def test_init_weights(self):
net = WTNetwork([[1]])
self.assertEqual(1, net.size)
self.assertTrue(np.array_equal([[1]], net.weights))
self.assertTrue(np.array_equal([0], net.thresholds))
self.assertIsNone(net.names)
net = WTNetwork([[1, 0], [0, 1]])
self.assertEqual(2, net.size)
self.assertTrue(np.array_equal([[1, 0], [0, 1]], net.weights))
self.assertTrue(np.array_equal([0, 0], net.thresholds))
self.assertIsNone(net.names)
net = WTNetwork([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
self.assertEqual(3, net.size)
self.assertTrue(np.array_equal(
[[1, 0, 0], [0, 1, 0], [0, 0, 1]], net.weights))
self.assertTrue(np.array_equal([0, 0, 0], net.thresholds))
self.assertIsNone(net.names)
net = WTNetwork(1)
self.assertEqual(1, net.size)
self.assertTrue(np.array_equal([[0]], net.weights))
self.assertTrue(np.array_equal([0], net.thresholds))
self.assertIsNone(net.names)
net = WTNetwork(2)
self.assertEqual(2, net.size)
self.assertTrue(np.array_equal([[0, 0], [0, 0]], net.weights))
self.assertTrue(np.array_equal([0, 0], net.thresholds))
self.assertIsNone(net.names)
def test_fission_yeast_numpy(self):
net = WTNetwork(
[[-1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, -1.0, -1.0, -1.0, 0.0, 0.0, 0.0, 0.0],
[-1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 1.0],
[-1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 1.0],
[0.0, 0.0, 0.0, 0.0, -1.0, 1.0, 0.0, 0.0, 0.0],
[0.0, 0.0, -1.0, -1.0, -1.0, 0.0, -1.0, 1.0, 0.0],
[0.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0],
[0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -1.0],
[0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.0]],
[0.0, -0.5, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0])
self.assertEqual(9, net.size)
self.assertEqual(512, len(list(net)))
init = np.asarray([1, 0, 1, 1, 0, 0, 1, 0, 0])
bio_sequence = np.asarray([[0, 0, 0, 0, 0, 0, 1, 0, 0],
[0, 1, 0, 0, 0, 0, 1, 0, 0],
[0, 1, 0, 0, 0, 0, 0, 1, 0],
[0, 1, 0, 0, 0, 1, 0, 1, 0],
[0, 1, 0, 0, 1, 1, 0, 1, 0],
[0, 0, 0, 0, 1, 0, 0, 1, 1],
[0, 0, 1, 1, 0, 0, 1, 0, 1],
[0, 0, 1, 1, 0, 0, 1, 0, 0]])
for expected in bio_sequence:
self.assertTrue(np.array_equal(expected, net.update(init)))
def test_different_matrix_without_trans(self):
net = WTNetwork([[1, -1], [0, 1]], [0.5, 0])
trans = list(map(net.decode, net.transitions))
for state in net:
with_trans = net.difference_matrix(state[:], transitions=trans)
without_trans = net.difference_matrix(state[:])
self.assertTrue(np.allclose(with_trans, without_trans, atol=1e-6))
def test_update_values_none(self):
net = WTNetwork([[1, 0], [-1, 1]], [0.5, 0.0],
theta=WTNetwork.positive_threshold)
xs = [0, 0]
self.assertEqual([0, 1], net.update(xs, values=None))
xs = [0, 0]
self.assertEqual([0, 1], net.update(xs, values={}))
def test_fission_yeast(self):
net = WTNetwork(
[[-1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, -1.0, -1.0, -1.0, 0.0, 0.0, 0.0, 0.0],
[-1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 1.0],
[-1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 1.0],
[0.0, 0.0, 0.0, 0.0, -1.0, 1.0, 0.0, 0.0, 0.0],
[0.0, 0.0, -1.0, -1.0, -1.0, 0.0, -1.0, 1.0, 0.0],
[0.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0],
[0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -1.0],
[0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.0]],
[0.0, -0.5, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0])
self.assertEqual(9, net.size)
self.assertEqual(512, len(list(net)))
init = [1, 0, 1, 1, 0, 0, 1, 0, 0]
bio_sequence = [[0, 0, 0, 0, 0, 0, 1, 0, 0],
[0, 1, 0, 0, 0, 0, 1, 0, 0],
[0, 1, 0, 0, 0, 0, 0, 1, 0],
[0, 1, 0, 0, 0, 1, 0, 1, 0],
[0, 1, 0, 0, 1, 1, 0, 1, 0],
[0, 0, 0, 0, 1, 0, 0, 1, 1],
[0, 0, 1, 1, 0, 0, 1, 0, 1],
[0, 0, 1, 1, 0, 0, 1, 0, 0]]
for expected in bio_sequence:
self.assertEqual(expected, net.update(init))
def test_state_space(self):
net = WTNetwork([[1]])
self.assertEqual(2, len(list(net)))
net = WTNetwork([[1, 0], [1, 1]])
self.assertEqual(4, len(list(net)))
net = WTNetwork([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
self.assertEqual(8, len(list(net)))
def test_average_difference_matrix_without_calc(self):
net = WTNetwork([[1, -1], [0, 1]], [0.5, 0])
states = list(net)
with_calc = net.average_sensitivity(states=deepcopy(states),
calc_trans=True)
without_calc = net.average_sensitivity(states=deepcopy(states),
calc_trans=False)
self.assertTrue(np.allclose(with_calc, without_calc, atol=1e-6))
def test_split_threshold(self):
xs = [0, 0, 0]
self.assertEqual(
[1, 0, 0], WTNetwork.split_threshold([1, -1, 0], xs))
self.assertEqual([1, 0, 0], xs)
xs = [1, 1, 1]
self.assertEqual(
[1, 0, 1], WTNetwork.split_threshold([1, -1, 0], xs))
self.assertEqual([1, 0, 1], xs)
def test_positive_threshold(self):
xs = [0, 0, 0]
self.assertEqual(
[1, 0, 1], WTNetwork.positive_threshold([1, -1, 0], xs))
self.assertEqual([1, 0, 1], xs)
xs = [1, 1, 1]
self.assertEqual(
[1, 0, 1], WTNetwork.positive_threshold([1, -1, 0], xs))
self.assertEqual([1, 0, 1], xs)
def test_update_values(self):
net = WTNetwork([[1, 0], [-1, 1]], [0.5, 0.0],
theta=WTNetwork.negative_threshold)
xs = [1, 1]
self.assertEqual([1, 1], net.update(xs, values={1: 1}))
net.theta = WTNetwork.positive_threshold
xs = [0, 0]
self.assertEqual([1, 1], net.update(xs, values={0: 1}))
def test_update_values_pin_clash(self):
net = WTNetwork([[1, 0], [-1, 1]], [0.5, 0.0],
theta=WTNetwork.positive_threshold)
with self.assertRaises(ValueError):
net.update([0, 0], pin=[0], values={0: 1})
with self.assertRaises(ValueError):
net.update([0, 0], pin=[1], values={1: 0})
with self.assertRaises(ValueError):
net.update([0, 0], pin=[1], values={0: 0, 1: 0})
with self.assertRaises(ValueError):
net.update([0, 0], pin=[1, 0], values={0: 0})
def test_init_thresholds(self):
with self.assertRaises(TypeError):
WTNetwork([[1]], theta=5)
net = WTNetwork([[1]])
self.assertEqual(WTNetwork.split_threshold, net.theta)
net = WTNetwork([[1]], theta=WTNetwork.negative_threshold)
self.assertEqual(WTNetwork.negative_threshold, net.theta)
net = WTNetwork([[1]], theta=WTNetwork.positive_threshold)
self.assertEqual(WTNetwork.positive_threshold, net.theta)
def test_neighbors_both_split_threshold(self):
net = WTNetwork(
[[-1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, -1.0, -1.0, -1.0, 0.0, 0.0, 0.0, 0.0],
[-1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 1.0],
[-1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 1.0],
[0.0, 0.0, 0.0, 0.0, -1.0, 1.0, 0.0, 0.0, 0.0],
[0.0, 0.0, -1.0, -1.0, -1.0, 0.0, -1.0, 1.0, 0.0],
[0.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0],
[0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -1.0],
[0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.0]],
[0.0, -0.5, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0])
self.assertEqual(net.neighbors(2), set([0, 1, 2, 5, 8]))
def test_neighbors_out_negative_threshold(self):
net = WTNetwork(
[[-1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, -1.0, -1.0, -1.0, 0.0, 0.0, 0.0, 0.0],
[-1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 1.0],
[-1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 1.0],
[0.0, 0.0, 0.0, 0.0, -1.0, 1.0, 0.0, 0.0, 0.0],
[0.0, 0.0, -1.0, -1.0, -1.0, 0.0, -1.0, 1.0, 0.0],
[0.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0],
[0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -1.0],
[0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.0]],
[0.0, -0.5, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0],
theta=WTNetwork.negative_threshold)
self.assertEqual(net.neighbors_out(2), set([1, 5]))
def test_update_pin_index_clash(self):
net = WTNetwork([[1, 0], [-1, 1]], [0.5, 0.0],
theta=WTNetwork.positive_threshold)
with self.assertRaises(ValueError):
net.update([0, 0], index=0, pin=[1])
with self.assertRaises(ValueError):
net.update([0, 0], index=1, pin=[1])
with self.assertRaises(ValueError):
net.update([0, 0], index=1, pin=[0, 1])
def test_transitions_wtnetwork(self):
net = WTNetwork(
weights=[[1, 0], [-1, 1]],
thresholds=[0.5, 0.0],
theta=WTNetwork.positive_threshold
)
self.assertEqual([2, 1, 2, 3], list(net.transitions))
def test_transitions_wtnetwork(self):
net = WTNetwork(weights=[[1, 0], [-1, 1]],
thresholds=[0.5, 0.0],
theta=WTNetwork.positive_threshold)
landscape = Landscape(net)
self.assertEqual(net, landscape.network)
self.assertEqual(2, landscape.size)
self.assertEqual([2, 1, 2, 3], list(landscape.transitions))
def test_transitions_wtnetwork(self):
"""
test ``transitions`` on WTNetworks
"""
net = WTNetwork(weights=[[1, 0], [-1, 1]],
thresholds=[0.5, 0.0],
theta=WTNetwork.positive_threshold)
got = transitions(net)
self.assertEqual([[0, 1], [1, 0], [0, 1], [1, 1]], got)
def test_transitions_wtnetwork_encoded(self):
"""
test ``transitions`` on WTNetworks; encoding the states
"""
net = WTNetwork(weights=[[1, 0], [-1, 1]],
thresholds=[0.5, 0.0],
theta=WTNetwork.positive_threshold)
got = transitions(net, encode=True)
self.assertEqual([2, 1, 2, 3], got)
def test_positive_threshold_scalar(self):
test = {
(1, 0): 1,
(0, 0): 1,
(-1, 0): 0,
(1, 1): 1,
(0, 1): 1,
(-1, 1): 0,
}
for x, s in test:
self.assertEqual(
test[(x, s)], WTNetwork.positive_threshold(x, s))
def test_neighbors_in_split_threshold(self):
net = WTNetwork(
[[-1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, -1.0, -1.0, -1.0, 0.0, 0.0, 0.0, 0.0],
[-1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 1.0],
[-1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 1.0],
[0.0, 0.0, 0.0, 0.0, -1.0, 1.0, 0.0, 0.0, 0.0],
[0.0, 0.0, -1.0, -1.0, -1.0, 0.0, -1.0, 1.0, 0.0],
[0.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0],
[0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -1.0],
[0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.0]],
[0.0, -0.5, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0])
self.assertEqual(net.neighbors_in(2), set([0, 1, 2, 5, 8]))
with self.assertRaises(IndexError):
self.assertEqual(net.neighbors_in(2.0))
with self.assertRaises(IndexError):
self.assertEqual(net.neighbors_in('2'))
def test_update_pin_invalid_indicies(self):
net = WTNetwork([[1, 0], [-1, 1]], [0.5, 0.0],
theta=WTNetwork.positive_threshold)
with self.assertRaises(IndexError):
net.update([0, 0], values={-3: 0})
with self.assertRaises(IndexError):
net.update([0, 0], values={2: 0})
def test_update_invalid_values(self):
net = WTNetwork([[1, 0], [-1, 1]], [0.5, 0.0],
theta=WTNetwork.positive_threshold)
with self.assertRaises(ValueError):
net.update([0, 0], values={0: 2})
with self.assertRaises(ValueError):
net.update([0, 0], values={0: -1})
def test_transitions_wtnetwork_pin(self):
net = WTNetwork(
weights=[[1, 0], [-1, 1]],
thresholds=[0.5, 0.0],
theta=WTNetwork.positive_threshold
)
net.landscape(pin=[1])
self.assertEqual([0, 1, 2, 3], list(net.transitions))
net.landscape(pin=[0])
self.assertEqual([2, 1, 2, 3], list(net.transitions))
net.landscape(pin=None)
self.assertEqual([2, 1, 2, 3], list(net.transitions))
def test_transitions_wtnetwork_values(self):
net = WTNetwork(
weights=[[1, 0], [-1, 1]],
thresholds=[0.5, 0.0],
theta=WTNetwork.positive_threshold
)
net.landscape(values={0: 1})
self.assertEqual([3, 1, 3, 3], list(net.transitions))
net.landscape(values={1: 0})
self.assertEqual([0, 1, 0, 1], list(net.transitions))
net.landscape(values={})
self.assertEqual([2, 1, 2, 3], list(net.transitions))
def test_trajectory_wtnetwork(self):
net = WTNetwork(weights=[[1, 0], [-1, 0]],
thresholds=[0.5, 0.0],
theta=WTNetwork.positive_threshold)
landscape = Landscape(net)
state = [0, 0]
got = landscape.trajectory(state)
self.assertEqual([0, 0], state)
self.assertEqual([[0, 0], [0, 1]], got)
got = landscape.trajectory(state, timesteps=3)
self.assertEqual([0, 0], state)
self.assertEqual([[0, 0], [0, 1], [0, 1], [0, 1]], got)
got = landscape.trajectory(state, encode=False)
self.assertEqual([0, 0], state)
self.assertEqual([[0, 0], [0, 1]], got)
got = landscape.trajectory(state, timesteps=3, encode=False)
self.assertEqual([0, 0], state)
self.assertEqual([[0, 0], [0, 1], [0, 1], [0, 1]], got)
got = landscape.trajectory(state, encode=True)
self.assertEqual([0, 0], state)
self.assertEqual([0, 2], got)
got = landscape.trajectory(state, timesteps=3, encode=True)
self.assertEqual([0, 0], state)
self.assertEqual([0, 2, 2, 2], got)
state = 0
got = landscape.trajectory(state)
self.assertEqual([0, 2], got)
got = landscape.trajectory(state, timesteps=3)
self.assertEqual([0, 2, 2, 2], got)
got = landscape.trajectory(state, encode=True)
self.assertEqual([0, 2], got)
got = landscape.trajectory(state, timesteps=3, encode=True)
self.assertEqual([0, 2, 2, 2], got)
got = landscape.trajectory(state, encode=False)
self.assertEqual([[0, 0], [0, 1]], got)
got = landscape.trajectory(state, timesteps=3, encode=False)
self.assertEqual([[0, 0], [0, 1], [0, 1], [0, 1]], got)
def test_update_pin(self):
net = WTNetwork([[1, 0], [-1, 1]], [0.5, 0.0])
net.theta = WTNetwork.negative_threshold
xs = [1, 1]
self.assertEqual([1, 0], net.update(xs, pin=[0]))
net.theta = WTNetwork.positive_threshold
xs = [0, 0]
self.assertEqual([0, 0], net.update(xs, pin=[1]))
def test_trajectory_wtnetwork(self):
"""
test ``trajectory`` on WTNetworks
"""
net = WTNetwork(weights=[[1, 0], [-1, 0]],
thresholds=[0.5, 0.0],
theta=WTNetwork.positive_threshold)
state = [0, 0]
got = trajectory(net, state)
self.assertEqual([0, 0], state)
self.assertEqual([[0, 0], [0, 1]], got)
got = trajectory(net, state, timesteps=3)
self.assertEqual([0, 0], state)
self.assertEqual([[0, 0], [0, 1], [0, 1], [0, 1]], got)
def test_trajectory_wtnetwork_encoded(self):
"""
test ``trajectory`` on WTNetworks; encoding the states
"""
net = WTNetwork(weights=[[1, 0], [-1, 0]],
thresholds=[0.5, 0.0],
theta=WTNetwork.positive_threshold)
state = [0, 0]
got = trajectory(net, state, encode=True)
self.assertEqual([0, 0], state)
self.assertEqual([0, 2], got)
got = trajectory(net, state, timesteps=3, encode=True)
self.assertEqual([0, 0], state)
self.assertEqual([0, 2, 2, 2], got)
def test_init_names(self):
with self.assertRaises(TypeError):
WTNetwork([[1]], names=5)
with self.assertRaises(ValueError):
WTNetwork([[1]], names=["A", "B"])
with self.assertRaises(ValueError):
WTNetwork([[1]], names=["A", "B"])
net = WTNetwork([[1]], names=["A"])
self.assertEqual(['A'], net.names)
net = WTNetwork([[1, 0], [1, 1]], names=['A', 'B'])
self.assertEqual(['A', 'B'], net.names)
net = WTNetwork([[1]], names="A")
self.assertEqual(['A'], net.names)
net = WTNetwork([[1, 0], [1, 1]], names="AB")
self.assertEqual(['A', 'B'], net.names)