def main():
"""Parse arguments, do the comparison, write to output."""
parser = argparse.ArgumentParser()
parser.description = "compare estimation of betweenness centralities to exact values"
parser.add_argument("epsilon", type=util.valid_interval_float, help="accuracy parameter")
parser.add_argument("delta", type=util.valid_interval_float, help="confidence parameter")
parser.add_argument("graph", help="graph file")
group = parser.add_mutually_exclusive_group()
group.add_argument("-a", "--approximate", action="store_true",
default=True, help="use approximate diameter when computing approximation of betweenness using VC-Dimension (default)")
group.add_argument("-d", "--diameter", type=util.positive_int, default=0,
help="value to use for the diameter")
group.add_argument("-e", "--exact", action="store_true", default=False,
help="use exact diameter when computing approximation of betweenness using VC-Dimension")
parser.add_argument("-m", "--maxconn", action="store_true", default=False,
help="if the graph is not weakly connected, only save the largest connected component")
parser.add_argument("-p", "--pickle", action="store_true", default=False,
help="use pickle reader for input file")
parser.add_argument("-r", "--resultfiles", nargs=4,
help="Use results files rather than recomputing betweenness. Files should be specified as 'exact_res vc_res bp_res gss_res'")
parser.add_argument("-s", "--samplesize", type=util.positive_int,
default=0, help="use specified sample size. Overrides epsilon, delta, and diameter computation")
parser.add_argument("-t", "--timeout", type=util.positive_int, default=3600,
help="Timeout computation after specified number of seconds (default 3600 = 1h, 0 = no timeout)")
parser.add_argument("-u", "--undirected", action="store_true", default=False,
help="consider the graph as undirected ")
parser.add_argument("-v", "--verbose", action="count", default=0,
help="increase verbosity (use multiple times for more verbosity)")
parser.add_argument("-w", "--write", nargs="?", default=False, const="auto",
help="write graph (and computed attributes) to file.")
args = parser.parse_args()
# Set the desired level of logging
util.set_verbosity(args.verbose)
# Seed the random number generator
random.seed()
# Read graph
if args.pickle:
G = util.read_graph(args.graph)
else:
G = converter.convert(args.graph, not args.undirected, args.maxconn)
if args.exact:
args.approximate = False
if not args.resultfiles:
(exact_stats, exact_betw) = brandes_exact.betweenness(G, args.write,
args.timeout)
if args.samplesize:
(vc_stats, vc_betw) = vc_sample.betweenness_sample_size(G,
args.samplesize, args.write, args.timeout)
(bp_stats, bp_betw) = brandespich_sample.betweenness_sample_size(G,
args.samplesize, args.write, args.timeout)
(gss_stats, gss_betw) = geisbergerss_sample.betweenness_sample_size(G,
args.samplesize, args.write, args.timeout)
else:
if args.diameter > 0:
(vc_stats, vc_betw) = vc_sample.betweenness(G, args.epsilon, args.delta,
args.diameter, args.write, args.timeout)
else:
(vc_stats, vc_betw) = vc_sample.betweenness(G, args.epsilon, args.delta,
args.approximate, args.write, args.timeout)
(bp_stats, bp_betw) = brandespich_sample.betweenness(G,
args.epsilon, args.delta, args.write, args.timeout)
(gss_stats, gss_betw) = geisbergerss_sample.betweenness(G,
args.epsilon, args.delta, args.write, args.timeout)
else:
(exact_stats, exact_betw) = util.read_stats_betw(args.result_files[0])
(vc_stats, vc_betw) = util.read_stats_betw(args.result_files[1])
(bp_stats, bp_betw) = util.read_stats_betw(args.result_files[2])
(gss_stats, gss_betw) = util.read_stats_betw(args.result_files[3])
#Compute useful graph statistics (mainly diameter)
if "diam" not in G.attributes():
diameter.diameter(G)
# If specified, write betweenness as vertex attributes, and time and
# diameter as graph attributes back to file
if args.write:
logging.info("Writing betweenness as vertex attributes and stats as graph attribute")
if args.write == "auto":
filename = os.path.splitext(args.graph)[0] + ("-undir" if args.undirected else "dir") + ".picklez"
G.write(filename)
else:
G.write(args.write)
# Compute error statistics
# It is not a problem to sort the error by value because we only compute
# aggregates.
# Normalize
#normalizer = math.pow(G.vcount(),2)-G.vcount()
#norm_exact_betw = [a/normalizer for a in exact_betw]
#norm_vc_betw = [a/normalizer for a in vc_betw]
#norm_bp_betw = [a/normalizer for a in bp_betw]
#norm_gss_betw = [a/normalizer for a in gss_betw]
#VC-STATISTICS
logging.info("Computing error statistics")
max_err = args.epsilon * G.vcount() * (G.vcount() - 1) / 2
vc_errs = sorted([abs(a - b) for a,b in zip(exact_betw,vc_betw)])
vc_stats["err_avg"] = sum(vc_errs) / G.vcount()
vc_stats["err_max"] = vc_errs[-1]
vc_stats["err_min"] = list(itertools.filterfalse(lambda x: x == 0, vc_errs))[0]
vc_stats["err_stddev"] = math.sqrt(sum([math.pow(err - vc_stats["err_avg"], 2) for err in vc_errs]) / (G.vcount() -1))
vc_stats["euc_dist"] = math.sqrt(sum([math.pow(a - b, 2) for a,b in zip(exact_betw,vc_betw)]))
vc_stats["wrong_eps"] = 0;
for i in range(G.vcount()):
err = abs(exact_betw[i] - vc_betw[i])
#if err > max_err:
#vc_stats["wrong_eps"] += 1
#if vc_stats["wrong_eps"] == 1:
#print("## VC wrong epsilon ##")
#print("{} {} {} {} {} {} {}".format(i, G.vs[i].degree(),
#exact_betw[i], vc_betw[i], bp_betw[i],
#err, err / (G.vcount() * (G.vcount() -1) / 2)))
#BP-STATISTICS
bp_errs = sorted([abs(a - b) for a,b in zip(exact_betw,bp_betw)])
bp_stats["err_avg"] = sum(bp_errs) / G.vcount()
bp_stats["err_max"] = max(bp_errs)
bp_stats["err_min"] = list(itertools.filterfalse(lambda x: x == 0, bp_errs))[0]
bp_stats["err_stddev"] = math.sqrt(sum([math.pow(err - bp_stats["err_avg"], 2) for err in bp_errs]) / (G.vcount() -1))
bp_stats["euc_dist"] = math.sqrt(sum([math.pow(a - b, 2) for a,b in zip(exact_betw,bp_betw)]))
bp_stats["wrong_eps"] = 0
for i in range(G.vcount()):
err = abs(exact_betw[i] - bp_betw[i])
#if err > max_err:
#bp_stats["wrong_eps"] += 1
#if bp_stats["wrong_eps"] == 1:
#print("## BP wrong epsilon ##")
#print("{} {} {} {} {} {} {}".format(i, G.vs[i].degree(),
#exact_betw[i], bp_betw[i], vc_betw[i], err, err / (G.vcount() * (G.vcount() -1) / 2)))
#GSS-STATISTICS
gss_errs = sorted([abs(a - b) for a,b in zip(exact_betw,gss_betw)])
gss_stats["err_avg"] = sum(gss_errs) / G.vcount()
gss_stats["err_max"] = max(gss_errs)
gss_stats["err_min"] = list(itertools.filterfalse(lambda x: x == 0, gss_errs))[0]
gss_stats["err_stddev"] = math.sqrt(sum([math.pow(err - gss_stats["err_avg"], 2) for err in gss_errs]) / (G.vcount() -1))
gss_stats["euc_dist"] = math.sqrt(sum([math.pow(a - b, 2) for a,b in zip(exact_betw,gss_betw)]))
gss_stats["wrong_eps"] = 0
for i in range(G.vcount()):
err = abs(exact_betw[i] - gss_betw[i])
#if err > max_err:
#gss_stats["wrong_eps"] += 1
#if gss_stats["wrong_eps"] == 1:
#print("## GSS wrong epsilon ##")
#print("{} {} {} {} {} {} {}".format(i, G.vs[i].degree(),
#exact_betw[i], gss_betw[i], vc_betw[i], err, err / (G.vcount() * (G.vcount() -1) / 2)))
# Print statistics to output as CSV
logging.info("Printing statistics")
print("graph,nodes,edges,diam,directed,epsilon,delta,sample_size")
print("{},{},{},{},{},{},{},{}".format(G["filename"], G.vcount(),
G.ecount(), G["diam"], G.is_directed(), args.epsilon, args.delta,
args.samplesize))
#csvkeys="epsilon, delta, sample_size, time, wrong_eps, err_avg, err_max, err_min, err_stddev, forward_touched_edges, backward_touched_edges, diameter_touched_edges, euc_dist, diameter, diam_type"
csvkeys="epsilon,delta,sample_size,time,wrong_eps,err_avg,err_stddev,forward_touched_edges,backward_touched_edges,diameter_touched_edges,euc_dist,diameter,diam_type"
print("type,", csvkeys)
print("vc,", util.dict_to_csv(vc_stats,csvkeys))
print("bp,", util.dict_to_csv(bp_stats,csvkeys))
print("gss,", util.dict_to_csv(gss_stats,csvkeys))
print("exact,", util.dict_to_csv(exact_stats,csvkeys))
def main():
"""Parse arguments, run experiments, collect results and stats, write to file."""
# Parse arguments
parser = argparse.ArgumentParser()
parser.description = "Perform experiment to compute exact betweenness centrality of all vertices in a graph using Brandes' algorithm"
parser.add_argument("runs",
type=util.positive_int,
default=20,
help="number of runs")
parser.add_argument("graph", help="graph file")
parser.add_argument("output", help="output file")
parser.add_argument(
"-m",
"--maxconn",
action="store_true",
default=False,
help=
"if the graph is not weakly connected, only save the largest connected component"
)
parser.add_argument("-p",
"--pickle",
action="store_true",
default=False,
help="use pickle reader for input file")
parser.add_argument(
"-t",
"--timeout",
type=util.positive_int,
default=3600,
help=
"Timeout computation after specified number of seconds (default 3600 = 1h, 0 = no timeout)"
)
parser.add_argument("-u",
"--undirected",
action="store_true",
default=False,
help="consider the graph as undirected ")
parser.add_argument(
"-v",
"--verbose",
action="count",
default=0,
help="increase verbosity (use multiple times for more verbosity)")
args = parser.parse_args()
# Set the desired level of logging
util.set_verbosity(args.verbose)
# Read graph
if args.pickle:
G = util.read_graph(args.graph)
else:
G = converter.convert(args.graph, not args.undirected, args.maxconn)
# Perform experiment multiple times
results = []
for i in range(args.runs):
logging.info("Run #%d", i)
results.append(brandes_exact.betweenness(G, False, args.timeout))
# Compute aggregate statistics about the experiments
stats = dict(results[0][0])
stats["graph"] = os.path.basename(args.graph)
stats["vertices"] = G.vcount()
stats["edges"] = G.ecount()
stats["runs"] = args.runs
del stats["time"]
times = sorted([x[0]["time"] for x in results])
stats["time_max"] = times[-1]
stats["time_min"] = times[0]
stats["time_avg"] = sum(times) / args.runs
if args.runs > 1:
stats["time_stddev"] = math.sqrt(
sum([math.pow(time - stats["time_avg"], 2)
for time in times]) / (args.runs - 1))
else:
stats["time_stddev"] = 0.0
csvkeys = "graph, runs, time_avg, time_stddev, time_max, time_min, forward_touched_edges, backward_touched_edges"
print(csvkeys)
print(util.dict_to_csv(stats, csvkeys))
# Write stats and results to output file
try:
with open(args.output, "wb") as output:
logging.info("Writing stats and results to %s", args.output)
pickle.dump((stats, results), output)
output.close()
except OSError as E:
logging.critical("Cannot write stats and results to %s: %s",
args.output, E.strerror)
sys.exit(2)
def main():
"""Parse arguments, run experiments, collect results and stats, write to file."""
# Parse arguments
parser = argparse.ArgumentParser()
parser.description = "Perform experiment to compute exact betweenness centrality of all vertices in a graph using Brandes' algorithm"
parser.add_argument("runs", type=util.positive_int, default=20, help="number of runs")
parser.add_argument("graph", help="graph file")
parser.add_argument("output", help="output file")
parser.add_argument("-m", "--maxconn", action="store_true", default=False,
help="if the graph is not weakly connected, only save the largest connected component")
parser.add_argument("-p", "--pickle", action="store_true", default=False,
help="use pickle reader for input file")
parser.add_argument("-t", "--timeout", type=util.positive_int, default=3600,
help="Timeout computation after specified number of seconds (default 3600 = 1h, 0 = no timeout)")
parser.add_argument("-u", "--undirected", action="store_true", default=False,
help="consider the graph as undirected ")
parser.add_argument("-v", "--verbose", action="count", default=0,
help="increase verbosity (use multiple times for more verbosity)")
args = parser.parse_args()
# Set the desired level of logging
util.set_verbosity(args.verbose)
# Read graph
if args.pickle:
G = util.read_graph(args.graph)
else:
G = converter.convert(args.graph, not args.undirected, args.maxconn)
# Perform experiment multiple times
results = []
for i in range(args.runs):
logging.info("Run #%d", i)
results.append(brandes_exact.betweenness(G, False, args.timeout))
# Compute aggregate statistics about the experiments
stats = dict(results[0][0])
stats["graph"]= os.path.basename(args.graph)
stats["vertices"] = G.vcount()
stats["edges"] = G.ecount()
stats["runs"] = args.runs
del stats["time"]
times = sorted([x[0]["time"] for x in results])
stats["time_max"] = times[-1]
stats["time_min"] = times[0]
stats["time_avg"] = sum(times) / args.runs
if args.runs > 1:
stats["time_stddev"] = math.sqrt(sum([math.pow(time -
stats["time_avg"], 2) for time in times]) / (args.runs - 1))
else:
stats["time_stddev"] = 0.0
csvkeys="graph, runs, time_avg, time_stddev, time_max, time_min, forward_touched_edges, backward_touched_edges"
print(csvkeys)
print(util.dict_to_csv(stats, csvkeys))
# Write stats and results to output file
try:
with open(args.output, "wb") as output:
logging.info("Writing stats and results to %s", args.output)
pickle.dump((stats, results), output)
output.close()
except OSError as E:
logging.critical("Cannot write stats and results to %s: %s",
args.output, E.strerror)
sys.exit(2)