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 cvxopt import spmatrix, matrix
from cvxopt.blas import copy
from lsqr import lsqr
from sys import argv, exit
import os.path
def smooth(boundary_list, cocycle_list):
dimension = max((max(d[1], d[2]) for d in boundary_list))
dimension += 1
# NB: D is a coboundary matrix; 1 and 2 below are transposed
D = spmatrix([d[0] for d in boundary_list],
[d[2] for d in boundary_list],
[d[1] for d in boundary_list], (dimension, dimension))
z = spmatrix([zz[0] for zz in cocycle_list],
[zz[1] for zz in cocycle_list],
[0 for zz in cocycle_list], (dimension, 1))
v1 = D * z
# print "D^2 is zero:", not bool(D*D)
# print "D*z is zero:", not bool(v1)
z = matrix(z)
def Dfun(x,y,trans = 'N'):
if trans == 'N':
copy(D * x, y)
elif trans == 'T':
copy(D.T * x, y)
else:
assert False, "Unexpected trans parameter"
tol = 1e-10
show = False
maxit = None
solution = lsqr(Dfun, matrix(z), show = show, atol = tol, btol = tol, itnlim = maxit)
v = z - D*solution[0]
# print sum(v**2)
# assert sum((D*v)**2) < tol and sum((D.T*v)**2) < tol, "Expected a harmonic cocycle"
if not (sum((D*v)**2) < tol and sum((D.T*v)**2) < tol):
print "Expected a harmonic cocycle:", sum((D*v)**2), sum((D.T*v)**2)
return solution[0], v
def vertex_values(solution, vertices):
values = [None]*len(vertices)
for i,v in vertices:
values[v] = solution[i]
return values
def read_list_file(filename):
list = []
with open(filename) as fp:
for line in fp.xreadlines():
if line.startswith('#'): continue
list.append(map(int, line.split()))
return list
if __name__ == '__main__':
if len(argv) < 4:
print "Usage: %s BOUNDARY COCYCLE VERTEXMAP" % argv[0]
exit()
boundary_filename = argv[1]
cocycle_filename = argv[2]
vertexmap_filename = argv[3]
boundary_list = read_list_file(boundary_filename)
cocycle_list = read_list_file(cocycle_filename)
vertexmap_list = read_list_file(vertexmap_filename)
solution, v = smooth(boundary_list, cocycle_list)
values = vertex_values(solution, vertexmap_list)
outfn = os.path.splitext(cocycle_filename)[0] + '.val'
with open(outfn, 'w') as f:
for i,v in enumerate(values):
f.write('%d %f\n' % (i,v))