def test_landscape_data(self):
net = ECA(30, size=5)
data_before_setup = net.landscape_data
self.assertEqual(data_before_setup.__dict__, {})
data_after_setup = net.landscape().landscape_data
self.assertEqual(data_before_setup.__dict__, {})
self.assertEqual(
list(data_after_setup.__dict__.keys()), ['transitions'])
data_after_expound = net.expound().landscape_data
self.assertEqual(data_before_setup.__dict__, {})
self.assertEqual(set(data_after_setup.__dict__.keys()), set([
"transitions",
"basins",
"basin_sizes",
"attractors",
"attractor_lengths",
"in_degrees",
"heights",
"recurrence_times",
"basin_entropy"
]))
self.assertEqual(set(data_after_expound.__dict__.keys()), set([
"transitions",
"basins",
"basin_sizes",
"attractors",
"attractor_lengths",
"in_degrees",
"heights",
"recurrence_times",
"basin_entropy"
]))
def test_fail_init(self):
with self.assertRaises(ValueError):
ECA(-1, 5)
with self.assertRaises(ValueError):
ECA(256, 5)
with self.assertRaises(TypeError):
ECA([1, 1, 0, 1, 1, 0, 0, 1])
with self.assertRaises(TypeError):
ECA("30", 5)
with self.assertRaises(TypeError):
ECA(30, "5")
with self.assertRaises(ValueError):
ECA(30, -1)
with self.assertRaises(ValueError):
ECA(30, 0)
with self.assertRaises(TypeError):
ECA(30, 5, boundary=[1, 2])
with self.assertRaises(ValueError):
ECA(30, 5, boundary=(1, 0, 1))
with self.assertRaises(ValueError):
ECA(30, 5, boundary=(1, 2))
def test_attractors_eca(self):
networks = [(ECA(30, 2), 3), (ECA(30, 3), 1), (ECA(30, 4), 4),
(ECA(30, 5), 2), (ECA(30, 6), 3), (ECA(110, 2), 1),
(ECA(110, 3), 1), (ECA(110, 4), 3), (ECA(110, 5), 1),
(ECA(110, 6), 3)]
for rule, size in networks:
self.assertEqual(size, len(rule.attractors))
def test_to_networkx_metadata(self):
net = ECA(30, 3)
net.boundary = (1, 0)
nx_net = net.network_graph()
self.assertEqual(nx_net.graph['code'], 30)
self.assertEqual(nx_net.graph['boundary'], (1, 0))
def test_update_long_time_open(self):
eca = ECA(45, 14, (0, 1))
lattice = [1, 1, 0, 1, 0, 0, 1, 0, 1, 0, 0, 1, 0, 1]
expected = [1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 1]
if lattice in eca:
for n in range(1000):
eca._unsafe_update(lattice)
self.assertEqual(expected, lattice)
def test_update_values_pin_clash(self):
eca = ECA(30, 5)
with self.assertRaises(ValueError):
eca.update([0, 0, 0, 0, 0], pin=[0], values={0: 1})
with self.assertRaises(ValueError):
eca.update([0, 0, 0, 0, 0], pin=[1], values={1: 0})
with self.assertRaises(ValueError):
eca.update([0, 0, 0, 0, 0], pin=[1], values={0: 0, 1: 0})
with self.assertRaises(ValueError):
eca.update([0, 0, 0, 0, 0], pin=[1, 0], values={0: 0})
def test_timeseries_eca(self):
for size in [5, 7, 11]:
rule = ECA(30, size)
time = 10
series = rule.timeseries(time)
self.assertEqual((size, 2**size, time + 1), series.shape)
for index, state in enumerate(rule):
traj = rule.trajectory(state, timesteps=time)
for t, expect in enumerate(traj):
got = series[:, index, t]
self.assertTrue(np.array_equal(expect, got))
def test_reproduce_open_ecas(self):
"""
Ensure that RewiredECAs can reproduce open ECAs
"""
reca = RewiredECA(30, boundary=(1, 0), size=7)
eca = ECA(30, size=7, boundary=(1, 0))
state = [0, 0, 0, 1, 0, 0, 0]
for _ in range(10):
expect = eca.update(np.copy(state))
got = reca.update(state)
self.assertTrue(np.array_equal(expect, got))
def test_basins_eca(self):
networks = [(ECA(30, 2), 3), (ECA(30, 3), 1), (ECA(30, 4), 4),
(ECA(30, 5), 2), (ECA(30, 6), 3), (ECA(110, 2), 1),
(ECA(110, 3), 1), (ECA(110, 4), 3), (ECA(110, 5), 1),
(ECA(110, 6), 3)]
for rule, size in networks:
self.assertEqual(rule.volume, len(rule.basins))
self.assertEqual(size, 1 + np.max(rule.basins))
unique = list(set(rule.basins))
unique.sort()
self.assertEqual(list(range(size)), unique)
def test_basin_entropy_eca(self):
networks = [(ECA(30, 2), 1.500000),
(ECA(30, 3), 0.000000),
(ECA(30, 4), 1.186278),
(ECA(30, 5), 0.337290),
(ECA(30, 6), 0.231872),
(ECA(110, 2), 0.000000),
(ECA(110, 3), 0.000000),
(ECA(110, 4), 1.561278),
(ECA(110, 5), 0.000000),
(ECA(110, 6), 1.469012)]
for net, entropy in networks:
self.assertAlmostEqual(entropy, net.basin_entropy, places=6)
def test_update_pin_index_clash(self):
eca = ECA(30, 2)
with self.assertRaises(ValueError):
eca.update([0, 0], index=0, pin=[1])
with self.assertRaises(ValueError):
eca.update([0, 0], index=1, pin=[1])
with self.assertRaises(ValueError):
eca.update([0, 0], index=1, pin=[0, 1])
def test_update_values_index_clash(self):
eca = ECA(30, 5)
with self.assertRaises(ValueError):
eca.update([0, 0, 0, 0, 0], index=0, values={0: 1})
with self.assertRaises(ValueError):
eca.update([0, 0, 0, 0, 0], index=1, values={1: 0})
with self.assertRaises(ValueError):
eca.update([0, 0, 0, 0, 0], index=1, values={0: 0, 1: 0})
def test_expound(self):
net = ECA(30, size=5)
before = net.landscape_data
after = net.expound().landscape_data
self.assertEqual(before.__dict__, {})
self.assertEqual(set(after.__dict__.keys()), set([
"transitions",
"basins",
"basin_sizes",
"attractors",
"attractor_lengths",
"in_degrees",
"heights",
"recurrence_times",
"basin_entropy"
]))
def test_transitions_eca(self):
net = ECA(30, 1)
self.assertEqual([0, 0], list(net.transitions))
net.size = 2
self.assertEqual([0, 1, 2, 0], list(net.transitions))
net.size = 3
self.assertEqual([0, 7, 7, 1, 7, 4, 2, 0], list(net.transitions))
net.size = 10
trans = net.transitions
self.assertEqual(1024, len(trans))
self.assertEqual([0, 515, 7, 517, 14, 525, 11,
521, 28, 543], list(trans[:10]))
self.assertEqual([18, 16, 13, 14, 10, 8, 7, 4, 2, 0],
list(trans[-10:]))
def test_transitions_eca_index(self):
net = ECA(30, 3)
net.landscape(index=1)
self.assertEqual([0, 3, 2, 1, 6, 5, 6, 5], list(net.transitions))
net.landscape(index=0)
self.assertEqual([0, 1, 3, 3, 5, 4, 6, 6], list(net.transitions))
net.landscape(index=None)
self.assertEqual([0, 7, 7, 1, 7, 4, 2, 0], list(net.transitions))
def test_transitions_eca_values(self):
net = ECA(30, 3)
net.landscape(values={0: 1})
self.assertEqual([1, 7, 7, 1, 7, 5, 3, 1], list(net.transitions))
net.landscape(values={1: 0})
self.assertEqual([0, 5, 5, 1, 5, 4, 0, 0], list(net.transitions))
net.landscape(values={})
self.assertEqual([0, 7, 7, 1, 7, 4, 2, 0], list(net.transitions))
def test_transitions_eca_pin(self):
net = ECA(30, 3)
net.landscape(pin=[1])
self.assertEqual([0, 5, 7, 3, 5, 4, 2, 2], list(net.transitions))
net.landscape(pin=[0])
self.assertEqual([0, 7, 6, 1, 6, 5, 2, 1], list(net.transitions))
net.landscape(pin=None)
self.assertEqual([0, 7, 7, 1, 7, 4, 2, 0], list(net.transitions))
def test_init(self):
for code in range(256):
for size in range(1, 5):
for left in range(2):
for right in range(2):
eca = ECA(code, size, (left, right))
self.assertEqual(code, eca.code)
self.assertEqual(size, eca.size)
self.assertEqual((left, right), eca.boundary)
def test_update_index_numpy(self):
eca = ECA(30, 5, (1, 1))
lattice = np.asarray([0, 0, 0, 0, 0])
eca.update(lattice, index=0)
self.assertTrue(np.array_equal([1, 0, 0, 0, 0], lattice))
lattice = np.asarray([0, 0, 0, 0, 0])
eca.update(lattice, index=1)
self.assertTrue(np.array_equal([0, 0, 0, 0, 0], lattice))
lattice = np.asarray([0, 0, 1, 0, 0])
eca.update(lattice, index=1)
self.assertTrue(np.array_equal([0, 1, 1, 0, 0], lattice))
def test_update_index(self):
eca = ECA(30, 5, (1, 1))
lattice = [0, 0, 0, 0, 0]
eca.update(lattice, index=0)
self.assertEqual([1, 0, 0, 0, 0], lattice)
lattice = [0, 0, 0, 0, 0]
eca.update(lattice, index=1)
self.assertEqual([0, 0, 0, 0, 0], lattice)
lattice = [0, 0, 1, 0, 0]
eca.update(lattice, index=1)
self.assertEqual([0, 1, 1, 0, 0], lattice)
def test_update_index_error(self):
eca = ECA(30, 2)
with self.assertRaises(IndexError):
eca.update([0, 0], index=2)
with self.assertRaises(IndexError):
eca.update([0, 0], index=-1)
def test_trajectory_too_short(self):
net = ECA(30, 3)
with self.assertRaises(ValueError):
net.trajectory([0, 0, 0], timesteps=-1)
with self.assertRaises(ValueError):
net.trajectory([0, 0, 0], timesteps=0)
def test_update_values(self):
eca = ECA(30, 5)
xs = [0, 0, 1, 0, 0]
self.assertEqual([0, 1, 0, 1, 0], eca.update(xs, values={2: 0}))
self.assertEqual([1, 0, 0, 0, 1], eca.update(xs, values={1: 0, 3: 0}))
self.assertEqual([0, 1, 0, 1, 0], eca.update(xs, values={-1: 0}))
eca.boundary = (1, 1)
xs = [0, 0, 0, 0, 0]
self.assertEqual([1, 0, 1, 0, 1], eca.update(xs, values={2: 1}))
def test_timeseries_too_short(self):
net = ECA(30, 3)
with self.assertRaises(ValueError):
net.timeseries(-1)
with self.assertRaises(ValueError):
net.timeseries(0)
def test_update_pin(self):
eca = ECA(30, 5)
xs = [0, 0, 1, 0, 0]
self.assertEqual([0, 0, 1, 1, 0], eca.update(xs, pin=[1]))
self.assertEqual([0, 0, 1, 0, 1], eca.update(xs, pin=[1]))
self.assertEqual([1, 0, 1, 0, 1], eca.update(xs, pin=[1]))
eca.boundary = (1, 1)
xs = [0, 0, 0, 0, 0]
self.assertEqual([1, 0, 0, 0, 0], eca.update(xs, pin=[-1]))
self.assertEqual([1, 1, 0, 0, 0], eca.update(xs, pin=[0, -1]))
def test_invalid_boundary(self):
eca = ECA(30, 5)
eca.boundary = (0, 0)
eca.boundary = None
with self.assertRaises(ValueError):
eca.boundary = (1, 1, 1)
with self.assertRaises(ValueError):
eca.boundary = (1, 2)
with self.assertRaises(TypeError):
eca.boundary = 1
with self.assertRaises(TypeError):
eca.boundary = [0, 1]
def test_attractor_lengths(self):
for code in [30, 110, 21, 43]:
for size in range(2, 7):
net = ECA(code, size)
lengths = list(map(len, net.attractors))
net.clear_landscape()
self.assertEqual(lengths, list(net.attractor_lengths))
for net in [s_pombe, s_cerevisiae, c_elegans]:
lengths = list(map(len, net.attractors))
net.clear_landscape()
self.assertEqual(lengths, list(net.attractor_lengths))
def test_invalid_size(self):
eca = ECA(30, 5)
eca.size = 8
with self.assertRaises(ValueError):
eca.size = -1
with self.assertRaises(ValueError):
eca.size = 0
with self.assertRaises(TypeError):
eca.size = "5"
def test_invalid_code(self):
eca = ECA(30, 5)
eca.code = 45
with self.assertRaises(ValueError):
eca.code = -1
with self.assertRaises(ValueError):
eca.code = 256
with self.assertRaises(TypeError):
eca.code = "30"
def test_in_degree(self):
for code in [30, 110, 21, 43]:
for size in range(2, 7):
net = ECA(code, size)
in_degrees = np.empty(net.volume, dtype=np.int)
for i in range(net.volume):
in_degrees[i] = np.count_nonzero(
net.transitions == i)
net.clear_landscape()
self.assertEqual(list(in_degrees), list(net.in_degrees))
for net in [s_pombe, s_cerevisiae, c_elegans]:
in_degrees = np.empty(net.volume, dtype=np.int)
for i in range(net.volume):
in_degrees[i] = np.count_nonzero(net.transitions == i)
net.clear_landscape()
self.assertEqual(list(in_degrees), list(net.in_degrees))
