Calling a matlab function with python subprocess.Popen

Hi,

I have a python code which runs a matlab function sussum(a,nx,ny) in the background with subprocess.Popen. I am not able to get it working. Because I'm unable to pass the input arguments to matlab correctly. Here is the python code:

     #!/usr/bin/env python

     import matlab.engine
     import scipy.io as sio
     import numpy as np
     import subprocess as sb

     nproc = 5
     input = sio.loadmat('sus_py.mat')

     totq = input['totq']
     nx,ny = input['nx'],input['ny']
     nq = totq+1
     nx,ny = matlab.int32(nx.tolist()) , matlab.int32(ny.tolist())

     iq = range(1,nq)
     gp = len(iq)/nproc
     list = [iq[j:j+nproc] for j in range(0,len(iq),nproc)]

     for g in range(0,len(list)):
         i = len(list[g])
         p = []
         for n in range(0,i):
             a = matlab.int32(list[g][n])
             fun = '-r "sussum(a,nx,ny); exit" '
             lmb = ['/usr/local/bin/matlab','-nodesktop','-nosplash','-nodisplay','-nojvm',fun]
             p.append(sb.Popen(lmb))
         for q in p:
             q.wait()

The python script executes in the command terminal of a cluster network, until it spits out the error message: Undefined function or variable 'a'.

I am sure that the matlab function sussum(a,nx,ny) works fine because I have tested it using Python-Matlab API as matlab.engine.start_matlab().sussum(a,nx,ny) and it gave the desired outputs. Any help in getting the python code running with subprocess.Popen() will be highly appreciated.

Answer 1

[Walter Roberson]

You need to convert the values of the variable to text and insert them at the appropriate place.

Or, you need to push the variables to the MATLAB engine and send the MATLAB engine a command. The method you are using now appears to use both the engine and a new MATLAB process.

[Shini Bhatt]

I'm not sure if I have understood what you are suggesting. Can you please provide an example by modifying my script above?

[Walter Roberson]

fun = '-r "sussum(%g,%g,%g); exit" ' % (a,nx,ny)

[Shini Bhatt]

Thanks! The edit you suggested works as long as nx,ny are 1-D or 2-D array. N-D array with N>2 has different structures in Matlab and Python, so matlab doesn't accept such inputs.

I found another answer that modifies python N-D arrays to be acceptable to matlab. Although, I haven't used this yet: https://www.mathworks.com/matlabcentral/answers/157347-convert-python-numpy-array-to-double