examples/pl-functions/lscubes.py
 author Dmitriy Morozov Tue, 26 Jan 2010 11:00:51 -0800 branch dev changeset 191 2d8fba6d1d58 child 276 4e136f6afbb5 permissions -rwxr-xr-x
Moved lsfiltration.py into examples/pl-functions + added lscubes.py example (cubical lower-star filtration)
```
#!/usr/bin/env python

from    dionysus        import CohomologyPersistence
from    cube            import Cube
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, cubes_filename, prime = 11):
vertices = []
with open(values_filename) as f:
for line in f:
if line.startswith('#'): continue
vertices.append(float(line.split()[0]))

fltr = []
with open(cubes_filename) as f:
for line in f:
if line.startswith('#'): continue
fltr.append(Cube(map(int, line.split())))
fltr.sort(lambda x,y: max_vertex_cmp(x,y,vertices))
for i,c in enumerate(fltr): c.data = i

ch = CohomologyPersistence(prime)
complex = {}

for c in fltr:
# print "%s: %s" % (c, " + ".join(map(str, c.boundary())))
# print complex
i,d = ch.add([complex[cb] for cb in c.boundary()], c.data)
complex[c] = i
if d:
birth = d
print c.dimension() - 1, max_vertex(fltr[birth], vertices), max_vertex(c, vertices)

if __name__ == '__main__':
if len(argv) < 3:
print "Usage: %s VERTICES CUBES" % argv[0]
print
print "Computes persistence of the lower star filtration of the cubical "
print "complex explicitly listed out in CUBES with vertex values given in VERTICES."
exit()

values = argv[1]
cubes = argv[2]

lsf(values, cubes)
```