examples/rips/rips.py
author Christos Mantoulidis <cmad@stanford.edu>
Tue, 04 Aug 2009 13:23:16 -0700
branchdev
changeset 156 f75fb57d2831
parent 130 580eaa850c4f
child 181 1ee6edc17cb6
permissions -rw-r--r--
Changed implementation of WeightedRips to store simplex values (max distance between simplices' vertices) as an invisible layer on top of each simplex object, so that the data() field of WeightedRips has been freed for use by the users again.

from    math        import fabs
from    dionysus    import Rips, Filtration, StaticPersistence #, enable_log

# Simple minded pairwise distance functor distance
class Distances:
    def __len__(self):
        return 5

    def __call__(self, x, y):
        return fabs(y-x)

dist = Distances()
r = Rips(dist)
lst = []
lst2 = []

#enable_log('rips')

r.generate(1, 3, lst.append)
r.generate(1, 3, lst2.append, [0,2,4])

print "Rips complex on all vertices:", lst
print "Rips complex on vertices [0,2,4]):", lst2

print "Values:", [map(r.eval, lst)]
print "Sorted:", sorted(lst, r.cmp)

cofaces = []
r.vertex_cofaces(2, 1, 3, cofaces.append)
print "Cofaces of vertex 2:", cofaces

cofaces = []
r.vertex_cofaces(2, 1, 3, cofaces.append, [0,2,4])
print "Cofaces of vertex 2 on vertices [0,2,4]:", cofaces

f = Filtration(lst, r.cmp)
p = StaticPersistence(f)
p.pair_simplices()
for s in p:
    print lst[f[p(s)]], s.sign()