def attractors(net, size=None, encode=True):
if not is_network(net):
raise TypeError("net must be a network or a networkx DiGraph")
elif is_fixed_sized(net) and size is not None:
raise ValueError("fixed sized networks require size is None")
elif not is_fixed_sized(net) and size is None:
raise ValueError("variable sized networks require a size")
if size is None:
g = net.to_networkx_graph()
encoder = net.state_space()._unsafe_encode
else:
g = net.to_networkx_graph(size)
encoder = net.state_space(size)._unsafe_encode
modules = list(nx.strongly_connected_components(g))
dag = nx.condensation(g)
dag_list = list(nx.topological_sort(dag))
attractors = {}
for module_number in dag_list:
parents = greatest_predecessors(dag, module_number)
if len(parents) == 0:
nodes = modules[module_number]
attractors[module_number] = {
'eff_module': nodes,
'attractors': attractors_brute_force(net, size, subgraph=nodes)
}
else:
parent_modules = [attractors[p]['eff_module'] for p in parents]
parent_attractors = [attractors[p]['attractors'] for p in parents]
parent = direct_sum(parent_modules, parent_attractors)
subgraph = modules[module_number]
attractors[module_number] = {
'eff_module':
parent[0] | subgraph,
'attractors':
attractors_brute_force(net,
size,
subgraph=subgraph,
parent=parent)
}
outputs = list(
filter(lambda m: len(list(dag.successors(m))) == 0, dag_list))
parent_modules = [attractors[o]['eff_module'] for o in outputs]
parent_attractors = [attractors[o]['attractors'] for o in outputs]
_, attractors = direct_sum(parent_modules, parent_attractors)
if encode:
return list(
map(lambda attractor: list(map(encoder, attractor)), attractors))
else:
return attractors
def test_is_fixed_sized(self):
"""
Ensure that RewiredECA is of fixed size
"""
from neet.interfaces import is_fixed_sized
self.assertTrue(is_fixed_sized(RewiredECA))
self.assertTrue(is_fixed_sized(RewiredECA(23, size=3)))
self.assertTrue(is_fixed_sized(RewiredECA(
30, wiring=[[-1, 0, 1], [0, 1, 2], [1, 2, 3]])))
def attractors_brute_force(net,
size=None,
subgraph=None,
parent=None,
encode=False):
if not is_network(net):
raise TypeError("net must be a network or a networkx DiGraph")
elif is_fixed_sized(net) and size is not None:
raise ValueError("fixed sized networks require size is None")
elif not is_fixed_sized(net) and size is None:
raise ValueError("variable sized networks require a size")
if size is None:
decoder = net.state_space().decode
else:
decoder = net.state_space(size).decode
mapping, trans = transitions(net,
size=size,
subgraph=subgraph,
parent=parent)
collapsed = [None] * len(trans)
for s, t in trans:
try:
collapsed[s] = t
except IndexError:
raise
assert (all(map(lambda x: x is not None, collapsed)))
cycles = attrs(collapsed)
if mapping is None:
if encode:
attractors = cycles
else:
attractors = []
for attr in cycles:
attractors.append(list(map(decoder, attr)))
elif encode:
attractors = []
for attr in cycles:
attractors.append(list(map(lambda state: mapping[state], attr)))
else:
attractors = []
for attr in cycles:
attractors.append(
list(map(lambda state: decoder(mapping[state]), attr)))
return attractors
def transitions(net, size=None, subgraph=None, parent=None):
if not is_network(net):
raise TypeError("net is not a network")
if is_fixed_sized(net):
if size is not None:
raise ValueError("size must be None for fixed sized networks")
size = net.size
state_space = net.state_space()
else:
if size is None:
raise ValueError(
"size must not be None for variable sized networks")
state_space = net.state_space(size)
encoder = state_space._unsafe_encode
if subgraph is None:
backward = None
trans = [None] * state_space.volume
for i, state in enumerate(state_space):
net._unsafe_update(state)
trans[i] = (i, encoder(state))
else:
if parent is None:
pin = [n for n in range(state_space.ndim) if n not in subgraph]
trans = [None] * 2**len(subgraph)
space = subspace(subgraph, size)
else:
parent_nodes, parent_attractors = parent
pin = [
n for n in range(state_space.ndim)
if n not in (subgraph | parent_nodes)
]
trans = [None
] * (sum(map(len, parent_attractors)) * 2**len(subgraph))
space = subspace(subgraph, size, dynamic_values=parent)
forward = {}
backward = {}
k = 0
for i, state in enumerate(space):
source = encoder(state)
net._unsafe_update(state, pin=pin)
target = encoder(state)
if source not in forward:
forward[source] = k
backward[k] = source
k += 1
if target not in forward:
forward[target] = k
backward[k] = target
k += 1
trans[i] = (forward[source], forward[target])
return backward, trans
def test_is_fixed_sized(self):
net = self.IsNetwork()
self.assertFalse(is_fixed_sized(net))
self.assertFalse(is_fixed_sized(type(net)))
not_net = self.IsNotNetwork()
self.assertFalse(is_fixed_sized(not_net))
self.assertFalse(is_fixed_sized(type(not_net)))
net = self.FixedSizeNetwork()
self.assertTrue(is_fixed_sized(net))
self.assertTrue(is_fixed_sized(type(net)))
not_net = self.NotFixedSizedNetwork()
self.assertFalse(is_fixed_sized(not_net))
self.assertFalse(is_fixed_sized(type(not_net)))
def test_is_fixed_sized(self):
from neet.interfaces import is_fixed_sized
self.assertTrue(is_fixed_sized(bnet.WTNetwork))
self.assertTrue(is_fixed_sized(bnet.WTNetwork([[1]])))
def test_is_not_fixed_sized(self):
from neet.interfaces import is_fixed_sized
self.assertFalse(is_fixed_sized(ca.ECA))
self.assertFalse(is_fixed_sized(ca.ECA(23)))
def test_is_fixed_sized(self):
from neet.interfaces import is_fixed_sized
self.assertTrue(is_fixed_sized(LogicNetwork([([0], {'0'})])))