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use hash on complete invariants instead of str
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@arashbm
arashbm committed Jul 17, 2024
1 parent 89784c6 commit 402b31c
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Showing 4 changed files with 71 additions and 78 deletions.
23 changes: 13 additions & 10 deletions pymnet/graphlets/graphlet_measures.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ def orbit_counts_all(net, n, nets, invs, auts, orbit_list, allowed_aspects="all"
max number of nodes
nets : dict (key: n_nodes, value: list of networks)
Graphlets, as produced by graphlets
invs : dict (key: str(complete invariant), value: tuple(n_nodes, net_index in nets))
invs : dict (key: complete invariant, value: tuple(n_nodes, net_index in nets))
complete invariants of the graphlets, as produced by graphlet
auts : dd (key: (n_nodes, net_index, node), value: node)
automorphisms, as produced by automorphism_orbits
Expand Down Expand Up @@ -71,17 +71,21 @@ def orbit_counts_all(net, n, nets, invs, auts, orbit_list, allowed_aspects="all"
processed.add(node0)
for node_comb in node_sets:
sub_net = pymnet.subnet(net, node_comb, layers)
ci_sub = str(
pymnet.get_complete_invariant(sub_net, allowed_aspects=allowed_aspects)
)
ci_sub = pymnet.get_complete_invariant(
sub_net, allowed_aspects=allowed_aspects)
if ci_sub not in invs:
raise KeyError(
"The network contains a graphlet not found in the pre-constructed complete invariant dictionary (invs). This can be caused by invs creation not being compatible with the attributes of the network. For example, the network might not be fully interconnected."
"The network contains a graphlet not found in the "
"pre-constructed complete invariant dictionary (invs). "
"This can be caused by invs creation not being compatible "
"with the attributes of the network. For example, the "
"network might not be fully interconnected."
)
i = invs[ci_sub][0]
j = invs[ci_sub][1]
nw = nets[i][j]
iso = pymnet.get_isomorphism(sub_net, nw, allowed_aspects=allowed_aspects)
iso = pymnet.get_isomorphism(
sub_net, nw, allowed_aspects=allowed_aspects)
for node in node_comb:
if node in iso[0]:
orbits[node, (i, j, auts[i, j, iso[0][node]])] += 1
Expand Down Expand Up @@ -165,7 +169,7 @@ def orbit_counts(
dictionary where the counts will be stored
auts : dd (key: (n_nodes, net_index, node), value: node)
automorphism orbits
invs : dict (key: str(complete invariant), value: tuple(n_nodes, net_index in nets))
invs : dict (key: complete invariant, value: tuple(n_nodes, net_index in nets))
complete invariants of the graphlets
orbit_list : list of orbits
allowed_aspects : list, string
Expand All @@ -179,9 +183,8 @@ def orbit_counts(
node_sets = touching_orbit_nodes(node0, net, n)
for nodes_s in node_sets:
sub_net = pymnet.subnet(net, nodes_s, layers)
ci_sub = str(
pymnet.get_complete_invariant(sub_net, allowed_aspects=allowed_aspects)
)
ci_sub = pymnet.get_complete_invariant(
sub_net, allowed_aspects=allowed_aspects)
i = invs[ci_sub][1]
n_nodes = invs[ci_sub][0]
nw = nets[n_nodes][i]
Expand Down
96 changes: 47 additions & 49 deletions pymnet/graphlets/graphlets.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -29,10 +29,10 @@ def graphlets(n, layers, n_l=None, couplings=None, allowed_aspects="all"):
-------
nets : dict (key: n_nodes, value: list of MultiplexNetwork objects)
graphlets
invariants : dict (key: str(complete invariant), value: tuple(index in 'nets': n_nodes, index in the list of multiplex networks))
invariants : dict (key: complete invariant, value: tuple(index in 'nets': n_nodes, index in the list of multiplex networks))
complete invariants of the graphlets, the values can be used to match the graphlets in 'nets'
"""
if n_l == None:
if n_l is None:
n_l = len(layers)

nets = {}
Expand All @@ -42,17 +42,18 @@ def graphlets(n, layers, n_l=None, couplings=None, allowed_aspects="all"):
for net_layers in itertools.combinations(layers, n_l):
layer_combs = layer_combinations(net_layers)
for layer_comb in layer_combs:
net = pymnet.MultiplexNetwork(couplings=couplings, fullyInterconnected=True)
net = pymnet.MultiplexNetwork(
couplings=couplings, fullyInterconnected=True)
for layer in layer_comb:
net[0, 1, layer] = 1

for layer in net_layers:
net.add_layer(layer)

ci = pymnet.get_complete_invariant(net, allowed_aspects=allowed_aspects)
ci_s = str(ci)
if not ci_s in invariants:
invariants[ci_s] = (2, len(nets2))
ci = pymnet.get_complete_invariant(
net, allowed_aspects=allowed_aspects)
if ci not in invariants:
invariants[ci] = (2, len(nets2))
nets2.append(net)

nets[2] = nets2
Expand All @@ -77,13 +78,13 @@ def graphlets(n, layers, n_l=None, couplings=None, allowed_aspects="all"):

for layer in net_layers:
new_net.add_layer(layer)
# check if isomorphic with a previous graph & add only if not isomorphic
# check if isomorphic with a previous graph & add only
# if not isomorphic
ci = pymnet.get_complete_invariant(
new_net, allowed_aspects=allowed_aspects
)
ci_s = str(ci)
if not ci_s in invariants:
invariants[ci_s] = (i + 1, len(nets_i_1))
if ci not in invariants:
invariants[ci] = (i + 1, len(nets_i_1))
nets_i_1.append(new_net)

nets[i + 1] = nets_i_1
Expand All @@ -106,8 +107,9 @@ def automorphism_orbits(nets, allowed_aspects="all"):
-------
auts : dict (key: (n_nodes, net_index, node), value: node_orbit_index)
Automorphism orbits. 'n_nodes' is the key in 'nets'. 'net_index' is the
index in the list of networks. 'node' is the node name in the given network.
'node_orbit_index' gets the same value for nodes that are in the same orbit.
index in the list of networks. 'node' is the node name in the given
network. 'node_orbit_index' gets the same value for nodes that are in
the same orbit.
"""

auts = dd()
Expand Down Expand Up @@ -189,7 +191,7 @@ def orbit_equations(n, nets, auts, invs, allowed_aspects="all"):
graphlets, as returned by graphlets
auts : dd (key: (n_nodes, net_index, node), value: node)
automorphisms, as returned by automorphism_orbits
invs : dict (key: str(complete invariant), value: tuple(n_nodes, net_index in nets))
invs : dict (key: complete invariant, value: tuple(n_nodes, net_index in nets))
complete invariants of the graphlets, as returned by graphlets
allowed_aspects : list, string
the aspects that can be permutated when computing isomorphisms
Expand Down Expand Up @@ -248,10 +250,8 @@ def orbit_equations(n, nets, auts, invs, allowed_aspects="all"):

comb_nets += add_e_nets
for comb_net in comb_nets:
ci_comb = str(
pymnet.get_complete_invariant(
comb_net[0], allowed_aspects=allowed_aspects
)
ci_comb = pymnet.get_complete_invariant(
comb_net[0], allowed_aspects=allowed_aspects
)
iso_net = invs[ci_comb]
iso = pymnet.get_isomorphism(
Expand All @@ -269,7 +269,7 @@ def orbit_equations(n, nets, auts, invs, allowed_aspects="all"):
iso_net[1],
auts[iso_net[0], iso_net[1], node_o],
)
if not new_orbit in new_orbits:
if new_orbit not in new_orbits:
new_orbits.add(new_orbit)
new_nets[new_orbit] = comb_net

Expand Down Expand Up @@ -337,9 +337,8 @@ def subtrahend(orbit1, orbit2, nets, auts, invs, allowed_aspects="all"):
for nodes_s in partition:
nodes_g = set(nodes_s) | set([the_node])
sub_net = pymnet.subnet(net1, nodes_g, layers)
ci_sub = str(
pymnet.get_complete_invariant(sub_net, allowed_aspects=allowed_aspects)
)
ci_sub = pymnet.get_complete_invariant(
sub_net, allowed_aspects=allowed_aspects)
if ci_sub in invs and invs[ci_sub] == (n_nodes2, orbit2[1]):
iso = pymnet.get_isomorphism(
sub_net, net2, allowed_aspects=allowed_aspects
Expand Down Expand Up @@ -439,7 +438,8 @@ def combine_orbits(orbit1, orbit2, nets, allowed_aspects="all"):
new_net[e[0], e[1], e[2], e[3]] = e[4]

new_nets.append(new_net)
ci = str(pymnet.get_complete_invariant(new_net, allowed_aspects=allowed_aspects))
ci = pymnet.get_complete_invariant(
new_net, allowed_aspects=allowed_aspects)
new_invs.add(ci)

if allowed_aspects != [0]:
Expand All @@ -453,10 +453,9 @@ def combine_orbits(orbit1, orbit2, nets, allowed_aspects="all"):
if e[0] != e[1]:
new_net[e[0], e[1], e[2], e[3]] = e[4]

ci = str(
pymnet.get_complete_invariant(new_net, allowed_aspects=allowed_aspects)
)
if not ci in new_invs:
ci = pymnet.get_complete_invariant(
new_net, allowed_aspects=allowed_aspects)
if ci not in new_invs:
new_nets.append(new_net)
new_invs.add(ci)

Expand Down Expand Up @@ -532,10 +531,9 @@ def merge_nodes(both_orbit_nodes, net, allowed_aspects="all"):
if neighbor[0] != node2:
new_net[node1, neighbor[0], layer, neighbor[1]] = 1

ci = str(
pymnet.get_complete_invariant(new_net, allowed_aspects=allowed_aspects)
)
if not ci in new_invs:
ci = pymnet.get_complete_invariant(
new_net, allowed_aspects=allowed_aspects)
if ci not in new_invs:
new_nets.append(new_net)
new_nets_and_nodes.append((new_net, both_orbit_nodes + [node1]))
new_invs.add(ci)
Expand Down Expand Up @@ -711,25 +709,27 @@ def coefficient_help(
net2 = nets[orbit2[0]][orbit2[1]]
n_nodes1 = len(net1.slices[0])

for node_comb in itertools.combinations(nodes, n_nodes1 - len(both_orbit_nodes)):
node_combs = itertools.combinations(
nodes, n_nodes1 - len(both_orbit_nodes))
for node_comb in node_combs:
nodes_s2 = nodes_a - set(node_comb)
nodes_s1 = (nodes_a - nodes_s2) | set(both_orbit_nodes)
sub1 = pymnet.subnet(net, nodes_s1, layers)
sub2 = pymnet.subnet(net, nodes_s2, layers)
ci_sub1 = str(
pymnet.get_complete_invariant(sub1, allowed_aspects=allowed_aspects)
)
ci_sub2 = str(
pymnet.get_complete_invariant(sub2, allowed_aspects=allowed_aspects)
)
if not ci_sub1 in invs or not ci_sub2 in invs:
ci_sub1 = pymnet.get_complete_invariant(
sub1, allowed_aspects=allowed_aspects)
ci_sub2 = pymnet.get_complete_invariant(
sub2, allowed_aspects=allowed_aspects)
if ci_sub1 not in invs or ci_sub2 not in invs:
continue
if invs[ci_sub1] == (orbit1[0], orbit1[1]) and invs[ci_sub2] == (
orbit2[0],
orbit2[1],
):
iso1 = pymnet.get_isomorphism(sub1, net1, allowed_aspects=allowed_aspects)
iso2 = pymnet.get_isomorphism(sub2, net2, allowed_aspects=allowed_aspects)
iso1 = pymnet.get_isomorphism(sub1, net1,
allowed_aspects=allowed_aspects)
iso2 = pymnet.get_isomorphism(sub2, net2,
allowed_aspects=allowed_aspects)
if the_node in iso1[0]:
iso_node1 = iso1[0][the_node]
else:
Expand All @@ -754,7 +754,7 @@ def orbit_name(node, net, nets, invs, auts, allowed_aspects="all"):
finds the name of the orbit given node and net
"""

ci = str(pymnet.get_complete_invariant(net, allowed_aspects=allowed_aspects))
ci = pymnet.get_complete_invariant(net, allowed_aspects=allowed_aspects)
i, j = invs[ci]
net_i = nets[i][j]
iso = pymnet.get_isomorphism(
Expand All @@ -765,9 +765,8 @@ def orbit_name(node, net, nets, invs, auts, allowed_aspects="all"):
return (i, j, k)


def partitions(
s, r
): # Gareth Rees https://stackoverflow.com/questions/14559946/producing-all-groups-of-fixed-length-combinations
# Gareth Rees https://stackoverflow.com/questions/14559946/producing-all-groups-of-fixed-length-combinations
def partitions(s, r):
"""
Generate partitions of the iterable `s` into subsets of size `r`.
Expand All @@ -787,9 +786,8 @@ def partitions(
yield (first_subset,) + p


def partitions_with_remainder(
s, r
): # Gareth Rees https://stackoverflow.com/questions/14559946/producing-all-groups-of-fixed-length-combinations
# Gareth Rees https://stackoverflow.com/questions/14559946/producing-all-groups-of-fixed-length-combinations
def partitions_with_remainder(s, r):
"""
Generate partitions of the iterable `s` into subsets of size
`r` plus a remainder.
Expand All @@ -800,7 +798,7 @@ def partitions_with_remainder(
[((0, 1, 2),), ((1, 2), (0,)), ((0, 2), (1,)), ((0, 1), (2,))]
"""
s = set(s)
for n in xrange(len(s), -1, -r): # n is size of remainder.
for n in range(len(s), -1, -r): # n is size of remainder.
if n == 0:
for p in partitions(s, r):
yield p
Expand Down
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