From c9f90cbf896b58a5716ee061e78de6abeb5f3d2f Mon Sep 17 00:00:00 2001
From: Yoann Dufresne <yoann.dufresne0@gmail.com>
Date: Wed, 29 Apr 2020 12:23:47 +0200
Subject: [PATCH] remove sum method to replace by a for: x2 speedup
---
deconvolution/dgraph/CliqueDGFactory.py | 3 ++-
experiments/clique_graph_eval.py | 16 +++++++++-------
2 files changed, 11 insertions(+), 8 deletions(-)
diff --git a/deconvolution/dgraph/CliqueDGFactory.py b/deconvolution/dgraph/CliqueDGFactory.py
index c30309b..9fd0564 100644
--- a/deconvolution/dgraph/CliqueDGFactory.py
+++ b/deconvolution/dgraph/CliqueDGFactory.py
@@ -67,7 +67,8 @@ class CliqueDGFactory(AbstractDGFactory):
observed_link = len(c1 & c2) # Intersections of the nodes are glued links
neighbor_intersection = clique_neighbors_set[c1_idx] & c2
neighbors_multiset = clique_neighbors_multiset[c1_idx]
- observed_link += sum(neighbors_multiset[x] for x in neighbor_intersection) # Sum the links between the cliques
+ for x in neighbor_intersection:
+ observed_link += neighbors_multiset[x] # Sum the links between the cliques
# Awaited links
d_approx = max(len(c1), len(c2))
diff --git a/experiments/clique_graph_eval.py b/experiments/clique_graph_eval.py
index f9697a1..3b85627 100644
--- a/experiments/clique_graph_eval.py
+++ b/experiments/clique_graph_eval.py
@@ -10,6 +10,8 @@ from deconvolution.dgraph.CliqueDGFactory import CliqueDGFactory
def parse_arguments():
parser = argparse.ArgumentParser(description="Tests on graph barcode")
parser.add_argument('barcode_graph', help='The barcode graph file. Must be a gexf formatted file.')
+ parser.add_argument('--threads', '-t', type=int, help="Number of threads to use (Set 1 for profiling)")
+ parser.add_argument('--verbose', '-v', action='store_true', help="Set the verbose flag")
args = parser.parse_args()
return args
@@ -77,10 +79,10 @@ def analyse_clique_graph(barcode_graph):
return continuous, len(clique_graph.nodes())
-def analyse_d_graphs(barcode_graph):
+def analyse_d_graphs(barcode_graph, threads=8, verbose=False):
# Generate udgs
factory = CliqueDGFactory(barcode_graph, 1)
- udg_per_node = factory.generate_all_dgraphs(threads=1)
+ udg_per_node = factory.generate_all_dgraphs(threads=threads, verbose=verbose)
# Remove duplicate udgs
udgs = {}
for udg_node_lst in udg_per_node.values():
@@ -100,12 +102,12 @@ def analyse_d_graphs(barcode_graph):
def main():
args = parse_arguments()
g = nx.read_gexf(args.barcode_graph)
+ # prev_time = time.time()
+ # continuous, total = analyse_clique_graph(g)
+ # print("cliques", time.time() - prev_time)
+ # print(continuous, "/", total)
prev_time = time.time()
- continuous, total = analyse_clique_graph(g)
- print("cliques", time.time() - prev_time)
- print(continuous, "/", total)
- prev_time = time.time()
- continuous, total = analyse_d_graphs(g)
+ continuous, total = analyse_d_graphs(g, threads=args.threads, verbose=args.verbose)
print("udgs", time.time() - prev_time)
print(continuous, "/", total)
--
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