navis-fastcore

Fast core functions for navis re-implemented in Cython.

The idea is that navis will use fastcore if installed and fall back to the pure-Python / numpy implementation if not.

Currently implemented:

• vertex similarity (Jarrell et al., 2012)
• shortest path from source to target (~40x faster than iGraph)
• geodesic distance matrix (up to 100x faster than scipy)

See further down for details.

Installation

I'm still figuring out the best way for building and packaging pre-compiled binaries (i.e. wheels). For now, you will need to compile it yourself during setup. This requires a C-compiler to be present (see here for a very brief explanation).

$ pip3 install git+git://github.com/navis-org/fastcore@main

Examples

>>> import numpy as np
>>> import navis
>>> import fastcore
>>> # Grab an example skeleton
>>> n = navis.example_neurons(1)
>>> # Time navis' scipy-based function for all-by-all geodesic distances
>>> %time m1 = navis.geodesic_matrix(n, weights=None)
CPU times: user 4.58 s, sys: 153 ms, total: 4.73 s
Wall time: 4.73 s
>>> # Time the analogous function in fastcore
>>> %time m2 = fastcore.geodesic_matrix(n.nodes.node_id.values, n.nodes.parent_id.values)
CPU times: user 2.17 s, sys: 173 ms, total: 2.35 s
Wall time: 258 ms
>>> # Make sure results are the same
>>> np.all(m1 == m2)
True

Troubleshooting

Compiler does not support openmp

We need openmp for threaded processing. Without it, this is not much faster than the pure numpy implementations. If your compiler does not support openmp, you will get an error along the lines of -fopenmp not supported. This happens e.g. on OSX if you use the clang bundled with XCode. In my case, I was able to work around it by installing llvm with homebrew and then adding a couple flags to my ~/.bash_profile to make sure the homebrew llvm is actually used:

export PATH="/usr/local/opt/llvm/bin:$PATH"
export LDFLAGS="-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib"
export CPPFLAGS="-I/usr/local/opt/llvm/include"

Develop

To compile the extensions in place:

$ python setup.py build_ext --inplace