How do I use mlabwrap to call a matlab function with cell arguments from python?

Question

Well, I was proud of myself that I got mlabwrap installed properly, but now I cannot get it to work with matlab cells. In python, lists are analogous to cells, so I figured I would input a list and mlabwrap would convert it to a cell. Unfortunately, it does not seem to work that way.

For example, I have a matlab m-file:

function list_test(x)
display(x);

In python, if I type

mlab.list_test([[1,2],[3,4]])

I get:

Thus, mlabwrap seems to take my two nested lists and turn them into a 2x2 matrix, which is not what I want.

When I try

mlab.list_test([[1,2],[3,4,5]])

then I get:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/Ben/.virtualenvs/test/lib/python2.7/site-packages/mlabwrap.py", line 607, in mlab_command
    return self._do(name, *args, **update({'nout':nout}, kwargs))
  File "/Users/Ben/.virtualenvs/test/lib/python2.7/site-packages/mlabwrap.py", line 534, in _do
    mlabraw.put(self._session,  argnames[-1], arg)
TypeError: a float is required

Clearly no dice.

If I have to, I imagine I could write some python code to convert lists into several 1-D arrays, feed the 1-D arrays into matlab using mlabwrap and write some matlab code to convert those 1-D arrays into cells. But this is messy, and I would like to know if there is an easier way. Can mlabwrap do this for me somehow?

Here are the details of my setup. OS: Mountain Lion (OS X 10.8), Python: 2.7, Matlab: 2010b, mlabwrap: 1.1

Has anyone experienced the same thing? Any ideas on how to get around it? There seems to be some machinery in mlabwrap for reading cells from matlab into python, but I am not sure if there is support for reading lists (cells) into matlab from python. — Stretch, Mar 27 '13 at 02:27

score 1 · Accepted Answer · answered May 30 '13 at 17:31

Unfortunately, mlabwrap has limited support for cell arrays; both when passing cell arrays into matlab, and when receiving cell arrays from matlab.

Here's the answer for your immediate question:

>>> from mlabwrap import mlab as matlab

>>> a = [[1, 2], [3, 4]]
>>> cell = matlab.mat2cell(array(a), [1, 1], [2])
>>> matlab.display(cell)

PROXY_VAL2__ = 

    [1x2 double]
    [1x2 double]

Note that this really only works with regularly-sized lists. I.e. [[1,2],[3,4]] works, but [[1,2],[3,4,5]] does not. This is because mlabwrap doesn't handle dtype=object arrays particularly well, instead requiring dtype=float arrays.

Let's swich over to matlab for a quick comparison:

>> display(cell)

cell = 

    [1x2 double]    [1x2 double]

Looks good! However, when we switch back to python, and try and actually access the cell array that we've created:

>>> cell[0][0]

error: Unable to get matrix from MATLAB(TM) workspace

>>> cell[0, 0]

error: Unsupported index type: <type 'tuple'>

>>> type(cell)
mlabwrap.MlabObjectProxy

Unfortunately, mlabwrap doesn't really allow access to the data stored in MlabObjectProxy objects. There are a few ways to try and get around this. You could write cell_insert and cell_pop functions in matlab. These should enable you to put python variables into an existing cell array, and get python-readable variables out from the cell array. Alternatively, you could write the cell array to a .mat file from matlab, and read it into python using scipy.io.loadmat()

Honestly, unless you absolutely need cell arrays for some reason, I would try and avoid using them through mlabwrap.

Ok. Thanks, Brent, for looking into this. For my application, the whole point of using cells is to use irregular length lists. After realizing that cells and structures would not work (easily), I decided to just bite the bullet and convert my matlab code to python. — Stretch, May 31 '13 at 00:45
No problem. I'm sorry about the needed port. If you feel the answer addresses your question sufficiently, would you accept it? — brentlance, May 31 '13 at 16:11
Thank you! If you have another mlabwrap question that's not getting answered, drop a comment here and I'll see it. — brentlance, Jun 01 '13 at 22:56

score 0 · Answer 2 · answered Nov 21 '19 at 18:58

If anyone reads this years later, there is in fact a basic support for cell arrays and char arrays, you just need to type this:

mlab._dont_proxy["cell"] = True

Before using your matlab command that returns a cell or char array. This was tested on https://github.com/aweinstein/mlabwrap and https://github.com/cpbotha/mlabwrap-purepy

How do I use mlabwrap to call a matlab function with cell arguments from python?

2 Answers2