# HG changeset patch
# User Dmitriy Morozov <dmitriy@mrzv.org>
# Date 1264532451 28800
# Node ID 2d8fba6d1d5820efcc9ac16b574f699cad95f929
# Parent 6edd7c861bc00f63ef2b17f90ef42bbf292a12ae
Moved lsfiltration.py into examples/pl-functions + added lscubes.py example (cubical lower-star filtration)
diff -r 6edd7c861bc0 -r 2d8fba6d1d58 examples/lsfiltration.py
--- a/examples/lsfiltration.py Tue Jan 12 14:36:38 2010 -0800
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,61 +0,0 @@
-#!/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()[1]))
-
- # 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)
diff -r 6edd7c861bc0 -r 2d8fba6d1d58 examples/pl-functions/cube.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/pl-functions/cube.py Tue Jan 26 11:00:51 2010 -0800
@@ -0,0 +1,40 @@
+def log2(x):
+ i = 0
+ while x:
+ x >>= 1
+ i += 1
+ return i-1
+
+class Cube:
+ def __init__(self, vertices):
+ self.vertices = vertices
+
+ def dimension(self):
+ return log2(len(self.vertices))
+
+ def boundary(self):
+ for i in xrange(self.dimension()):
+ for side in [0,1]:
+ vertices = []
+ for idx in xrange(len(self.vertices)/2):
+ # Insert i-th bit equal to side
+ v = (idx & ~(2**i-1)) << 1
+ if side: v |= 2**i
+ v |= (idx & (2**i - 1))
+ vertices.append(self.vertices[v])
+ yield Cube(vertices)
+
+ def __hash__(self):
+ return hash(tuple(self.vertices))
+
+ def __eq__(self, other):
+ return self.vertices == other.vertices
+
+ def __repr__(self):
+ return " ".join(map(str, self.vertices))
+
+
+if __name__ == '__main__':
+ c = Cube(['a', 'b', 'c', 'd'])
+ print c
+ for sb in c.boundary(): print sb
diff -r 6edd7c861bc0 -r 2d8fba6d1d58 examples/pl-functions/lscubes.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/pl-functions/lscubes.py Tue Jan 26 11:00:51 2010 -0800
@@ -0,0 +1,56 @@
+#!/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):
+ # Read vertices
+ vertices = []
+ with open(values_filename) as f:
+ for line in f:
+ if line.startswith('#'): continue
+ vertices.append(float(line.split()[0]))
+
+ # Read cubes
+ 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)
diff -r 6edd7c861bc0 -r 2d8fba6d1d58 examples/pl-functions/lsfiltration.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/pl-functions/lsfiltration.py Tue Jan 26 11:00:51 2010 -0800
@@ -0,0 +1,61 @@
+#!/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)