examples/rips/rips-pairwise.py
author Dmitriy Morozov <dmitriy@mrzv.org>
Wed, 29 Apr 2009 10:16:03 -0700
branchdev
changeset 132 2a737609b8bf
parent 126 3c3e77ac43d2
child 145 ee096f207dfb
permissions -rw-r--r--
Cleaned up simplex comparison functions, rip-pairwise.py outputs a diagram, auxilliary add_simplices() + remove_simplices() for zigzags

#/usr/bin/env python


from    dionysus    import Rips, PairwiseDistances, StaticPersistence, Filtration, points_file, \
                           ExplicitDistances, data_dim_cmp
from    sys         import argv, exit
import  time


if len(argv) < 4:
    print "Usage: %s POINTS SKELETON MAX" % argv[0]
    exit()

filename = argv[1]
skeleton = int(argv[2])
max = float(argv[3])

points = [p for p in points_file(filename)]
distances = PairwiseDistances(points)
distances = ExplicitDistances(distances)           # speeds up generation of the Rips complex at the expense of memory usage
rips = Rips(distances)
print time.asctime(), "Rips initialized"

simplices = []
rips.generate(skeleton, max, simplices.append)
print time.asctime(), "Generated complex: %d simplices" % len(simplices)

# While this step is unnecessary (Filtration below can be passed rips.cmp), 
# it greatly speeds up the running times
for s in simplices: s.data = rips.eval(s)
print time.asctime(), simplices[0], '...', simplices[-1]

f = Filtration(simplices, data_dim_cmp)             # could be rips.cmp if s.data for s in simplices is not set
print time.asctime(), "Set up filtration"

p = StaticPersistence(f)
print time.asctime(), "Initialized StaticPersistence"

p.pair_simplices()
print time.asctime(), "Simplices paired"

print "Outputting persistence diagram"
for i in p:
    if i.sign():
        b = simplices[f[p(i)]]

        if b.dimension() >= skeleton: continue

        if i == i.pair:
            print b.dimension(), b.data, "inf"
            continue

        d = simplices[f[p(i.pair)]]
        print b.dimension(), b.data, d.data