Update: Check if all graphs have edge(s) in ShorestPath.

gklearn/kernels/shortest_path.py

@@ -17,6 +17,7 @@ from itertools import product
 from multiprocessing import Pool
 from tqdm import tqdm
 import numpy as np
+import networkx as nx
 from gklearn.utils.parallel import parallel_gm, parallel_me
 from gklearn.utils.utils import getSPGraph
 from gklearn.kernels import GraphKernel
@@ -35,6 +36,7 @@ class ShortestPath(GraphKernel):
 
 
 	def _compute_gm_series(self):
+		self._all_graphs_have_edges(self._graphs)
 		# get shortest path graph of each graph.
 		if self._verbose >= 2:
 			iterator = tqdm(self._graphs, desc='getting sp graphs', file=sys.stdout)
@@ -60,6 +62,7 @@ class ShortestPath(GraphKernel):
 
 
 	def _compute_gm_imap_unordered(self):
+		self._all_graphs_have_edges(self._graphs)
 		# get shortest path graph of each graph.
 		pool = Pool(self._n_jobs)
 		get_sp_graphs_fun = self._wrapper_get_sp_graphs
@@ -92,6 +95,7 @@ class ShortestPath(GraphKernel):
 
 
 	def _compute_kernel_list_series(self, g1, g_list):
+		self._all_graphs_have_edges([g1] + g_list)
 		# get shortest path graphs of g1 and each graph in g_list.
 		g1 = getSPGraph(g1, edge_weight=self._edge_weight)
 		if self._verbose >= 2:
@@ -114,6 +118,7 @@ class ShortestPath(GraphKernel):
 
 
 	def _compute_kernel_list_imap_unordered(self, g1, g_list):
+		self._all_graphs_have_edges([g1] + g_list)
 		# get shortest path graphs of g1 and each graph in g_list.
 		g1 = getSPGraph(g1, edge_weight=self._edge_weight)
 		pool = Pool(self._n_jobs)
@@ -156,6 +161,7 @@ class ShortestPath(GraphKernel):
 
 
 	def _compute_single_kernel_series(self, g1, g2):
+		self._all_graphs_have_edges([g1] + [g2])
 		g1 = getSPGraph(g1, edge_weight=self._edge_weight)
 		g2 = getSPGraph(g2, edge_weight=self._edge_weight)
 		kernel = self._sp_do(g1, g2)
@@ -327,4 +333,10 @@ class ShortestPath(GraphKernel):
 	def _wrapper_sp_do(self, itr):
 		i = itr[0]
 		j = itr[1]
-		return i, j, self._sp_do(G_gs[i], G_gs[j])
+		return i, j, self._sp_do(G_gs[i], G_gs[j])
+
+
+	def _all_graphs_have_edges(self, graphs):
+		for G in graphs:
+			if nx.number_of_edges(G) == 0:
+				raise ValueError('Not all graphs have edges!!!')