Calling MATLAB through Shell with Python Script Issues

Question

I'm having an issue with this call I can't seem to resolve:

os.system('matlab -nodisplay -nosplash -r \"processFates;dlmwrite(\'' + FWHM + ' ' + volume      + ' ' + key + ' ' + str(numTrials) + '\", min_timing)\"')

FWHM, volume, key are all strings. I keep getting the error of an extra ) but it seems like I need all of them here.

Sam Roberts · Accepted Answer · 2013-07-03 09:54:40Z

2

Let's try this with some values:

>>> FWHM, volume, key, numTrials, min_timing = 'a', 'b', 'c', 'd', 'e'
>>> print('matlab -nodisplay -nosplash -r \"processFates;dlmwrite(\'' + FWHM + ' ' + volume      + ' ' + key + ' ' + str(numTrials) + '\", min_timing)\"')
matlab -nodisplay -nosplash -r "processFates;dlmwrite('a b c d", min_timing)"

See that double quote after the d? That should probably be a single quote. Also, the min_timing you're passing is the literal string min_timing, not the variable you're expecting.

Using subprocess.Popen instead of os.system you can avoid some of these problems with escaping by not relying on the shell and passing the arguments as strings directly:

command = "processFates; dlmwrite('%s %s %s %s', %s)" % (FWHM, volume, key, numTrials, min_timing)
proc = subprocess.Popen(['matlab', '-nodisplay', '-nosplash', '-r', command])

edited Jul 3, 2013 at 9:54

Sam Roberts

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answered Jul 2, 2013 at 21:42

mata

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3 Comments

alvarezcl Over a year ago

Ah I see okay. But matlab still doesn't seem to be executing dlmwrite still.

mata Over a year ago

this suggests that your syntax of the dlmwrite command is not right, you should need to have commas between the parameters, and quote the string parameters... I just indicated the problems with the shell syntax. I don't use matlab, so I can't really help you with that.

alvarezcl Over a year ago

Okay. So the first one you fixed is actually giving me the result I needed without using the subprocess module. Matlab would process my parameters but not tell me it did anything (which is weird) but it works. Thanks!

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