[Neuroimaging] Using Python libs from MATLAB

[Marmaduke Woodman]

hi all,

I'm a dev behind the Virtual Brain (TVB) a neuroimaging simulation library,
written in Python. As part of an effort to reach out to some users stuck in
MATLAB, I've been testing MATLAB's recent *official* support for Python
(2014b+). It is notably better than the many other attempts because it
appears to use Py's C API to expose objects and methods as MATLAB objects
and methods instead of just providing eval/exec.

Generally it's working, but there are some workarounds to avoid segfaults,
errors and lack of stdout/err. I've started to collect a series of tips and
workarounds and figured there might be common interest in the community for
a "helper" library so all our projects can benefit from a larger user base,
and maybe ease the transition for potential Python users.

The most important in order,

- Anything touching HDF5 must use exactly the same version as MATLAB or
segfault
- Scipy.io.{save,load}mat segfault
- C++ extension modules whose exception model doesn't match MATLAB's,
segfault on exception
- Linalg segfault unless using MKL (which is what MATLAB uses)
- stdout/err and logging must be redirecting to mexPrintf via a ctypes
monkey patch
- Numpy/MATLAB array conversion is O(1) op, but can probably be made zero
copy with a ctypes + lib mx workaround

Aside from these (for which I sent a service request to MathWorks), it's
working well and we (TVB) expect our next release to include demo scripts
in MATLAB.

So, again, if there is common interest in collecting notes and a helper
library to monkey patch around the segfaults, it'd be great to not do this
alone ;)

cheers,
Marmaduke
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