Move reverse Cuthill-McKee algorithm to utils.

Adjust example.
Addresses #530

--HG--
rename : examples/algorithms/rcm.py => networkx/utils/rcm.py

1 files changed, 26 insertions, 77 deletions

diff --git a/examples/algorithms/rcm.py b/examples/algorithms/rcm.py
index 3b0060a5..9bf781c6 100644
--- a/examples/algorithms/rcm.py
+++ b/examples/algorithms/rcm.py
@@ -2,82 +2,31 @@
 # Copyright (C) 2011 by 
 # Aric Hagberg <aric.hagberg@gmail.com>
 # BSD License
-from operator import itemgetter
 import networkx as nx
-__author__ = """\n""".join(['Aric Hagberg (hagberg@lanl.gov)'])
-__all__ = ['cuthill_mckee_ordering',
-           'reverse_cuthill_mckee_ordering']
+from networkx.utils import reverse_cuthill_mckee_ordering
 
-def cuthill_mckee_ordering(G, start=None):
-    for g in nx.connected_component_subgraphs(G):
-        for n in connected_cuthill_mckee_ordering(g, start):
-            yield n
-
-def reverse_cuthill_mckee_ordering(G, start=None):
-    return reversed(list(cuthill_mckee_ordering(G, start=start)))
-
-def connected_cuthill_mckee_ordering(G, start=None):
-    if start is None:
-        (_, start) = find_pseudo_peripheral_node_pair(G)
-    yield start
-    visited = set([start])
-    stack = [(start, iter(G[start]))]
-    while stack:
-        parent,children = stack[0]
-        if parent not in visited:
-            yield parent
-        try:
-            child = next(children)
-            if child not in visited:
-                yield child
-                visited.add(child)
-                # add children to stack, sorted by degree (lowest first)
-                nd = sorted(G.degree(G[child]).items(), key=itemgetter(1))
-                children = (n for n,d in nd)
-                stack.append((child,children))
-        except StopIteration:
-            stack.pop(0)
-
-def find_pseudo_peripheral_node_pair(G, start=None):
-    if start is None:
-        u = next(G.nodes_iter())
-    else:
-        u = start
-    lp = 0
-    v = u 
-    while True:
-        spl = nx.shortest_path_length(G, v)
-        l = max(spl.values())
-        if l <= lp: 
-            break
-        lp = l
-        farthest = [n for n,dist in spl.items() if dist==l]
-        v, deg = sorted(G.degree(farthest).items(), key=itemgetter(1))[0]
-    return u, v
-    
-if __name__=='__main__':
-    import networkx as nx
-    # example from 
-    # http://www.boost.org/doc/libs/1_37_0/libs/graph/example/cuthill_mckee_ordering.cpp
-    G = nx.Graph([(0,3),(0,5),(1,2),(1,4),(1,6),(1,9),(2,3),
-            (2,4),(3,5),(3,8),(4,6),(5,6),(5,7),(6,7)])
-    rcm = list(reverse_cuthill_mckee_ordering(G,start=0))    
-    assert(rcm==[9, 1, 4, 6, 7, 2, 8, 5, 3, 0])
-    rcm = list(reverse_cuthill_mckee_ordering(G))    
-    assert(rcm==[0, 8, 5, 7, 3, 6, 4, 2, 1, 9])
-    print "ordering",rcm
-    # build low-bandwidth numpy matrix
-    try:
-        import numpy as np
-        print "matrix"
-        A = nx.to_numpy_matrix(G)
-        print A
-        x,y = np.nonzero(A)
-        print("bandwidth:",np.abs(x-y).max())
-        B = nx.to_numpy_matrix(G,nodelist=rcm)
-        print("low-bandwidth matrix")
-        print B
-        x,y = np.nonzero(B)
-        print("bandwidth:",np.abs(x-y).max())
-    except:
-        pass
+import networkx as nx
+# example from 
+# http://www.boost.org/doc/libs/1_37_0/libs/graph/example/cuthill_mckee_ordering.cpp
+G = nx.Graph([(0,3),(0,5),(1,2),(1,4),(1,6),(1,9),(2,3),
+        (2,4),(3,5),(3,8),(4,6),(5,6),(5,7),(6,7)])
+rcm = list(reverse_cuthill_mckee_ordering(G,start=0))    
+assert(rcm==[9, 1, 4, 6, 7, 2, 8, 5, 3, 0])
+rcm = list(reverse_cuthill_mckee_ordering(G))    
+assert(rcm==[0, 8, 5, 7, 3, 6, 4, 2, 1, 9])
+print "ordering",rcm
+# build low-bandwidth numpy matrix
+try:
+    import numpy as np
+    print "unordered matrix"
+    A = nx.to_numpy_matrix(G)
+    print A
+    x,y = np.nonzero(A)
+    print("bandwidth:",np.abs(x-y).max())
+    B = nx.to_numpy_matrix(G,nodelist=rcm)
+    print("low-bandwidth matrix")
+    print B
+    x,y = np.nonzero(B)
+    print("bandwidth:",np.abs(x-y).max())
+except:
+    pass