Is it possible to import and use third party matlab functions/packages in python?

I would like to call functions from packages that are imported in Matlab in Python using the MATLAB Engine API for Python. The import/setup work for the package I want to use is contained in load_javaplex.m:

% This script prepares the javaplex library for use

clc; clear all; close all;
%clear import;

javaaddpath('./lib/javaplex.jar');
import edu.stanford.math.plex4.*;

javaaddpath('./lib/plex-viewer.jar');
import edu.stanford.math.plex_viewer.*;

cd './utility';
addpath(pwd);
cd '..';

fprintf('DONE');
% This last line calls a function to test the library
api.Plex4.createExplicitSimplexStream()

In Python I tried the following:

import matlab.engine
eng = matlab.engine.start_matlab()

# prepare javaplex library for use
eng.load_javaplex(nargout=0)
eng.api.Plex4.createExplicitSimplexStream()

When the load_javaplex.m runs it successfully calls api.Plex4.createExplicitSimplexStream(), so we know the package is working in Matlab. But calling eng.api.Plex4.createExplicitSimplexStream() results in an undefined function error (output from running the Python code above):

DONE
ans =

edu.stanford.math.plex4.streams.impl.ExplicitSimplexStream@5e894fec

Undefined function or variable 'api.Plex4.createExplicitSimplexStream'.

Traceback (most recent call last):
  File "/Users/alex/PycharmProjects/SeniorResearchProject/Code/sandbox/test2.py", line 6, in <module>
    eng.api.Plex4.createExplicitSimplexStream()
  File "/Users/alex/anaconda/lib/python2.7/site-packages/matlab/engine/matlabengine.py", line 84, in __call__
    _stderr, feval=True).result()
  File "/Users/alex/anaconda/lib/python2.7/site-packages/matlab/engine/futureresult.py", line 68, in result
    return self.__future.result(timeout)
  File "/Users/alex/anaconda/lib/python2.7/site-packages/matlab/engine/fevalfuture.py", line 82, in result
    self._result = pythonengine.getFEvalResult(self._future,self._nargout, None, out=self._out, err=self._err)
matlab.engine.MatlabExecutionError: Undefined function or variable 'api.Plex4.createExplicitSimplexStream'.

Process finished with exit code 1

Is there a way to call these third party functions from Python?

Answer 1

[Robert Snoeberger]

It looks like your problem is with import. I don't think the import that executes in your script, load_javaplex, is available when you try to call createExplicitSimplexStream. Try using the full name instead of the shortened name. I would guess that the full name is edu.stanford.math.plex4.api.Plex4.createExplicitSimplexStream. Example:

% Use the full name
eng.edu.stanford.math.plex4.api.Plex4.createExplicitSimplexStream()

[Alexander Williams]

This does work, but the matlab engine api is unable to handle the custom datatype (a java object) returned by the function call:

Traceback (most recent call last):
  File "/Users/alex/PycharmProjects/SeniorResearchProject/Code/sandbox/test2.py", line 8, in <module>
    eng.edu.stanford.math.plex4.api.Plex4.createExplicitSimplexStream()
  File "/Users/alex/anaconda/lib/python2.7/site-packages/matlab/engine/matlabengine.py", line 84, in __call__
    _stderr, feval=True).result()
  File "/Users/alex/anaconda/lib/python2.7/site-packages/matlab/engine/futureresult.py", line 68, in result
    return self.__future.result(timeout)
  File "/Users/alex/anaconda/lib/python2.7/site-packages/matlab/engine/fevalfuture.py", line 82, in result
    self._result = pythonengine.getFEvalResult(self._future,self._nargout, None, out=self._out, err=self._err)
TypeError: unsupported data type returned from MATLAB

I think I will just keep all calls to the java library in matlab code for now. Since you did technically answer my question I accepted. Thanks for responding!

Answer 2

[Bo Li]

It looks that "api.Plex4.createExplicitSimplexStream()" is a Java API and it works when it is called by Python Engine as part of load_javaplex.m, while calling eng.api.Plex4.createExplicitSimplexStream() directly from Python fails.

Python Engine works as the MATLAB command "feval" does:

http://www.mathworks.com/help/matlab/ref/feval.html

Most likely, calling "feval('api.Plex4.createExplicitSimplexStream')" in MATLAB will also fail. In such case, besides wrapping the Java API inside a M function, you may also invoke the Java API with eval in Python:

>>>eng.eval('api.Plex4.createExplicitSimplexStream', nargout=0)

[Alexander Williams]

eng.eval('api.Plex4.createExplicitSimplexStream', nargout=0)

results in

matlab.engine.MatlabExecutionError: Undefined variable "api" or class "api.Plex4.createExplicitSimplexStream".

I have decided to keep all calls to the java package in matlab code because of the issue mentioned in my comment above.