[GraphIndex] Create graph index directly from scipy matrix. (#87)

* create synthetic data with scipy.

* changes as comments

python/dgl/data/citation_graph.py

@@ -206,10 +206,33 @@ def get_gnp_generator(args):
         return nx.fast_gnp_random_graph(n, p, seed, True)
     return _gen
 
+class ScipyGraph(object):
+    """A simple graph object that uses scipy matrix."""
+    def __init__(self, mat):
+        self._mat = mat
+
+    def get_graph(self):
+        return self._mat
+
+    def number_of_nodes(self):
+        return self._mat.shape[0]
+
+    def number_of_edges(self):
+        return self._mat.getnnz()
+
+def get_scipy_generator(args):
+    n = args.syn_gnp_n
+    p = (2 * np.log(n) / n) if args.syn_gnp_p == 0. else args.syn_gnp_p
+    def _gen(seed):
+        return ScipyGraph(sp.random(n, n, p, format='coo'))
+    return _gen
+
 def load_synthetic(args):
     ty = args.syn_type
     if ty == 'gnp':
         gen = get_gnp_generator(args)
+    elif ty == 'scipy':
+        gen = get_scipy_generator(args)
     else:
         raise ValueError('Unknown graph generator type: {}'.format(ty))
     return GCNSyntheticDataset(

python/dgl/graph_index.py

@@ -3,7 +3,7 @@ from __future__ import absolute_import
 import ctypes
 import numpy as np
 import networkx as nx
-import scipy.sparse as sp
+import scipy
 
 from ._ffi.base import c_array
 from ._ffi.function import _init_api
@@ -600,30 +600,59 @@ class GraphIndex(object):
         return GraphIndex(handle)
 
 class SubgraphIndex(GraphIndex):
-    def __init__(self, handle, parent, induced_nodes, induced_edges):
-        super().__init__(handle)
+    """Graph index for subgraph.
 
+    Parameters
+    ----------
+    handle : GraphIndexHandle
+        The capi handle.
+    paranet : GraphIndex
+        The parent graph index.
+    induced_nodes : utils.Index
+        The parent node ids in this subgraph.
+    induced_edges : utils.Index
+        The parent edge ids in this subgraph.
+    """
+    def __init__(self, handle, parent, induced_nodes, induced_edges):
+        super(SubgraphIndex, self).__init__(handle)
         self._parent = parent
         self._induced_nodes = induced_nodes
         self._induced_edges = induced_edges
 
     def add_nodes(self, num):
+        """Add nodes. Disabled because SubgraphIndex is read-only."""
         raise RuntimeError('Readonly graph. Mutation is not allowed.')
 
     def add_edge(self, u, v):
+        """Add edges. Disabled because SubgraphIndex is read-only."""
         raise RuntimeError('Readonly graph. Mutation is not allowed.')
 
     def add_edges(self, u, v):
+        """Add edges. Disabled because SubgraphIndex is read-only."""
         raise RuntimeError('Readonly graph. Mutation is not allowed.')
 
-    @property
-    def induced_edges(self):
-        return self._induced_edges
-
     @property
     def induced_nodes(self):
+        """Return parent node ids.
+
+        Returns
+        -------
+        utils.Index
+            The parent node ids.
+        """
         return self._induced_nodes
 
+    @property
+    def induced_edges(self):
+        """Return parent edge ids.
+
+        Returns
+        -------
+        utils.Index
+            The parent edge ids.
+        """
+        return self._induced_edges
+
 def disjoint_union(graphs):
     """Return a disjoint union of the input graphs.
 
@@ -697,8 +726,25 @@ def create_graph_index(graph_data=None, multigraph=False):
 
     handle = _CAPI_DGLGraphCreate(multigraph)
     gi = GraphIndex(handle)
-    if graph_data is not None:
+
+    if graph_data is None:
+        return gi
+
+    # scipy format
+    if isinstance(graph_data, scipy.sparse.spmatrix):
+        try:
+            gi.from_scipy_sparse_matrix(graph_data)
+            return gi
+        except:
+            raise Exception('Graph data is not a valid scipy sparse matrix.')
+
+    # networkx - any format
+    try:
         gi.from_networkx(graph_data)
+    except:
+        raise Exception('Error while creating graph from input of type "%s".'
+                         % type(graph_data))
+
     return gi
 
 _init_api("dgl.graph_index")