my coding...

Now that the loop appears to be running though, what I've found is that it processes the first participant in my ID list but then fails to call the function (task1) again for the second participant in the ID list. I get the error:

Output argument "task1" (and maybe others) not assigned during call to "scriptname".
Error in loop (line 12)
result = scriptname(ID{nSubject},Visit{nVisit");

Any idea why it won't repeat the loop?

[Matt J]

Yes, it is complaining that you've written the function,

function task1 = scriptname(ID,Visit)

declaring that an output variable called task1 will be returned, but task1 is never created anywhere within the body of scriptname.

[Caitlin Ridgewell]

Excellent point, Matt. I'll look into how to improve my script so it's written appropriately and doesn't have this problem anymore. Thanks for pointing that out!

Answer 1

[Matt J]

     result = scriptname(ID{nSubject},Visit{nVisit});