How to get the output of a matlab script in python

Question

I am performing a matlab calculation through python. For this purpose, I use the following command:

retcode=subprocess.call["matlab","-nosplash","nodesktop","-wait","-r","run('matlabscript.m')","quit;"])

by running this command line in python, a matlab session opens and I can start to execute the aforementioned script 'matlabscript.m'. Is there a way to get the output of the execution of this script into python? retcode, does not contain anything unless a single number. I have tried to use subprocess.check_output instead, but I cannot get anything. Basically, when I execute the aforementioned sript a casename is going to be created and specified.

Have you tried subprocess.Popen with stdout=subprocess.PIPE and the communicate method? — cdarke
– cdarke, Commented Jun 17, 2015 at 14:53
@AaronHall: it's not an answer because the question specifically requires subprocess.call, not Popen. — cdarke
– cdarke, Commented Jun 17, 2015 at 15:11
@cdarke read the source, same thing: hg.python.org/cpython/file/8667c26e2bec/Lib/subprocess.py#l552 — Aaron Hall
– Aaron Hall ♦, Commented Jun 17, 2015 at 15:36
I think that communicate method is when you would like to insert the sequence of commands to specify when the matlab script runs. Are you certain about the usage of this command? — Domenico di Cugno
– Domenico di Cugno, Commented Jun 17, 2015 at 15:45

cdarke · Accepted Answer · 2015-06-17 15:52:45Z

1

I suggest you use Popen. I don't have matlab, so I can't test your exact command, but try this:

import subprocess

cmd = ["matlab", "-nosplash", "no desktop", "-wait", "r", "run('matlabscript.m')","quit;"]

proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
(output, error) = proc.communicate()

if error:
    print "error:", error

print "output:", output

# if you need this:
retcode = proc.returncode

If a huge amount of output is produced then this could potentially crash, its a judgement only you can make.

Note that subprocess.communicate() is also used for stdin.

answered Jun 17, 2015 at 15:52

cdarke

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2 Comments

Domenico di Cugno Over a year ago

I may need to clarify that the output that I need is whatever comes out or is typed into the cmd of matlab. It is this the information that I want to get returned into python. By the way, by following your method, the output I get is empty.

cdarke Over a year ago

@DomenicodiCugno: I'm assuming your phrase "output" means stdout, the standard output stream. If it is sent somewhere else then you will have to capture it some other way. This could be why check_output does not work. Did you get anything through the error (stderr) stream? Can you confirm what you mean by output?

notorious.no · Accepted Answer · 2015-06-17 14:59:47Z

0

You could use subprocess.check_output which will wait for the result:

subprocess.check_output(["matlab","-nosplash","nodesktop","-wait","-r","run('matlabscript.m')","quit;"])

answered Jun 17, 2015 at 14:59

notorious.no

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1 Comment

Kevin Over a year ago

I agree that this is a step in the right direction. But apparently "I have tried to use subprocess.check_output instead, but I cannot get anything", so something else is going on.

Markus · Accepted Answer · 2015-06-17 19:10:48Z

If you're using Matlab >= R2014b, you can simply use the Matlab Engine for Python provided by Mathworks.

>>> import matlab.engine
>>> worker = matlab.engine.start_matlab()
>>> a = worker.eval('rand(10,10)')
>>> print(a)
[[0.8147236863931789,0.15761308167754828,0.6557406991565868,0.7060460880196088,0.43874435965639824,0.27602507699857837,0.7512670593056529,0.8407172559836625,0.35165950706299676,0.07585428956306361],[0.9057919370756192,0.9705927817606157,0.035711678574189554,0.031832846377420676,0.3815584570930084,0.6797026768536748,0.2550951154592691,0.25428217897153105,0.8308286278962909,0.05395011866660715],[0.12698681629350606,0.9571669482429456,0.8491293058687771,0.27692298496088996,0.7655167881490024,0.6550980039738407,0.5059570516651424,0.8142848260688164,0.5852640911527243,0.5307975530089727],[0.9133758561390194,0.4853756487228412,0.9339932477575505,0.04617139063115394,0.7951999011370632,0.16261173519463057,0.699076722656686,0.2435249687249893,0.5497236082911395,0.7791672301020112],[0.6323592462254095,0.8002804688888001,0.6787351548577735,0.09713178123584754,0.1868726045543786,0.11899768155837664,0.8909032525357985,0.9292636231872278,0.91719366382981,0.934010684229183],[0.09754040499940952,0.14188633862721534,0.7577401305783334,0.8234578283272926,0.48976439578823106,0.49836405198214295,0.9592914252054443,0.34998376598480874,0.28583901882037355,0.12990620847373013],[0.2784982188670484,0.421761282626275,0.7431324681249162,0.694828622975817,0.4455862007108995,0.9597439585160811,0.5472155299638031,0.19659525043120818,0.7572002291107213,0.5688236608721927],[0.5468815192049838,0.9157355251890671,0.39222701953416816,0.31709948006086053,0.6463130101112646,0.3403857266661332,0.13862444282867914,0.25108385797603106,0.7537290942784953,0.4693906410582058],[0.9575068354342976,0.7922073295595544,0.6554778901775566,0.9502220488383549,0.7093648308580726,0.5852677509797773,0.14929400555905747,0.6160446761466392,0.38044584697535666,0.011902069501241397],[0.9648885351992765,0.959492426392903,0.17118668781156177,0.03444608050290876,0.7546866819823609,0.22381193949113698,0.25750825412373646,0.47328884890272926,0.5678216407252211,0.3371226443988815]]

As an alternative, switch to GNU Octave and simple use Oct2Py.

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