pyfof 0.1.5

Friends-of-friends cluster finding in python

pyfof

Friends of Friends cluster finding in python.

This implements the friends-of-friends algorithm to find clusters of points, accelerated with an R*-tree.

Requirements

• c++11 complient compiler
• Cython (for the development version only)
• numpy
• boost

Installation

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.

Examples

Two Gaussian blobs

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()

A more complicated example