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Fast Overlap

A tiny cython library to calculate the pairwise overlap of all cell masks between two time points. Created for use in https://github.com/Hekstra-Lab/microutil/

Install

pip install fast-overlap

Development

Installation

python setup.py build_ext -i

To really remove stuff and build + test:

rm *.so build/ fast_overlap.cpp -rf && python setup.py build_ext -i && python test_speedup.py

On Mac

You need to compile python extensions with the same compiler used to compile python. So on mac you should use clang. However the apple distributed clang doesn't include openmp so you should either use g++ locally (which seems to work for some reason, but doesn't for built wheels) or use homebrew clang as in the github workflows.

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