Speedup get_edges (#132)

nngt/core/graph.py

@@ -868,39 +868,44 @@ def get_edges(self, attribute=None, value=None, source_node=None,
             self.edge_id((source_node, target_node))
             edges = np.array([[source_node, target_node]])
         else:
-            # we need to use the adjacency matrix, get its subparts,
-            # then use the list of nodes to get the original ids back
-            # to do that we first convert source/target_node to lists
-            # (note that this has no significant speed impact)
-            src, tgt = None, None
-
-            if source_node is None:
-                src = np.array(
-                    [i for i in range(self.node_nb())], dtype=int)
-            elif is_integer(source_node):
-                src = np.array([source_node], dtype=int)
+            if source_node is None or target_node is None:
+                # backend-specific implementation for source or target
+                edges = self._get_edges(source_node=source_node,
+                                        target_node=target_node)
             else:
-                src = np.sort(source_node)
+                # we need to use the adjacency matrix, get its subparts,
+                # then use the list of nodes to get the original ids back
+                # to do that we first convert source/target_node to lists
+                # (note that this has no significant speed impact)
+                src, tgt = None, None
+
+                if source_node is None:
+                    src = np.array(
+                        [i for i in range(self.node_nb())], dtype=int)
+                elif is_integer(source_node):
+                    src = np.array([source_node], dtype=int)
+                else:
+                    src = np.sort(source_node)
 
-            if target_node is None:
-                tgt = np.array(
-                    [i for i in range(self.node_nb())], dtype=int)
-            elif is_integer(target_node):
-                tgt = np.array([target_node], dtype=int)
-            else:
-                tgt = np.sort(target_node)
+                if target_node is None:
+                    tgt = np.array(
+                        [i for i in range(self.node_nb())], dtype=int)
+                elif is_integer(target_node):
+                    tgt = np.array([target_node], dtype=int)
+                else:
+                    tgt = np.sort(target_node)
 
-            mat = self.adjacency_matrix()
+                mat = self.adjacency_matrix()
 
-            nnz = mat[src].tocsc()[:, tgt].nonzero()
+                nnz = mat[src].tocsc()[:, tgt].nonzero()
 
-            edges = np.array([src[nnz[0]], tgt[nnz[1]]], dtype=int).T
+                edges = np.array([src[nnz[0]], tgt[nnz[1]]], dtype=int).T
 
-            # remove reciprocal if graph is undirected
-            if not self.is_directed():
-                edges.sort()
+                # remove reciprocal if graph is undirected
+                if not self.is_directed():
+                    edges.sort()
 
-                edges = _unique_rows(edges)
+                    edges = _unique_rows(edges)
 
         # check attributes
         if attribute is None:

nngt/core/gt_graph.py

@@ -465,6 +465,38 @@ def edges_array(self):
 
         return edges[order, :2]
 
+    def _get_edges(self, source_node=None, target_node=None):
+        g = self._graph
+
+        edges = set()
+
+        if source_node is not None:
+            if is_integer(source_node):
+                return g.get_out_edges(source_node)
+
+            for s in source_node:
+                if g.is_directed():
+                    edges.update((tuple(e) for e in g.get_out_edges(s)))
+                else:
+                    for e in g.get_all_edges(s):
+                        if tuple(e[::-1]) not in edges:
+                            edges.add(tuple(e))
+
+            return list(edges)
+
+        if is_integer(target_node):
+            return g.get_in_edges(target_node)
+
+        for t in target_node:
+            if g.is_directed():
+                edges.update((tuple(e) for e in g.get_in_edges(t)))
+            else:
+                for e in g.get_all_edges(t):
+                    if tuple(e[::-1]) not in edges:
+                        edges.add(tuple(e))
+
+        return list(edges)
+
     def new_node(self, n=1, neuron_type=1, attributes=None, value_types=None,
                  positions=None, groups=None):
         '''

nngt/core/ig_graph.py

@@ -319,6 +319,23 @@ def edges_array(self):
         g = self._graph
         return np.array([(e.source, e.target) for e in g.es], dtype=int)
 
+    def _get_edges(self, source_node=None, target_node=None):
+        g = self._graph
+
+        edges = None
+
+        if source_node is None:
+            if is_integer(target_node):
+                edges = g.es.select(_target_eq=target_node)
+            else:
+                edges = g.es.select(_target_in=target_node)
+        elif is_integer(source_node):
+            edges = g.es.select(_source_eq=source_node)
+        else:
+            edges = g.es.select(_source_in=source_node)
+
+        return [e.tuple for e in edges]
+
     def new_node(self, n=1, neuron_type=1, attributes=None, value_types=None,
                  positions=None, groups=None):
         '''

nngt/core/nngt_graph.py

@@ -404,6 +404,46 @@ def edges_array(self):
         '''
         return np.asarray(list(self._graph._unique), dtype=int)
 
+    def _get_edges(self, source_node=None, target_node=None):
+        g = self._graph
+
+        edges = None
+
+        if source_node is not None:
+            source_node = \
+                [source_node] if is_integer(source_node) else source_node
+
+            if g.is_directed():
+                edges = [e for e in g._unique if e[0] in source_node]
+            else:
+                edges = set()
+
+                for e in g._unique:
+                    if e[0] in source_node or e[1] in source_node:
+                        if e[::-1] not in edges:
+                            edges.add(e)
+
+                edges = list(edges)
+
+            return edges
+
+        target_node = \
+            [target_node] if is_integer(target_node) else target_node
+
+        if g.is_directed():
+            edges = [e for e in g._unique if e[1] in target_node]
+        else:
+            edges = set()
+
+            for e in g._unique:
+                if e[0] in target_node or e[1] in target_node:
+                    if e[::-1] not in edges:
+                        edges.add(e)
+
+            edges = list(edges)
+
+        return edges
+
     def is_connected(self):
         raise NotImplementedError("Not available with 'nngt' backend, please "
                                   "install a graph library (networkx, igraph, "

nngt/core/nx_graph.py

@@ -390,6 +390,24 @@ def edges_array(self):
 
         return edges
 
+    def _get_edges(self, source_node=None, target_node=None):
+        g = self._graph
+
+        if source_node is not None:
+            source_node = \
+                [source_node] if is_integer(source_node) else source_node
+
+            return list(
+                g.out_edges(source_node) if g.is_directed()
+                else g.edges(source_node))
+
+        target_node = \
+            [target_node] if is_integer(target_node) else target_node
+
+        return list(
+            g.in_edges(target_node) if g.is_directed()
+            else g.edges(target_node))
+
     def new_node(self, n=1, neuron_type=1, attributes=None, value_types=None,
                  positions=None, groups=None):
         '''

testing/test_basics.py

@@ -588,10 +588,13 @@ def test_get_edges():
 
     g.new_edges(edges)
 
-    assert np.array_equal(g.get_edges(source_node=[0, 1]), edges[:3])
-    assert np.array_equal(g.get_edges(target_node=[0, 1]), edges[:2])
-    assert np.array_equal(g.get_edges(source_node=[0, 2], target_node=[0, 1]),
-                          [(0, 1)])
+    def to_set(ee):
+        return {tuple(e) for e in ee}
+
+    assert to_set(g.get_edges(source_node=[0, 1])) == to_set(edges[:3])
+    assert to_set(g.get_edges(target_node=[0, 1])) == to_set(edges[:2])
+    assert to_set(g.get_edges(source_node=[0, 2],
+                  target_node=[0, 1])) == {(0, 1)}
 
     # undirected
     g = nngt.Graph(4, directed=False)
@@ -602,14 +605,13 @@ def test_get_edges():
 
     res = [(0, 1), (1, 2)]
 
-    assert np.array_equal(g.get_edges(source_node=[0, 1]), res)
-    assert np.array_equal(g.get_edges(target_node=[0, 1]), res)
-    assert np.array_equal(g.get_edges(source_node=[0, 2], target_node=[0, 1]),
-                          res)
+    assert to_set(g.get_edges(source_node=[0, 1])) == to_set(res)
+    assert to_set(g.get_edges(target_node=[0, 1])) == to_set(res)
+    assert to_set(g.get_edges(source_node=[0, 2],
+                              target_node=[0, 1])) == to_set(res)
 
-    assert np.array_equal(g.get_edges(source_node=0, target_node=1), [(0, 1)])
-    assert np.array_equal(g.get_edges(source_node=0, target_node=[0, 1]),
-                          [(0, 1)])
+    assert to_set(g.get_edges(source_node=0, target_node=1)) == {(0, 1)}
+    assert to_set(g.get_edges(source_node=0, target_node=[0, 1])) == {(0, 1)}
 
 
 @pytest.mark.mpi_skip