Path conflicts

A frequent cause of errors is that MATLAB calls 'the wrong' function that has the same name as the intended one. This is called shadowing and the precise file MATLAB uses depends on MATLAB's function precedence order.

For this reason you should be very careful in the way you use paths on shared rigs. Here is a list of things to avoid:

Don't ever call savepath from your functions and more generally avoid changing the rig paths.
Avoid putting your functions in the userpath (usually <User>\Documents\MATLAB) because this folder is by default at the top of the MATLAB path list.
Avoid changing directory in your functions
Don't start an experiment before checking your current working directory.

Note that Rigbox doesn't need to be in any specific directory to work, and besides addRigboxPaths, no code will permanently change the working directory or search path.

Checking your working directory
Calling custom functions
When to add paths
Reset on startup
Etc.

Checking your working directory

It's good idea to make sure your working directory is somewhere safe before starting your experiment. To check you working directory type pwd into the command window. To change into MATLAB's default directory (<User>\Documents\MATLAB), call cd(userpath). To check which file is being used, call the function which with the name of the function your investigating, e.g. which choiceWorld.

Calling custom functions

If changing paths, etc. is unavoidable, make sure you leave everything in the state it was in afterwards.

One way is to temporarily change directory using onCleanup, which will execute even if your function encounters an error:

origDir = pwd; % Get current working directory
mess = onCleanup(@() cd(origDir)); % When exiting the function, change back to original dir
cd(fullfile('my', 'path')) % Change directory to containing mySpecialFunction.m is
mySpecialFunction() % Call your function

When returning, MATLAB clears all a function's variables, including `mess`, whose delete method calls the anonymous function @() cd(origDir)

Another way is to use fileFunction, which temporarily adds the file to the MATLAB path, then removes it after the function is called. This is useful if you need to call a custom function just once:

mySpecialFunction = fileFunction(['my' filesep 'path'], 'mySpecialFunction.m'); % Return function wrapper
% [...]
mySpecialFunction() % Call your function

When to add paths

Changing directory and adding paths can affect performance as MATLAB has to rehash all its file and function caches. If you're constantly calling a special function there are two things to consider. Your expDef is run only twice per experiment so not being on the path doesn't really affect performance, and Rigbox deals with this for you. However if in your expDef a function that is called with scan or map is changing the paths, consider refactoring your code, e.g. making whatever function you need to call a local function. Another option is to create a MATLAB package. That way your function is in its own namespace and you will most likely avoid these sorts of conflicts. For example say I have a function called ls that I need to constantly call. If I put it in +john\ls.m then I can add it to the paths and safely call it without worrying about conflicts:

addpath('+john') % Add this package to the search path
john.ls() % Call +john\ls.m
ls() % Call MATLAB's builtin ls

Reset on startup

Another way to avoid these conflicts occuring over time is to reset your paths each time MATLAB starts up. You can do this by adding the following to MATLAB's startup script:

disp 'Resetting paths...'
restoredefaultpath % Restore all paths to factory state

userDir = winqueryreg('HKEY_CURRENT_USER',...
  'Software\Microsoft\Windows\CurrentVersion\Explorer\Shell Folders', ...
  'Personal'); % Get the user directory path, e.g. <User>\Documents

% Change these paths to your install locations
rigbox_path = fullfile(userDir, 'Github', 'rigbox');
ptb_path = fullfile(userDir, 'PTB', 'Psychtoolbox');

% Add Psychtoolbox paths
disp '...'
disp 'Adding PsychToolbox paths...'
cd(ptb_path)
state = pause('off');
SetupPsychtoolbox;
pause(state);

% Add Rigbox paths
disp 'Adding Rigbox paths...'
cd(rigbox_path)
addRigboxPaths('Strict', false)

% Return to default working directory
cd(userpath)
clear variables
home % Hide command output history

Etc.

Author: Miles Wells

v1.0.0