matpy

Call Python from MATLAB

Source

This package is based on work originally done by Stanislaw Adaszewski. You can find his original work on his blog. His license is included below and in py.cpp.

Modifications

This repository puts the code under public source control for the first time, and adds a build script which deals with some build issues with the default instructions on the original blog. Pull requests are welcome.

License

Copyright (c) 2012, STANISLAW ADASZEWSKI
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
    * Redistributions of source code must retain the above copyright
      notice, this list of conditions and the following disclaimer.
    * Redistributions in binary form must reproduce the above copyright
      notice, this list of conditions and the following disclaimer in the
      documentation and/or other materials provided with the distribution.
    * Neither the name of STANISLAW ADASZEWSKI nor the
      names of its contributors may be used to endorse or promote products
      derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL STANISLAW ADASZEWSKI BE LIABLE FOR ANY
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Python Version

Currently, the only python version suppoted and testsed for is python 2.7.9.

Types supported to Import and Export

String
Unicode String (Import only)
int8
uint8
int16
uint16
int32
uint32
int64
uint64
single
double
logical
Matlab structs
- structs are exported as python dictionary such that each field is a key in the dictionary and has a corresponding list of values, one for each of the elements of the struct.
- only dictionaries in this form can be imported as structs.
- ex. s =
```
1x2 struct array with fields:
      f1
      f2

s(1) =
      f1: 'v1'
      f2: 'v2'
s(2) =
      f1: 'v3'
      f2: 'v4'

would be exported as:
{'f1': ['v1', 'v3'], 'f2': ['v2', 'v4']}
```
Matlab cells
- cells are exported as a list of objects

Some simple examples

Running a python command with matpy must have the following format:

py('eval', 'python command here')

An example

>> py('eval', 'print "hello, world"')
hello, world

This is a simple example of exporting a variable to python, changing it, and importing the new value.

>> test = 3

test =

     3

>> py_export test
>> py('eval', 'test = test + 3')
>> py_import test
>> test

test =

     6

The example below shows that exporting a simple value to python is represted in python as a single value in a 2d array

>> test = 4

test =

     4

>> py_export test
>> py('eval', 'print test')
[[ 4.]]
>> py('eval', 'print test[0][0]')
4.0

Here's the example of using the py shell

>> test = 5

test =

     5

>> py_export test
>> py_shell
py> print "hello, world"
hello, world
py> print test
[[ 5.]]
py> 1 + 1
py> print 1 + 1
2
py> if test[0][0] < 10: print "hi, again"
hi, again
py> exit

Here's an example of exporting a struct to python, note how it is represented in python

>> test2 = struct('field1', 'value1', 'field2', 'value2');
>> test2(2) = struct('field1', 'value3', 'field2', 'value4');
>> test2(1)

ans =

    field1: 'value1'
    field2: 'value2'

>> test2(2)

ans =

    field1: 'value3'
    field2: 'value4'

>> py_export test2
>> py_shell
py> print test2
{'field2': ['value2', 'value4'], 'field1': ['value1', 'value3']}

Troubleshooting

Compilation Problems

Can't find MATLAB

If you are getting errors similar to

make: mexext: Command not found
make: mex: Command not found

It is possible that the Makefile cannot locate your MATLAB. To Fix, try adding something like this to your ~/.bash_profile export MATPATH=[path to matlab] for example export MATPATH=/Applications/MATLAB_R2012b.app/bin/matlab worked for me.

Can't find Python

If you are getting errors similar to

py.cpp:27:10: fatal error: 'Python.h' file not found
#include <Python.h>
          ^

It is possible that your which python doesn't point to a specific python that we want. You may have to set in your ~/.bash_profile export PYPATH=[path to .pyenv]/versions/[your version]/bin/python for example export PYPATH=~/.pyenv/versions/2.7.9/bin/python worked for me.

Warnings

If your last line after compiling is,


7 warnings generated.

then everything is working as should.

Pointing to the right python

By default, matpy will build with the systems default python. If you want it to reference a specific python, you'll need to make a file ~/.matpyrc and set the python you want matlab to use (and only that string), for example I have /Users/samuelmassinon/.pyenv/versions/2.7.9/bin/python as the only line in my ~/.matpyrc file.

-lpython[version] cannot be found

Your python must link to the appropriate .dylib file. If you are using pyenv it is possible that you can install a version of python that does not include the .dylib file. To fix this, remove the version and then get the version of python using env PYTHON_CONFIGURE_OPTS="--enable-shared" LD_LIBRARY_PATH=~/.pyenv/versions/[version]/lib/ pyenv install -k [version]. For example, I used env PYTHON_CONFIGURE_OPTS="--enable-shared" LD_LIBRARY_PATH=~/.pyenv/versions/2.7.9/lib/ pyenv install -k 2.7.9.

The .dylib file should be located in the /lib directory.

san-santra/matpy