Use get_iters function instead of tqdm in StructuralSP.

gklearn/kernels/graph_kernel.py

@@ -37,7 +37,7 @@ class GraphKernel(object):
 			elif len(graphs[0]) == 0:
 				raise Exception('The graph list given is empty. No computation was performed.')
 			else:
-				self._graphs = [g.copy() for g in graphs[0]]
+				self._graphs = [g.copy() for g in graphs[0]] # @todo: might be very slow.
 				self._gram_matrix = self._compute_gram_matrix()
 				self._gram_matrix_unnorm = np.copy(self._gram_matrix)
 				if self._normalize:

gklearn/kernels/structural_sp.py

@@ -14,7 +14,7 @@ import sys
 from itertools import product
 # from functools import partial
 from multiprocessing import Pool
-from tqdm import tqdm
+from gklearn.utils import get_iters
 # import networkx as nx
 import numpy as np
 from gklearn.utils.parallel import parallel_gm, parallel_me
@@ -41,10 +41,7 @@ class StructuralSP(GraphKernel):
 	def _compute_gm_series(self):
 		# get shortest paths of each graph in the graphs.
 		splist = []
-		if self._verbose >= 2:
-			iterator = tqdm(self._graphs, desc='getting sp graphs', file=sys.stdout)
-		else:
-			iterator = self._graphs
+		iterator = get_iters(self._graphs, desc='getting sp graphs', file=sys.stdout, verbose=(self._verbose >= 2))
 		if self._compute_method == 'trie':
 			for g in iterator:
 				splist.append(self._get_sps_as_trie(g))
@@ -57,10 +54,9 @@ class StructuralSP(GraphKernel):
 
 		from itertools import combinations_with_replacement
 		itr = combinations_with_replacement(range(0, len(self._graphs)), 2)
-		if self._verbose >= 2:
-			iterator = tqdm(itr, desc='Computing kernels', file=sys.stdout)
-		else:
-			iterator = itr
+		len_itr = int(len(self._graphs) * (len(self._graphs) + 1) / 2)
+		iterator = get_iters(itr, desc='Computing kernels', file=sys.stdout,
+					   length=len_itr, verbose=(self._verbose >= 2))
 		if self._compute_method == 'trie':
 			for i, j in iterator:
 				kernel = self._ssp_do_trie(self._graphs[i], self._graphs[j], splist[i], splist[j])
@@ -91,11 +87,9 @@ class StructuralSP(GraphKernel):
 			get_sps_fun = self._wrapper_get_sps_trie
 		else:
 			get_sps_fun = self._wrapper_get_sps_naive
-		if self.verbose >= 2:
-			iterator = tqdm(pool.imap_unordered(get_sps_fun, itr, chunksize),
-							desc='getting shortest paths', file=sys.stdout)
-		else:
-			iterator = pool.imap_unordered(get_sps_fun, itr, chunksize)
+		iterator = get_iters(pool.imap_unordered(get_sps_fun, itr, chunksize),
+						desc='getting shortest paths', file=sys.stdout,
+						length=len(self._graphs), verbose=(self._verbose >= 2))
 		for i, sp in iterator:
 			splist[i] = sp
 		pool.close()
@@ -122,10 +116,8 @@ class StructuralSP(GraphKernel):
 		# get shortest paths of g1 and each graph in g_list.
 		sp1 = get_shortest_paths(g1, self._edge_weight, self._ds_infos['directed'])
 		splist = []
-		if self._verbose >= 2:
-			iterator = tqdm(g_list, desc='getting sp graphs', file=sys.stdout)
-		else:
-			iterator = g_list
+		iterator = get_iters(g_list, desc='getting sp graphs', file=sys.stdout,
+					verbose=(self._verbose >= 2))
 		if self._compute_method == 'trie':
 			for g in iterator:
 				splist.append(self._get_sps_as_trie(g))
@@ -135,10 +127,8 @@ class StructuralSP(GraphKernel):
 
 		# compute kernel list.
 		kernel_list = [None] * len(g_list)
-		if self._verbose >= 2:
-			iterator = tqdm(range(len(g_list)), desc='Computing kernels', file=sys.stdout)
-		else:
-			iterator = range(len(g_list))
+		iterator = get_iters(range(len(g_list)), desc='Computing kernels',
+					   file=sys.stdout, length=len(g_list), verbose=(self._verbose >= 2))
 		if self._compute_method == 'trie':
 			for i in iterator:
 				kernel = self._ssp_do_trie(g1, g_list[i], sp1, splist[i])
@@ -166,11 +156,9 @@ class StructuralSP(GraphKernel):
 			get_sps_fun = self._wrapper_get_sps_trie
 		else:
 			get_sps_fun = self._wrapper_get_sps_naive
-		if self.verbose >= 2:
-			iterator = tqdm(pool.imap_unordered(get_sps_fun, itr, chunksize),
-							desc='getting shortest paths', file=sys.stdout)
-		else:
-			iterator = pool.imap_unordered(get_sps_fun, itr, chunksize)
+		iterator = get_iters(pool.imap_unordered(get_sps_fun, itr, chunksize),
+						desc='getting shortest paths', file=sys.stdout,
+						length=len(g_list), verbose=(self._verbose >= 2))
 		for i, sp in iterator:
 			splist[i] = sp
 		pool.close()