"Converting" Numpy arrays to Matlab and vice versa

Question

Sure, just use scipy.io.savemat

As an example:

import numpy as np
import scipy.io

x = np.linspace(0, 2 * np.pi, 100)
y = np.cos(x)

scipy.io.savemat('test.mat', dict(x=x, y=y))

Similarly, there's scipy.io.loadmat.

You then load this in matlab with load test.

Alteratively, as @JAB suggested, you could just save things to an ascii tab delimited file (e.g. numpy.savetxt). However, you'll be limited to 2 dimensions if you go this route. On the other hand, ascii is the universial exchange format. Pretty much anything will handle a delimited text file.

A simple solution, without passing data by file or external libs.

Numpy has a method to transform ndarrays to list and matlab data types can be defined from lists. So, when can transform like:

np_a = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
mat_a = matlab.double(np_a.tolist())

From matlab to python requires more attention. There is no built-in function to convert the type directly to lists. But we can access the raw data, which isn't shaped, but plain. So, we use reshape (to format correctly) and transpose (because of the different way MATLAB and numpy store data). That's really important to stress: Test it in your project, mainly if you are using matrices with more than 2 dimensions. It works for MATLAB 2015a and 2 dims.

np_a = np.array(mat_a._data.tolist())
np_a = np_a.reshape(mat_a.size).transpose()

Here's a solution that avoids iterating in python, or using file IO - at the expense of relying on (ugly) matlab internals:

import matlab
# This is actually `matlab._internal`, but matlab/__init__.py
# mangles the path making it appear as `_internal`.
# Importing it under a different name would be a bad idea.
from _internal.mlarray_utils import _get_strides, _get_mlsize

def _wrapper__init__(self, arr):
    assert arr.dtype == type(self)._numpy_type
    self._python_type = type(arr.dtype.type().item())
    self._is_complex = np.issubdtype(arr.dtype, np.complexfloating)
    self._size = _get_mlsize(arr.shape)
    self._strides = _get_strides(self._size)[:-1]
    self._start = 0

    if self._is_complex:
        self._real = arr.real.ravel(order='F')
        self._imag = arr.imag.ravel(order='F')
    else:
        self._data = arr.ravel(order='F')

_wrappers = {}
def _define_wrapper(matlab_type, numpy_type):
    t = type(matlab_type.__name__, (matlab_type,), dict(
        __init__=_wrapper__init__,
        _numpy_type=numpy_type
    ))
    # this tricks matlab into accepting our new type
    t.__module__ = matlab_type.__module__
    _wrappers[numpy_type] = t

_define_wrapper(matlab.double, np.double)
_define_wrapper(matlab.single, np.single)
_define_wrapper(matlab.uint8, np.uint8)
_define_wrapper(matlab.int8, np.int8)
_define_wrapper(matlab.uint16, np.uint16)
_define_wrapper(matlab.int16, np.int16)
_define_wrapper(matlab.uint32, np.uint32)
_define_wrapper(matlab.int32, np.int32)
_define_wrapper(matlab.uint64, np.uint64)
_define_wrapper(matlab.int64, np.int64)
_define_wrapper(matlab.logical, np.bool_)

def as_matlab(arr):
    try:
        cls = _wrappers[arr.dtype.type]
    except KeyError:
        raise TypeError("Unsupported data type")
    return cls(arr)

The observations necessary to get here were:

• Matlab seems to only look at type(x).__name__ and type(x).__module__ to determine if it understands the type
• It seems that any indexable object can be placed in the ._data attribute

Unfortunately, matlab is not using the _data attribute efficiently internally, and is iterating over it one item at a time rather than using the python memoryview protocol :(. So the speed gain is marginal with this approach.

scipy.io.savemat or scipy.io.loadmat does NOT work for matlab arrays --v7.3. But the good part is that matlab --v7.3 files are hdf5 datasets. So they can be read using a number of tools, including numpy.

For python, you will need the h5py extension, which requires HDF5 on your system.

import numpy as np, h5py 
f = h5py.File('somefile.mat','r') 
data = f.get('data/variable1') 
data = np.array(data) # For converting to numpy array

Some time ago I faced the same problem and wrote the following scripts to allow easy copy and pasting of arrays back and forth from interactive sessions. Obviously only practical for small arrays, but I found it more convenient than saving/loading through a file every time:

Matlab -> Python

Python -> Matlab