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Installing MedPy with GraphCut support#

The GraphCut functionalities of MedPy depend on the max-flow/min-cut library by Boykov and Kolmogorov. During installation, MedPy will try to compile it and its python wrappers. If the compilation fails, MedPy will be installed without the GraphCut module. To enable the GraphCut functionality of MedPy, the dependencies of the library must be met before installing MedPy (although it can always be simply re-installed).

Dependencies#

  • Boost.Python

  • g++

  • gcc

These dependencies can be found in the repositories of all major distribution. For e.g. Ubuntu, you can simply call:

sudo apt-get install libboost-python-dev build-essential

Then install MedPy the usual way.

Troubleshooting#

If you experience an error like ModuleNotFoundError: No module named ‘medpy.graphcut.maxflow’, this usually means that the graphcut module has not been compiled successfully. To check the error log, try re-installing MedPy with:

pip install medpy --no-cache-dir --force-reinstall -v

In the logs, you might see the following warning:

2021-06-30T11:07:32,684   ***************************************************************************
2021-06-30T11:07:32,685   WARNING: The medpy.graphcut.maxflow external C++ package could not be compiled, all graphcut functionality will be disabled. You might be missing Boost.Python or some build essentials like g++.
2021-06-30T11:07:32,685   Failure information, if any, is above.
2021-06-30T11:07:32,685   I'm retrying the build without the graphcut C++ module now.
2021-06-30T11:07:32,685   ***************************************************************************

The error should be detailed in the lines just above.

Usually, it is a problem with the linking of the (lib)boost_python3 lib. There are some inconsistent naming conventions around, rendering the file undiscoverable to MedPy.

On Ubuntu, you should be able to locate your libboost_python3x.so under /usr/lib/x86_64-linux-gnu/. If your shared library file is named differently than MedPy expects, you might have to create a softlink like, e.g.:

sudo ln -s libboost_python38.so libboost_python3.so
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