Seg3D Pages

Web pages for Seg3D

View the Project on GitHub SCIInstitute/Seg3D

Installing packages

If there is an installation of the packages with other python builds on the machine, the system path can be used to use those packages. There are many ways to install packages in Python. pip is an easy way that is usually included with Python.

Installing pip

If pip is not installed for the Seg3D installation of python, follow these directions. Be sure to use the python included in the Seg3D application. With OS x versions, it is in Seg3D2.app/Contents/Frameworks/Python.framework/Versions/Current/bin.

Installing numpy, scipy, and other major packages

Make sure that the package is found in Seg3D2.app/Contents/Frameworks/Python.framework/Versions/Current/lib/python3.4/site-packages.

Installing Matlab engine for Python in Seg3D

In the terminal: cd "matlab_root"/extern/engines/python Seg3D2.app/Contents/Frameworks/Python.framework/Versions/Current/bin/python3.4 setup.py build --build-base="builddir" install --prefix="installdir"

Make sure that the package (matlab and matlabengineforpython-…) is found in Seg3D2.app/Contents/Frameworks/Python.framework/Versions/Current/lib/python3.4/site-packages

Full instructions are located on the mathworks site.

Matlab engine in Seg3D (through Python)

In Seg3D, Matlab code and functions can be run using the Matlab engine for Python in the python console or Python interface. To do so, make sure that the Matlab engine is installed (previous section).

To run the Matlab engine in the Python console in Seg3D, the DYLD_LIBRARY_PATH environment variable needs to be set to find python libraries and the matlab engine:

export DYLD_LIBRARY_PATH="path"/Seg3D2.app/Contents/Frameworks/Python.framework/Versions/Current/lib: "matlab_root"/extern/engines/python/dist/matlab/

This can be added to the .bashrc file or you could try the /etc/launchd.conf file.

Full documentation for the Matlab engine can be found on the mathworks site.