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Commit 16bdbf15 authored by Tiago Peixoto's avatar Tiago Peixoto
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minimize_nested_blockmodel_dl(): Fix issues with clabel for graphs with filtered vertices

parent fe27ada4
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Showing with 71 additions and 69 deletions
src/graph_tool/community/blockmodel.py
View file @ 16bdbf15
......@@ -181,7 +181,7 @@ class BlockState(object):
self.clabel = self.g.own_property(clabel.copy("int"))
else:
self.clabel = self.g.new_vertex_property("int")
self.clabel.a = clabel
self.clabel.fa = clabel
else:
self.clabel = self.g.new_vertex_property("int")
......@@ -1340,7 +1340,7 @@ def greedy_shrink(state, B, **kwargs):
curr_B = (state.wr.a > 0).sum()
if _bm_test():
assert curr_B == len(set(state.b.a)), (curr_B, len(set(state.b.a)))
assert curr_B == len(set(state.b.fa)), (curr_B, len(set(state.b.fa)))
if verbose:
print("merging, B=%d" % curr_B, "left:", curr_B - B,
......@@ -1727,7 +1727,7 @@ def multilevel_minimize(state, B, nsweeps=10, adaptive_sweeps=True, epsilon=0,
# check cache for previous results
if b_cache is not None and Bi in b_cache:
if _bm_test():
assert (state.clabel.a == b_cache[Bi][1].clabel.a).all(), "wrong clabel in cache"
assert (state.clabel.fa == b_cache[Bi][1].clabel.fa).all(), "wrong clabel in cache"
assert state._BlockState__check_clabel(), "clabel already invalidated before cache"
assert b_cache[Bi][1]._BlockState__check_clabel(), "clabel already invalidated after cache"
state = b_cache[Bi][1].copy()
......@@ -1759,7 +1759,7 @@ def multilevel_minimize(state, B, nsweeps=10, adaptive_sweeps=True, epsilon=0,
nstate = state.copy(b=state.get_nonoverlap_blocks(), overlap=False)
assert nstate.B <= nstate.N
nstate = multilevel_minimize(nstate, B=Bi, verbose=verbose, **kwargs)
nstate = nstate.copy(overlap=True, clabel=state.clabel.a)
nstate = nstate.copy(overlap=True, clabel=state.clabel.fa)
unilevel_minimize(nstate, **kwargs)
if nstate.B > Bi:
......@@ -2236,7 +2236,7 @@ def minimize_blockmodel_dl(g, deg_corr=True, overlap=False, ec=None,
minimize_state.init = False
if min_B is None:
min_B = state.clabel.a.max() + 1
min_B = state.clabel.fa.max() + 1
if verbose:
print("Overlapping minimization starting from B=", max_B)
......
src/graph_tool/community/covariate_blockmodel.py
View file @ 16bdbf15
......@@ -247,7 +247,7 @@ class CovariateBlockState(BlockState):
max_BE=self.max_BE)
else:
base_u, node_index = self.__get_base_u(u)
state = OverlapBlockState(u, b=u.vp["b"].a,
state = OverlapBlockState(u, b=u.vp["b"].fa,
B=B,
vweight=u.vp["weight"],
node_index=node_index,
......@@ -499,7 +499,7 @@ class CovariateBlockState(BlockState):
vweight=self.vweight if vweight is None else vweight,
b=self.b if b is None else b,
B=(self.B if b is None else None) if B is None else B,
clabel=(self.clabel.a if self.overlap else self.clabel) if clabel is None else clabel,
clabel=(self.clabel.fa if self.overlap else self.clabel) if clabel is None else clabel,
deg_corr=self.deg_corr if deg_corr is None else deg_corr,
overlap=self.overlap if overlap is None else overlap,
layers=self.layers if layers is None else layers,
......@@ -727,7 +727,7 @@ def init_layer_confined(g, ec):
tmp_state = tmp_state.copy(overlap=True)
be = tmp_state.get_edge_blocks()
ba = ungroup_vector_property(be, [0])[0]
ba.a = ba.a + ec.a * (ba.a.max() + 1)
ba.fa = ba.fa + ec.fa * (ba.fa.max() + 1)
continuous_map(ba)
be = group_vector_property([ba, ba])
return be
\ No newline at end of file
src/graph_tool/community/nested_blockmodel.py
View file @ 16bdbf15
......@@ -111,7 +111,7 @@ class NestedBlockState(object):
clabel=self.clabel,
max_BE=max_BE)
self.clabel = state.clabel.copy()
state.clabel.a = 0
state.clabel.fa = 0
else:
state = BlockState(g, B=Bl, b=bl,
eweight=ecount,
......@@ -132,7 +132,7 @@ class NestedBlockState(object):
max_BE=max_BE)
if overlap:
self.clabel = state.clabel.copy()
state.clabel.a = 0
state.clabel.fa = 0
else:
......@@ -170,7 +170,7 @@ class NestedBlockState(object):
ec = g.own_property(self.ec.copy()) if self.ec is not None else None
bstack = self.get_bstack()
return self.copy(g=g, eweight=eweight, vweight=vweight, clabel=clabel,
ec=ec, bs=[s.vp.b.a for s in bstack])
ec=ec, bs=[s.vp.b.fa for s in bstack])
def copy(self, g=None, eweight=None, vweight=None, bs=None, ec=None,
layers=None, deg_corr=None, overlap=None, clabel=None, **kwargs):
......@@ -178,18 +178,20 @@ class NestedBlockState(object):
have the same meaning as in the constructor.."""
if bs is None:
bs = [s.b.a for s in self.levels]
bs = [s.b.fa for s in self.levels]
if overlap is None:
overlap = self.overlap
elif self.overlap and not overlap:
raise ValueError("Cannot automatically convert overlapping nested state to nonoverlapping")
elif not self.overlap and overlap:
s = self.levels[0].copy(overlap=True)
bs[0] = s.b.a
bs[0] = s.b.fa
if deg_corr is None:
deg_corr = self.deg_corr
if layers is None:
layers = self.layers
if clabel is None:
clabel = self.clabel
return NestedBlockState(self.g if g is None else g,
self.eweight if eweight is None else eweight,
self.vweight if vweight is None else vweight,
......@@ -206,7 +208,7 @@ class NestedBlockState(object):
eweight=self.eweight,
vweight=self.vweight,
overlap=self.overlap,
bs=[array(s.b.a) for s in self.levels],
bs=[array(s.b.fa) for s in self.levels],
clabel=self.clabel,
deg_corr=self.deg_corr,
max_BE=self.levels[0].max_BE,
......@@ -253,12 +255,12 @@ class NestedBlockState(object):
if self.levels[j].wr.a.min() == 0:
print("WARNING: empty blocks at level", j)
if self.levels[j].b.a.max() + 1 != self.levels[j].B:
print("WARNING: b.max() + 1 != B at level", j, self.levels[j].b.max() + 1, self.levels[j].B)
if self.levels[j].b.fa.max() + 1 != self.levels[j].B:
print("WARNING: b.max() + 1 != B at level", j, self.levels[j].b.fa.max() + 1, self.levels[j].B)
for j in range(len(self.levels) - 1):
B = self.levels[j].b.a.max() + 1
B = self.levels[j].b.fa.max() + 1
bg_state = self.levels[j].get_block_state(b=self.levels[j+1].b.copy(),
overlap=self.overlap == "full",
deg_corr=self.deg_corr == "full")[0]
......@@ -275,20 +277,20 @@ class NestedBlockState(object):
print("N, B:", bg_state.N, bg_state.B)
print("N, B:", self.levels[j + 1].N, self.levels[j + 1].B)
print("similarity:", similarity(bg_state.g, self.levels[j+1].g))
print("b:", bg_state.b.a)
print("b:", self.levels[j+1].b.a)
print("b:", bg_state.b.fa)
print("b:", self.levels[j+1].b.fa)
print("wr:", bg_state.wr.a)
print("wr:", self.levels[j+1].wr.a)
print("wr:", bg_state.wr.fa)
print("wr:", self.levels[j+1].wr.fa)
print("mrs:", bg_state.mrs.a)
print("mrs:", self.levels[j+1].mrs.a)
print("mrs:", bg_state.mrs.fa)
print("mrs:", self.levels[j+1].mrs.fa)
print("eweight:", bg_state.eweight.a)
print("eweight:", self.levels[j+1].eweight.a)
print("eweight:", bg_state.eweight.fa)
print("eweight:", self.levels[j+1].eweight.fa)
print("vweight:", bg_state.vweight.a)
print("vweight:", self.levels[j+1].vweight.a)
print("vweight:", bg_state.vweight.fa)
print("vweight:", self.levels[j+1].vweight.fa)
assert abs(S1 - S2) < 1e-6 and not isnan(S2) and not isnan(S1), "inconsistency at level %d after %s of level %d, different entropies (%g, %g)" % (j, op, l, S1, S2)
......@@ -297,15 +299,15 @@ class NestedBlockState(object):
# verify hierarchy / clabel consistency
clabel = self.__project_partition(0, j)
self.levels[0].clabel.a = self.clabel.a
self.levels[0].clabel.fa = self.clabel.fa
assert self.levels[0]._BlockState__check_clabel(), "inconsistency at level %d after %s of level %d, clabel invalidated" % (j + 1, op, l)
self.levels[0].clabel.a = 0
self.levels[0].clabel.fa = 0
# verify hierarchy consistency
clabel = self.__project_partition(j, j + 1)
self.levels[0].clabel.a = self.clabel.a
self.levels[0].clabel.fa = self.clabel.fa
assert self.levels[0]._BlockState__check_clabel(), "inconsistency at level %d after %s of level %d, partition not compatible with upper level" % (j + 1, op, l)
self.levels[0].clabel.a = 0
self.levels[0].clabel.fa = 0
def __rebuild_level(self, l, b, clabel=None):
......@@ -320,7 +322,7 @@ class NestedBlockState(object):
old_b = b.copy()
state = self.levels[l].copy(b=b, clabel=clabel.a)
state = self.levels[l].copy(b=b, clabel=clabel.fa)
self.levels[l] = state
if l == 0:
self.clabel = state.g.own_property(self.clabel) # for CovariateBlockState
......@@ -334,8 +336,8 @@ class NestedBlockState(object):
self.levels.append(None)
self.levels[l + 1] = bstate
self.levels[l].clabel.a = 0
self.levels[l + 1].clabel.a = 0
self.levels[l].clabel.fa = 0
self.levels[l + 1].clabel.fa = 0
# if l + 1 < len(self.levels) - 1:
# self.levels[l + 1].clabel = self.__project_partition(l + 1, l + 2)
......@@ -354,22 +356,22 @@ class NestedBlockState(object):
if abs(bstate.entropy() - self.levels[l + 2].entropy()) > 1e-6:
print("********************** inconsistent rebuild! **************************")
print(bstate.b.a)
print(self.levels[l + 2].b.a)
print(bstate.b.fa)
print(self.levels[l + 2].b.fa)
print(bstate.wr.a)
print(self.levels[l + 2].wr.a)
print(bstate.eweight.a)
print(self.levels[l + 2].eweight.a)
print(bstate.eweight.fa)
print(self.levels[l + 2].eweight.fa)
nclabel = self.__project_partition(l, l + 1)
print(nclabel.a)
print(clabel.a)
print(self.levels[l].b.a)
print(self.levels[l+1].b.a)
print(self.levels[l+2].b.a)
print(bstate.b.a)
print(nclabel.fa)
print(clabel.fa)
print(self.levels[l].b.fa)
print(self.levels[l+1].b.fa)
print(self.levels[l+2].b.fa)
print(bstate.b.fa)
print ("DS", l, l + 1, bstate.entropy(), self.levels[l + 2].entropy())
B = self.levels[l].B
......@@ -516,7 +518,7 @@ class NestedBlockState(object):
l -= 1
else:
b = self.levels[l].b.copy()
state = self.levels[0].copy(b=b.a)
state = self.levels[0].copy(b=b.fa)
return state
def merge_layers(self, l_src, l_tgt, revert=False):
......@@ -624,7 +626,7 @@ def nested_mcmc_sweep(state, beta=1., c=1., dl=False, sequential=True,
# propagate externally imposed clabel at the bottom
cclabel = state._NestedBlockState__propagate_clabel(l)
cclabel.a += clabel.a * (cclabel.a.max() + 1)
cclabel.fa += clabel.fa * (cclabel.fa.max() + 1)
continuous_map(cclabel)
bstate.clabel = cclabel
......@@ -635,7 +637,7 @@ def nested_mcmc_sweep(state, beta=1., c=1., dl=False, sequential=True,
sequential=sequential, parallel=parallel,
verbose=verbose)
bstate.clabel.a = 0
bstate.clabel.fa = 0
rets.append(ret)
return rets
......@@ -673,7 +675,7 @@ def replace_level(l, state, min_B=None, max_B=None, max_b=None, nsweeps=10,
if l > 0 or max_B is None:
max_B = bstate.N
min_B = max(min_B, state.clabel.a.max() + 1)
min_B = max(min_B, state.clabel.fa.max() + 1)
# constraint partitions not to invalidate upper layers
if l < len(state.levels) - 1:
......@@ -682,25 +684,25 @@ def replace_level(l, state, min_B=None, max_B=None, max_b=None, nsweeps=10,
clabel = bstate.g.new_vertex_property("int")
assert min_B <= max_B, (min_B, max_B, bstate.B, bstate.N, g.num_vertices(),
state.clabel.a.max() + 1, clabel.a.max() + 1, l)
state.clabel.fa.max() + 1, clabel.fa.max() + 1, l)
# propagate externally imposed clabel at the bottom
cclabel = state._NestedBlockState__propagate_clabel(l)
assert cclabel.a.max() <= state.clabel.a.max(), (cclabel.a.max(), state.clabel.a.max())
cclabel.a += clabel.a * (cclabel.a.max() + 1)
assert cclabel.fa.max() <= state.clabel.fa.max(), (cclabel.fa.max(), state.clabel.fa.max())
cclabel.fa += clabel.fa * (cclabel.fa.max() + 1)
continuous_map(cclabel)
min_B = max(min_B, cclabel.a.max() + 1)
min_B = max(min_B, cclabel.fa.max() + 1)
assert min_B <= max_B, (min_B, max_B, bstate.B, bstate.N, g.num_vertices(),
cclabel.a.max() + 1, state.clabel.a.max() + 1, clabel.a.max() + 1, l)
cclabel.fa.max() + 1, state.clabel.fa.max() + 1, clabel.fa.max() + 1, l)
if _bm_test():
assert bstate._BlockState__check_clabel(), "invalid clabel before minimize!"
nested_dl = l < len(state.levels) - 1
state.levels[l].clabel.a = cclabel.a
state.levels[l].clabel.fa = cclabel.fa
Sb = get_b_dl(state.levels[l],
dense=(l > 0 and state.deg_corr != "full") or dense,
......@@ -709,14 +711,14 @@ def replace_level(l, state, min_B=None, max_B=None, max_b=None, nsweeps=10,
nested_overlap=state.overlap == "full",
dl_ent=dl_ent)
state.levels[l].clabel.a = 0
state.levels[l].clabel.fa = 0
if _bm_test():
assert clabel.a.max() + 1 <= min_B
assert clabel.fa.max() + 1 <= min_B
if l == 0 and max_b is not None:
istate = state.levels[0].copy(b=max_b.copy(),
clabel=cclabel.a if state.overlap else cclabel)
clabel=cclabel.fa if state.overlap else cclabel)
if _bm_test():
assert istate._BlockState__check_clabel(), "invalid clabel!"
if istate.B > max_B:
......@@ -749,7 +751,7 @@ def replace_level(l, state, min_B=None, max_B=None, max_b=None, nsweeps=10,
epsilon=epsilon,
max_B=max_B,
min_B=min_B,
clabel=cclabel if not bstate.overlap else cclabel.a,
clabel=cclabel if not bstate.overlap else cclabel.fa,
max_BE=bstate.max_BE,
dl=dl,
dense=(l > 0 and state.deg_corr != "full") or dense,
......@@ -769,7 +771,7 @@ def replace_level(l, state, min_B=None, max_B=None, max_b=None, nsweeps=10,
ignore_degrees=state.ignore_degrees if l == 0 else None)
if _bm_test():
assert (res.clabel.a == cclabel.a).all(), (res.clabel.a, cclabel.a)
assert (res.clabel.fa == cclabel.fa).all(), (res.clabel.fa, cclabel.fa)
assert res._BlockState__check_clabel(), "invalid clabel after minimize!"
Sf = get_b_dl(res,
......@@ -779,10 +781,10 @@ def replace_level(l, state, min_B=None, max_B=None, max_b=None, nsweeps=10,
nested_overlap=state.overlap == "full",
dl_ent=dl_ent)
res.clabel.a = 0
res.clabel.fa = 0
if state.ec is not None:
for s in res.states:
s.clabel.a = 0
s.clabel.fa = 0
b = res.b
kept = False
......@@ -1331,7 +1333,7 @@ def init_nested_state(g, Bs, ec=None, deg_corr=True, overlap=False,
deg_corr=deg_corr == "full")[0]
if B == 1:
bstate.copy(b=bstate.g.new_vertex_property("int").a)
bstate.copy(b=bstate.g.new_vertex_property("int").fa)
else:
bstate = multilevel_minimize(bstate, B, nsweeps=nsweeps,
epsilon=epsilon,
......@@ -1636,12 +1638,12 @@ def minimize_nested_blockmodel_dl(g, Bs=None, bs=None, min_B=None,
nmerge_sweeps=nmerge_sweeps, dl=dl,
sequential=sequential, parallel=parallel,
confine_layers=confine_layers)
bs = [array(s.b.a) for s in state.levels]
bs[0] = array(bstate.b.a)
bs = [array(s.b.fa) for s in state.levels]
bs[0] = array(bstate.b.fa)
del bstate
else:
bstates = [bstate.copy(overlap=True) for bstate in state.levels]
bs = [array(s.b.a) for s in bstates]
bs = [array(s.b.fa) for s in bstates]
del bstates
if nonoverlap_init != "full":
......
src/graph_tool/community/overlap_blockmodel.py
View file @ 16bdbf15
......@@ -202,13 +202,13 @@ class OverlapBlockState(BlockState):
if isinstance(clabel, PropertyMap):
# if clabel is a property map, we will assume it constraints the *nodes*
if _bm_test():
assert len(clabel.a) < self.g.num_vertices()
assert len(clabel.fa) < self.g.num_vertices()
self.clabel = self.node_index.copy()
pmap(self.clabel, clabel.copy("int"))
else:
# if clabel is an array, we will assume it constraints the *half-edges*
self.clabel = self.g.new_vertex_property("int")
self.clabel.a = clabel
self.clabel.fa = clabel
else:
self.clabel = self.g.new_vertex_property("int")
......@@ -266,7 +266,7 @@ class OverlapBlockState(BlockState):
vweight=self.vweight if vweight is None else vweight,
b=self.b if b is None else b,
B=(self.B if b is None else None) if B is None else B,
clabel=self.clabel.a if clabel is None else clabel,
clabel=self.clabel.fa if clabel is None else clabel,
deg_corr=self.deg_corr if deg_corr is None else deg_corr,
base_g=self.base_g,
half_edges=self.half_edges,
......@@ -296,7 +296,7 @@ class OverlapBlockState(BlockState):
vweight=self.vweight,
b=self.b,
B=self.B,
clabel=array(self.clabel.a),
clabel=array(self.clabel.fa),
deg_corr=self.deg_corr,
base_g=self.base_g,
half_edges=self.half_edges,
......
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