def group_edges(cs):
plus = []
minus = []
pairs = []
gc.disable()
for current, cl1 in enumerate(cs.clusters):
update_status(
float(current) / len(cs.clusters), "Grouping all edges...")
bib1 = tuple(cl1.bibs)[0]
pointers = cl1.out_edges
for bib2 in xrange(len(cl1.out_edges)):
val = pointers[bib2]
if val[0] not in Bib_matrix.special_numbers:
if val[0] > edge_cut_prob:
pairs.append((bib1, bib2, val))
elif val[0] == Bib_matrix.special_symbols['+']:
plus.append((bib1, bib2))
elif val[0] == Bib_matrix.special_symbols['-']:
minus.append((bib1, bib2))
else:
assert val[0] == Bib_matrix.special_symbols[
None], "Invalid Edge"
update_status_final("Finished with the edge grouping.")
bibauthor_print(
"Positive edges: %d, Negative edges: %d, Value edges: %d." %
(len(plus), len(minus), len(pairs)))
gc.enable()
return plus, minus, pairs
def group_edges(cs):
plus = []
minus = []
pairs = []
for current, cl1 in enumerate(cs.clusters):
update_status(float(current) / len(cs.clusters), "Grouping all edges...")
bib1 = tuple(cl1.bibs)[0]
pointers = cl1.out_edges
for bib2 in xrange(len(cl1.out_edges)):
val = pointers[bib2]
if val[0] not in special_numbers:
if val[0] > edge_cut_prob:
pairs.append((bib1, bib2, val))
elif val[0] == special_symbols["+"]:
plus.append((bib1, bib2))
elif val[0] == special_symbols["-"]:
minus.append((bib1, bib2))
else:
assert val[0] == special_symbols[None]
update_status_final("Finished with the edge grouping.")
bibauthor_print("Positive edges: %d, Negative edges: %d, Value edges: %d." % (len(plus), len(minus), len(pairs)))
return plus, minus, pairs
def group_edges(cs):
plus = []
minus = []
pairs = []
gc.disable()
interval = 1000
for current, cl1 in enumerate(cs.clusters):
if (current % interval) == 0:
update_status(float(current) / len(cs.clusters), "Grouping all edges...")
bib1 = tuple(cl1.bibs)[0]
pointers = cl1.out_edges
for bib2 in xrange(len(cl1.out_edges)):
val = pointers[bib2]
if val[0] not in Bib_matrix.special_numbers:
if val[0] > edge_cut_prob:
pairs.append((bib1, bib2, val))
elif val[0] == Bib_matrix.special_symbols['+']:
plus.append((bib1, bib2))
elif val[0] == Bib_matrix.special_symbols['-']:
minus.append((bib1, bib2))
else:
assert val[0] == Bib_matrix.special_symbols[None], "Invalid Edge"
update_status_final("Finished with the edge grouping.")
bibauthor_print("Positive edges: %d, Negative edges: %d, Value edges: %d."
% (len(plus), len(minus), len(pairs)))
gc.enable()
return plus, minus, pairs
def main():
"""Main function """
try:
import bibauthorid_daemon as daemon
except ImportError:
bibauthor_print("Hmm...No Daemon process running.")
return
daemon.bibauthorid_daemon()
def main():
"""Main function """
try:
import bibauthorid_daemon as daemon
except ImportError:
bibauthor_print("Hmm...No Daemon process running.")
return
daemon.bibauthorid_daemon()
def tortoise_last_name(name, pure=False):
lname = generate_last_name_cluster_str(name)
names = create_lastname_list_from_personid()
names = filter(lambda x: x[0] == name, names)
if names:
pids = names[0][1]
bibauthor_print("Found %s(%s), %d pids" % (name, lname, len(pids)))
disambiguate_last_name(pids, lname, pure, False)
else:
bibauthor_print("Sorry, %s(%s) not found in the last name clusters" % (name, lname))
def disambiguate(cluster_set):
'''
Updates personid from a list of personids, sharing common
last name, and this last name.
'''
bibs = sum(len(c.bibs) for c in cluster_set.clusters)
expected = bibs * (bibs - 1) / 2
bibauthor_print("Start working on %s. Total number of bibs: %d, "
"maximum number of comparisons: %d"
% (cluster_set.last_name, bibs, expected))
wedge(cluster_set)
cluster_set.store()
def prepare_matirx(cluster_set, force):
if bconfig.DEBUG_CHECKS:
assert cluster_set._debug_test_hate_relation()
assert cluster_set._debug_duplicated_recs()
matr = ProbabilityMatrix()
matr.load(cluster_set.last_name, load_map=True, load_matrix=False)
if not force and matr.is_up_to_date(cluster_set):
bibauthor_print("Cluster %s is up-to-date and therefore will not be computed."
% cluster_set.last_name)
# nothing to do
return False
matr.load(cluster_set.last_name, load_map=False, load_matrix=True)
matr.recalculate(cluster_set)
matr.store(cluster_set.last_name)
return True
def prepare_matirx(cluster_set, force):
if bconfig.DEBUG_CHECKS:
assert cluster_set._debug_test_hate_relation()
assert cluster_set._debug_duplicated_recs()
matr = ProbabilityMatrix()
matr.load(cluster_set.last_name, load_map=True, load_matrix=False)
if not force and matr.is_up_to_date(cluster_set):
bibauthor_print(
"Cluster %s is up-to-date and therefore will not be computed." %
cluster_set.last_name)
# nothing to do
return False
matr.load(cluster_set.last_name, load_map=False, load_matrix=True)
matr.recalculate(cluster_set)
matr.store(cluster_set.last_name)
return True
def do_wedge(cluster_set, deep_debug=False):
'''
Rearranges the cluster_set acoarding to be values in the probability_matrix.
The deep debug option will produce a lot of output. Avoid using it with more
than 20 bibs in the cluster set.
'''
def decide(cl1, cl2):
score1 = compare_to(cl1, cl2)
score2 = compare_to(cl2, cl1)
return compare_to_final_bounds(score1, score2)
def compare_to(cl1, cl2):
pointers = [cl1.out_edges[v] for v in cl2.bibs]
assert pointers, "Wedge: no edges between clusters!"
vals, probs = zip(*pointers)
avg = sum(vals) / len(vals)
if avg > eps:
nvals = ((val / avg)**prob for val, prob in pointers)
else:
return 0
coeff = gini(nvals)
weight = sum(starmap(mul, pointers)) / sum(probs)
wedge_print("Wedge: Decide: vals = %s, probs = %s" %
(str(vals), str(probs)))
wedge_print("Wedge: Decide: coeff = %f, weight = %f" % (coeff, weight))
return coeff * weight
def gini(arr):
arr = sorted(arr, reverse=True)
dividend = sum(starmap(mul, izip(arr, xrange(1, 2 * len(arr), 2))))
divisor = len(arr) * sum(arr)
return float(dividend) / divisor
def compare_to_final_bounds(score1, score2):
return score1 + score2 > bconfig.WEDGE_THRESHOLD
def edge_sorting(edge):
'''
probability + certainty / 10
'''
return edge[2][0] + edge[2][1] / 10.
bib_map = create_bib_2_cluster_dict(cluster_set)
plus_edges, minus_edges, edges = group_edges(cluster_set)
for i, (bib1, bib2) in enumerate(plus_edges):
update_status(
float(i) / len(plus_edges), "Agglomerating obvious clusters...")
cl1 = bib_map[bib1]
cl2 = bib_map[bib2]
if cl1 != cl2 and not cl1.hates(cl2):
join(cl1, cl2)
cluster_set.clusters.remove(cl2)
for v in cl2.bibs:
bib_map[v] = cl1
update_status_final("Agglomerating obvious clusters done.")
for i, (bib1, bib2) in enumerate(minus_edges):
update_status(
float(i) / len(minus_edges), "Dividing obvious clusters...")
cl1 = bib_map[bib1]
cl2 = bib_map[bib2]
if cl1 != cl2 and not cl1.hates(cl2):
cl1.quarrel(cl2)
update_status_final("Dividing obvious clusters done.")
bibauthor_print("Sorting the value edges.")
edges = sorted(edges, key=edge_sorting, reverse=True)
interval = 1000
wedge_print("Wedge: New wedge, %d edges." % len(edges))
for current, (v1, v2, unused) in enumerate(edges):
if (current % interval) == 0:
update_status(float(current) / len(edges), "Wedge...")
assert unused != '+' and unused != '-', "Signed edge after filter!"
wedge_print("Wedge: poped new edge: Verts = %s, %s Value = (%f, %f)" %
(v1, v2, unused[0], unused[1]))
cl1 = bib_map[v1]
cl2 = bib_map[v2]
if cl1 != cl2 and not cl1.hates(cl2):
if deep_debug:
export_to_dot(
cluster_set,
"/tmp/%s%d.dot" % (cluster_set.last_name, current),
bib_map, (v1, v2, unused))
if decide(cl1, cl2):
wedge_print("Wedge: Joined!")
join(cl1, cl2)
cluster_set.clusters.remove(cl2)
for v in cl2.bibs:
bib_map[v] = cl1
else:
wedge_print("Wedge: Quarreled!")
cl1.quarrel(cl2)
elif cl1 == cl2:
wedge_print("Wedge: Clusters already joined!")
else:
wedge_print("Wedge: Clusters hate each other!")
update_status_final("Wedge done.")
bibauthor_print("")
if deep_debug:
export_to_dot(cluster_set, "/tmp/%sfinal.dot" % cluster_set.last_name,
bib_map)
def do_wedge(cluster_set, deep_debug=False):
'''
Rearranges the cluster_set acoarding to be values in the probability_matrix.
The deep debug option will produce a lot of output. Avoid using it with more
than 20 bibs in the cluster set.
'''
bib_map = create_bib_2_cluster_dict(cluster_set)
plus_edges, minus_edges, edges = group_edges(cluster_set)
interval = 1000
for i, (bib1, bib2) in enumerate(plus_edges):
if (i % interval) == 0:
update_status(float(i) / len(plus_edges), "Agglomerating obvious clusters...")
cl1 = bib_map[bib1]
cl2 = bib_map[bib2]
if cl1 != cl2 and not cl1.hates(cl2):
join(cl1, cl2)
cluster_set.clusters.remove(cl2)
for v in cl2.bibs:
bib_map[v] = cl1
update_status_final("Agglomerating obvious clusters done.")
interval = 1000
for i, (bib1, bib2) in enumerate(minus_edges):
if (i % interval) == 0:
update_status(float(i) / len(minus_edges), "Dividing obvious clusters...")
cl1 = bib_map[bib1]
cl2 = bib_map[bib2]
if cl1 != cl2 and not cl1.hates(cl2):
cl1.quarrel(cl2)
update_status_final("Dividing obvious clusters done.")
bibauthor_print("Sorting the value edges.")
edges = sorted(edges, key=_edge_sorting, reverse=True)
interval = 500000
wedge_print("Wedge: New wedge, %d edges." % len(edges))
for current, (v1, v2, unused) in enumerate(edges):
if (current % interval) == 0:
update_status(float(current) / len(edges), "Wedge...")
assert unused != '+' and unused != '-', PID()+"Signed edge after filter!"
cl1 = bib_map[v1]
cl2 = bib_map[v2]
idcl1 = cluster_set.clusters.index(cl1)
idcl2 = cluster_set.clusters.index(cl2)
#keep the ids low!
if idcl1 > idcl2:
idcl1, idcl2 = idcl2, idcl1
cl1, cl2 = cl2, cl1
wedge_print("Wedge: popped new edge: Verts = (%s,%s) from (%s, %s) Value = (%f, %f)" % (idcl1, idcl2, v1, v2, unused[0], unused[1]))
if cl1 != cl2 and not cl1.hates(cl2):
if deep_debug:
export_to_dot(cluster_set, "/tmp/%s%d.dot" % (cluster_set.last_name, current), bib_map, (v1, v2, unused))
decision, value = _decide(cl1, cl2)
if decision:
wedge_print("Wedge: Joined %s to %s with %s"% (idcl1, idcl2, value))
join(cl1, cl2)
cluster_set.clusters.remove(cl2)
for v in cl2.bibs:
bib_map[v] = cl1
else:
wedge_print("Wedge: Quarreled %s from %s with %s " % (idcl1, idcl2, value))
cl1.quarrel(cl2)
elif cl1 == cl2:
wedge_print("Wedge: Clusters already joined! (%s,%s)" % (idcl1, idcl2))
else:
wedge_print("Wedge: Clusters hate each other! (%s,%s)" % (idcl1, idcl2))
update_status_final("Wedge done.")
bibauthor_print("")
if deep_debug:
export_to_dot(cluster_set, "/tmp/%sfinal.dot" % cluster_set.last_name, bib_map)
def do_wedge(cluster_set, deep_debug=False):
'''
Rearranges the cluster_set acoarding to be values in the probability_matrix.
The deep debug option will produce a lot of output. Avoid using it with more
than 20 bibs in the cluster set.
'''
def decide(cl1, cl2):
score1 = compare_to(cl1, cl2)
score2 = compare_to(cl2, cl1)
return compare_to_final_bounds(score1, score2)
def compare_to(cl1, cl2):
pointers = [cl1.out_edges[v] for v in cl2.bibs]
assert pointers, "Wedge: no edges between clusters!"
vals, probs = zip(*pointers)
avg = sum(vals) / len(vals)
if avg > eps:
nvals = ((val / avg) ** prob for val, prob in pointers)
else:
return 0
coeff = gini(nvals)
weight = sum(starmap(mul, pointers)) / sum(probs)
wedge_print("Wedge: Decide: vals = %s, probs = %s" % (str(vals), str(probs)))
wedge_print("Wedge: Decide: coeff = %f, weight = %f" % (coeff, weight))
return coeff * weight
def gini(arr):
arr = sorted(arr, reverse=True)
dividend = sum(starmap(mul, izip(arr, xrange(1, 2 * len(arr), 2))))
divisor = len(arr) * sum(arr)
return float(dividend) / divisor
def compare_to_final_bounds(score1, score2):
return score1 + score2 > bconfig.WEDGE_THRESHOLD
def edge_sorting(edge):
'''
probability + certainty / 10
'''
return edge[2][0] + edge[2][1] / 10.
bib_map = create_bib_2_cluster_dict(cluster_set)
plus_edges, minus_edges, edges = group_edges(cluster_set)
for i, (bib1, bib2) in enumerate(plus_edges):
update_status(float(i) / len(plus_edges), "Agglomerating obvious clusters...")
cl1 = bib_map[bib1]
cl2 = bib_map[bib2]
if cl1 != cl2 and not cl1.hates(cl2):
join(cl1, cl2)
cluster_set.clusters.remove(cl2)
for v in cl2.bibs:
bib_map[v] = cl1
update_status_final("Agglomerating obvious clusters done.")
for i, (bib1, bib2) in enumerate(minus_edges):
update_status(float(i) / len(minus_edges), "Dividing obvious clusters...")
cl1 = bib_map[bib1]
cl2 = bib_map[bib2]
if cl1 != cl2 and not cl1.hates(cl2):
cl1.quarrel(cl2)
update_status_final("Dividing obvious clusters done.")
bibauthor_print("Sorting the value edges.")
edges = sorted(edges, key=edge_sorting, reverse=True)
interval = 1000
wedge_print("Wedge: New wedge, %d edges." % len(edges))
for current, (v1, v2, unused) in enumerate(edges):
if (current % interval) == 0:
update_status(float(current) / len(edges), "Wedge...")
assert unused != '+' and unused != '-', "Signed edge after filter!"
wedge_print("Wedge: poped new edge: Verts = %s, %s Value = (%f, %f)" % (v1, v2, unused[0], unused[1]))
cl1 = bib_map[v1]
cl2 = bib_map[v2]
if cl1 != cl2 and not cl1.hates(cl2):
if deep_debug:
export_to_dot(cluster_set, "/tmp/%s%d.dot" % (cluster_set.last_name, current), cluster_set.mapping, (v1, v2, unused))
if decide(cl1, cl2):
wedge_print("Wedge: Joined!")
join(cl1, cl2)
cluster_set.clusters.remove(cl2)
for v in cl2.bibs:
bib_map[v] = cl1
else:
wedge_print("Wedge: Quarreled!")
cl1.quarrel(cl2)
elif cl1 == cl2:
wedge_print("Wedge: Clusters already joined!")
else:
wedge_print("Wedge: Clusters hate each other!")
update_status_final("Wedge done.")
bibauthor_print("")
if deep_debug:
export_to_dot(cluster_set, "/tmp/%sfinal.dot" % cluster_set.last_name, cluster_set.mapping)
