Call Python function from MATLAB

Question

I need to call a Python function from MATLAB. how can I do this?

Answer 1

Since MATLAB seamlessly integrates with Java, you can use Jython to write your script and call that from MATLAB (you may have to add a thin pure JKava wrapper to actually call the Jython code). I never tried it, but I can't see why it won't work.

Answer 2

This seems to be a suitable method to "tunnel" functions from Python to MATLAB:

http://code.google.com/p/python-matlab-wormholes/

The big advantage is that you can handle ndarrays with it, which is not possible by the standard output of programs, as suggested before. (Please correct me, if you think this is wrong - it would save me a lot of trouble :-) )

Answer 3

Try this MEX file for ACTUALLY calling Python from MATLAB not the other way around as others suggest. It provides fairly decent integration : http://algoholic.eu/matpy/

You can do something like this easily:

[X,Y]=meshgrid(-10:0.1:10,-10:0.1:10);
Z=sin(X)+cos(Y);
py_export('X','Y','Z')
stmt = sprintf(['import matplotlib\n' ...
'matplotlib.use(''Qt4Agg'')\n' ...
'import matplotlib.pyplot as plt\n' ...
'from mpl_toolkits.mplot3d import axes3d\n' ...
'f=plt.figure()\n' ...
'ax=f.gca(projection=''3d'')\n' ...
'cset=ax.plot_surface(X,Y,Z)\n' ...
'ax.clabel(cset,fontsize=9,inline=1)\n' ...
'plt.show()']);
py('eval', stmt);

Answer 4

You could embed your Python script in a C program and then MEX the C program with MATLAB but that might be a lot of work compared dumping the results to a file.

You can call MATLAB functions in Python using PyMat. Apart from that, SciPy has several MATLAB duplicate functions.

But if you need to run Python scripts from MATLAB, you can try running system commands to run the script and store the results in a file and read it later in MATLAB.

Answer 5

I had a similar requirement on my system and this was my solution:

In MATLAB there is a function called perl.m, which allows you to call perl scripts from MATLAB. Depending on which version you are using it will be located somewhere like

C:\Program Files\MATLAB\R2008a\toolbox\matlab\general\perl.m

Create a copy called python.m, a quick search and replace of perl with python, double check the command path it sets up to point to your installation of python. You should now be able to run python scripts from MATLAB.

Example

A simple squared function in python saved as "sqd.py", naturally if I was doing this properly I'd have a few checks in testing input arguments, valid numbers etc.

import sys

def squared(x):
    y = x * x
    return y

if __name__ == '__main__':
    x = float(sys.argv[1])
    sys.stdout.write(str(squared(x)))

Then in MATLAB

>> r=python('sqd.py','3.5')
r =
12.25
>> r=python('sqd.py','5')
r =
25.0
>>

Answer 6

As @dgorissen said, Jython is the easiest solution.

Just install Jython from the homepage.

Then:

javaaddpath('/path-to-your-jython-installation/jython.jar')

import org.python.util.PythonInterpreter;

python = PythonInterpreter; %# takes a long time to load!
python.exec('import some_module');
python.exec('result = some_module.run_something()');
result = python.get('result');

See the documentation for some examples.

Beware: I never actually worked with Jython and it seems that the standard library one may know from CPython is not fully implemented in Jython!

Small examples I tested worked just fine, but you may find that you have to prepend your Python code directory to sys.path.

Answer 7

Since Python is a better glue language, it may be easier to call the MATLAB part of your program from Python instead of vice-versa.

Check out Mlabwrap.

Answer 8

With Matlab 2014b python libraries can be called directly from matlab. A prefix py. is added to all packet names:

>> wrapped = py.textwrap.wrap("example")

wrapped = 

  Python list with no properties.

    ['example']

Answer 9

Like Daniel said you can run python commands directly from Matlab using the py. command. To run any of the libraries you just have to make sure Malab is running the python environment where you installed the libraries:

On a Mac:

• Open a new terminal window;

• type: which python (to find out where the default version of python is installed);

• Restart Matlab;

• type: pyversion('/anaconda2/bin/python'), in the command line (obviously replace with your path).
• You can now run all the libraries in your default python installation.

For example:

py.sys.version;

py.sklearn.cluster.dbscan

Answer 10

Starting from Matlab 2014b Python functions can be called directly. Use prefix py, then module name, and finally function name like so:

result = py.module_name.function_name(argument1, argument2, ...);

Make sure to add the script to the Python search path when calling from Matlab if you are in a different working directory than that of the Python script.

---

Introduction

The source code below explains how to call a function from a Python module from a Matlab script.

It is assumed that MATLAB and Python are already installed (along with NumPy in this particular example).

Exploring the topic I landed on this link (MATLAB 2014b Release Notes) on the MathWorks website which indicated that it is possible starting from Matlab R2014b.

Instructions

In the example below it is assumed the current working directory will have the following structure:

our_module
  |
  +-> our_script.py
matlab_scripts
  |
  +-> matlab_script.m

Start with a simple script our_module/our_script.py:

import numpy

def our_function(text):
    print('%s %f' % (text, numpy.nan))

It has one function which prints the string passed to it as a parameter, followed by NaN (not-a-number) value.

Keep it in its own directory our_module.

Next, go to Matlab and navigate to the current working directory where the Python module (our_module) is located.

Call the function from the Python module with the following statement:

py.our_module.our_script.our_function('Hello')

This will have the expected outcome:

>> py.our_module.our_script.our_function('Hello')
Hello nan
>>

However, a matlab_script.m file in a matlab_scripts directory (created next to the our_module directory) with only the above statement will result in the following outcome:

>> matlab_script
Undefined variable "py" or class "py.our_module.our_script.our_function".

Error in matlab_script (line 1)
py.our_module.our_script.our_function('Hello')
>>

Looking for the solution I found a page entitled Undefined variable "py" or function "py.command" which helped to troubleshoot this error.

Assuming there is no typo in the script it recommends adding the base directory to Python's search path.

Therefore, the correct content of the Matlab script should be:

[own_path, ~, ~] = fileparts(mfilename('fullpath'));
module_path = fullfile(own_path, '..');
python_path = py.sys.path;
if count(python_path, module_path) == 0
    insert(python_path, int32(0), module_path);
end
py.our_module.our_script.our_function('Hello')

It obtains the location of the Python module, finds the base path of that module, accesses the Python search path, checks if the base path is already included and inserts it otherwise.

Running the corrected script will result in the same expected output as before.

Here is another helpful link to get you going.

Answer 11

A little known (and little documented) fact about MATLAB's system() function: On unixoid systems it uses whatever interpreter is given in the environment variable SHELL or MATLAB_SHELL at the time of starting MATLAB. So if you start MATLAB with

SHELL='/usr/bin/python' matlab

any subsequent system() calls will use Python instead of your default shell as an interpreter.

Answer 12

I've adapted the perl.m to python.m and attached this for reference for others, but I can't seem to get any output from the Python scripts to be returned to the MATLAB variable :(

Here is my M-file; note I point directly to the Python folder, C:\python27_64, in my code, and this would change on your system.

function [result status] = python(varargin)
cmdString = '';
for i = 1:nargin
    thisArg = varargin{i};
    if isempty(thisArg) || ~ischar(thisArg)
        error('MATLAB:python:InputsMustBeStrings', 'All input arguments must be valid strings.');
    end
    if i==1
        if exist(thisArg, 'file')==2
            if isempty(dir(thisArg))
                thisArg = which(thisArg);
            end
        else
            error('MATLAB:python:FileNotFound', 'Unable to find Python file: %s', thisArg);
        end
    end
  if any(thisArg == ' ')
    thisArg = ['"', thisArg, '"'];
  end
  cmdString = [cmdString, ' ', thisArg];
end
errTxtNoPython = 'Unable to find Python executable.';
if isempty(cmdString)
  error('MATLAB:python:NoPythonCommand', 'No python command specified');
elseif ispc
  pythonCmd = 'C:\python27_64';
  cmdString = ['python' cmdString];  
  pythonCmd = ['set PATH=',pythonCmd, ';%PATH%&' cmdString];
  [status, result] = dos(pythonCmd)
else
  [status ignore] = unix('which python'); %#ok
  if (status == 0)
    cmdString = ['python', cmdString];
    [status, result] = unix(cmdString);
  else
    error('MATLAB:python:NoExecutable', errTxtNoPython);
  end
end
if nargout < 2 && status~=0
  error('MATLAB:python:ExecutionError', ...
        'System error: %sCommand executed: %s', result, cmdString);
end

EDIT :

Worked out my problem the original perl.m points to a Perl installation in the MATLAB folder by updating PATH then calling Perl. The function above points to my Python install. When I called my function.py file, it was in a different directory and called other files in that directory. These where not reflected in the PATH, and I had to easy_install my Python files into my Python distribution.

Answer 13

The simplest way to do this is to use MATLAB's system function.

So basically, you would execute a Python function on MATLAB as you would do on the command prompt (Windows), or shell (Linux):

system('python pythonfile.py')

The above is for simply running a Python file. If you wanted to run a Python function (and give it some arguments), then you would need something like:

system('python pythonfile.py argument')

For a concrete example, take the Python code in Adrian's answer to this question, and save it to a Python file, that is test.py. Then place this file in your MATLAB directory and run the following command on MATLAB:

system('python test.py 2')

And you will get as your output 4 or 2^2.

Note: MATLAB looks in the current MATLAB directory for whatever Python file you specify with the system command.

This is probably the simplest way to solve your problem, as you simply use an existing function in MATLAB to do your bidding.