calling TRex from MATLAB

[schlurch1]

Hello mooch (&everybody else), I am really enjoying TRex, especially for being so fast. Thereby i would like to integrate in my analysis and call it from MATLAB. This generally works with using the system function:
system(['call', 'C:\Python\Anaconda3', '\Scripts\activate.bat tracking & ', 'C:\Python\Anaconda3\envs\tracking\bin', '\trex.exe'])

but i cannot manage to set parameters, which is usually done with the '-' (i.e. sth like: -i -meta_real_width ....) any idea which command has to be used?

MATLAB itself states: "You can specify a file to be opened using ./trex -i " - but this did not work

Best Regards

[schlurch1]

never mind, i made it! fyi:

system(['call ', 'C:\Python\Anaconda3', '\Scripts\activate.bat tracking & ', ...
'C:\Python\Anaconda3\envs\tracking\bin', '\trex.exe ', ...
'-i ', input2, ...
'-meta_real_width ', meta_real_width, ...
'-blob_size_ranges ', blob_size_ranges, ...
'-track_max_individuals ', track_max_individuals, ...
'-track_threshold ', track_threshold, ...
'-nowindow ', nowindow, ...
'-output_dir', output, ...
'auto_quit', autoquit, ...
'&'])

Do not forget to place a space at the end of every parameter call and also at the end of the parameter itself

[mooch443]

Yes, this is more or less what I would have suggested. The syntax used in TRex of -parameter value is a very typical Unix/Linux syntax for passing arguments, where Windows would probably use /parameter value or something like that.

And I suppose if those spaces are really necessary there, it's because the only thing that system, given an array of strings, does, is probably to "".join(array). If that is true though, you may be missing a couple. E.g. -output_dir and missing a dash at auto_quit. :-)