Friends of Friends cluster finding in python.
This implements the friends-of-friends algorithm to find clusters of points, accelerated with an R*-tree.
If your boost installation is in a normal place you should just be able to install the latest release of the package directly from PyPI
pip install pyfof
If that fails then you will need to tell pip where to find your boost include
directory. This can be done by creating a file in your home directory called
.pydistutils.cfg containing:
[build_ext]
include_dirs=/path/to/boost/include/directory
and then running the above command.
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.cm as cm
import pyfof
npts = 10000
data = np.vstack((np.random.normal(-1,0.2,(npts/2,2)),\
np.random.normal(1,0.2,(npts/2,2))))
groups = pyfof.friends_of_friends(data, 0.4)
colors = cm.rainbow(np.linspace(0, 1, len(groups)))
for g,c in zip(groups, colors):
plt.scatter(data[g,0], data[g,1], color=c, s=3)
plt.show()
