NF: GraphPartiton new method index_as_node_names to retrieve index(partition) as node names and not as ints

Author: CindeeM

brainx/modularity.py

@@ -95,6 +95,7 @@ def __init__(self, graph, index):
         # Store the nodes as a set of contiguous integers (indices into
         #the adjacency_matrix), needed for many operations
         self._node_set = set(range(self.num_nodes))
+        self._node_names = graph.nodes()
         ## raise useful error if index is missing nodes in graph
         self._check_allnodes_in_index(graph)
 
@@ -510,8 +511,9 @@ def random_mod(self):
         num_mods=len(self)
 
 
-        # Make a random choice bounded between 0 and 1, less than 0.5 means we will split the modules
-        # greater than 0.5 means we will merge the modules.
+        # Make a random choice bounded between 0 and 1, 
+        #   less than 0.5 means we will split the modules
+        #   greater than 0.5 means we will merge the modules.
 
         if num_mods >= self.num_nodes-1: ### CG: why are we subtracting 1 here?
             coin_flip = 1 #always merge if each node is in a separate module
@@ -611,6 +613,15 @@ def store_best(self):
         #Store references to the original graph and label dict
         self.bestindex = copy.deepcopy(self.index)
 
+    def index_as_node_names(self):
+        """ index by default contains references to integers represented the
+        nodes as indexed in the adjacency matrix defined in the original graph. 
+        This will return the index (partition) using the graph node names"""
+        named_part = []
+        for nmod, part in self.index.iteritems():
+            named_part.append([self._node_names[x] for x in part])
+        return named_part
+            
     def check_integrity(self, partition):
         """ Raises error if partition structure contains
         empty partitions or Nan values"""

brainx/tests/test_modularity.py

@@ -55,7 +55,18 @@ def test_graphpartition():
     graph.add_edge('c','d')
     index = {0:set([0,1]), 1:set([2,3])}
     gpart = mod.GraphPartition(graph, index)
+    assert gpart._node_set == set([0,1,2,3])
 
+def test_index_as_node_names():
+    graph = nx.Graph()
+    graph.add_edge('a','b')
+    graph.add_edge('c','d')
+    ## NOTE network x does not store names as added
+    ## for this graph ['a', 'c', 'b', 'd']
+    index = {0:set([0,2]), 1:set([1,3])}
+    gpart = mod.GraphPartition(graph, index)
+    named_index = gpart.index_as_node_names()
+    assert ['a','b'] in named_index
 
 def test_random_modular_graph_between_fraction():
     """Test for graphs with non-zero between_fraction"""