MATLAB: Calling python modules that matlab can’t import

MATLABmatpynumpyopencvpilpymexpythonpython-matlab-wormholespythoncallscikit learnscikit-imagescipy

i'm the author of this SO question. the problem came down to needing python libraries (PIL, opencv, scipy) that either:

depend on later versions of libraries than matlab ships (libtiff.5.dylib, libgfortran.3.dylib), or
include identifiers starting with underscore (_), which i guess matlab doesn't allow (why?)

what options do i have for how to proceed?

i'm guessing that attempting to compile PIL/opencv/scipy against matlab's libraries would be extremely painful.

i've found the following 3rd party python-from-matlab bridges — is this my best route?

matpy — numpy.ndarray integration
pymex — numpy.ndarray integration, less recent development, but also looks good
pythoncall — even older, looks less polished
wormholes — also old, ndarray's only, bidirectional over TCP

are there others to consider? opinions/experience on which is most promising for this scenario? i'm guessing matpy…

Best Answer

this solves it:

~$ DYLD_INSERT_LIBRARIES=/opt/local/lib/libgcc/libgfortran.3.dylib:/opt/local/lib/libtiff.5.dylib /Applications/MATLAB_R2015a.app/bin/matlab

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i ran into a possible explanation from this SO question that references trying to import opencv:

dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/cv2.so, 2): Library not loaded: /opt/local/lib/libtiff.5.dylib
    Referenced from: /opt/local/lib/libopencv_highgui.2.4.dylib
    Reason: Incompatible library version: libopencv_highgui.2.4.dylib requires version 8.0.0 or later, but libtiff.5.dylib provides version 6.0.0

perhaps matlab executes system calls in some way that links against its old versions of libraries rather than the up to date ones you have installed?

you don't say whether the script runs fine when executed from a regular shell?

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