Added code to expose the persistence_diagram class, the bottleneck_distance function and the point class to python.
Most of the commonly used methods for each class have been exported.
The constructor for point now requires that a data argument be provided along with x and y coord. This needs to be made optional.
The constructor for persistence_diagram could possibly be rewritten as well.
#!/usr/bin/env python
from dionysus import Simplex, Filtration, StaticPersistence, vertex_cmp
from sys import argv, exit
def max_vertex(s, vertices):
return max((vertices[v] for v in s.vertices))
def max_vertex_cmp(s1, s2, vertices):
m1 = max_vertex(s1, vertices)
m2 = max_vertex(s2, vertices)
return cmp(m1, m2) or cmp(s1.dimension(), s2.dimension())
def lsf(values_filename, simplices_filename):
# Read vertices
vertices = []
with open(values_filename) as f:
for line in f:
if line.startswith('#'): continue
vertices.append(float(line.split()[0]))
# Read simplices
fltr = Filtration()
with open(simplices_filename) as f:
for line in f:
if line.startswith('#'): continue
fltr.append(Simplex(map(int, line.split())))
fltr.sort(lambda x,y: max_vertex_cmp(x,y,vertices))
# Compute persistence
p = StaticPersistence(fltr)
p.pair_simplices()
# Output the persistence diagram
smap = p.make_simplex_map(fltr)
for i in p:
if not i.sign(): continue
b = smap[i]
d = smap[i.pair()]
if i.unpaired():
print b.dimension(), max_vertex(b, vertices), "inf"
continue
print b.dimension(), max_vertex(b, vertices), max_vertex(d, vertices)
if __name__ == '__main__':
if len(argv) < 3:
print "Usage: %s VERTICES SIMPLICES" % argv[0]
print
print "Computes persistence of the lower star filtration of the simplicial "
print "complex explicitly listed out in SIMPLICES with vertex values given in VERTICES."
exit()
values = argv[1]
simplices = argv[2]
lsf(values, simplices)