author:Pauli Virtanen <>

Python embedded inside Matlab.

Conversion of basic types + numeric array types between Python and Matlab is provided.


This is still in relatively early stages of work, but I have used it for example for loading HDF5 files using PyTables. (Since frankly, Matlab’s HDF5 support has been quite inadequate.)

Also, this code has been tested only on Linux platforms.


  • Evaluate python string:

    pythoncall('eval', command)

    command is a string containing the Python program to run. It is run in the __main__ module.

  • Get variable values from the Python space:

    [value1, value2, ...] = pythoncall('get', varname1, varname2, ...)

    This gets variables from the top-level of __main__ module.

  • Set variable values to the Python space:

    pythoncall('set', varname1, value1, varname2, value2, ...)

    This sets variables to the top-level of __main__ module.

Compilation (important!)

Note that Matlab apparently dlopens its extensions with RTLD_GLOBAL disabled. This means that if you load the Python interpreter inside Matlab without extra tricks, any extensions modules loaded by Python will not be able to see Python symbols. Which means that they do not work, which is especially annoying since you surely would like to use for example numpy.

To work around this nasty limitation, pythoncall.c has an equally nasty hack: it explicitly loads symbols in the Python library to its own “namespace”, by dlopening the Python library file. To do this, it needs to know the location of Python’s file. Have a look at the Makefile and fix the location of LIBPYTHON to match your version of Python.

While you’re at it, also change -DNUMPY to -DNUMARRAY or -DNUMERIC if you use one of the earlier array libraries of Python.

Type conversion

The whole point of having Python inside Matlab is to have easy conversion of variables. In pythoncall this goes as follows:

From To
Python int Matlab 1x1 int32
Python float Matlab 1x1 double
Python complex Matlab 1x1 double complex
Python bool Matlab 1x1 logical
Python dict Matlab 1x1 struct array. Field names: repr(key)
Python object array Matlab cell array
Python array Matlab array
Python sequence Matlab 1xN cell array
Python None Matlab empty cell array
Python other Matlab empty cell array + warning
Matlab cell array Python list if one-dim, otherwise python object array
Matlab char array Python string if one-dim, otherwise python numeric array
Matlab struct array Python dict. If 1x1, values are converted directly. If not scalar, values are python arrays/obj-arrays, same size as the struct.
Matlab array Python array
Matlab other Python None + warning