def test_cylindrical_space(self):
s = space.Space(periodic_boundaries=((-1.0, 4.0), (-1.0, 4.0), (-1.0,
4.0)))
self.assertEqual(s.distances(self.A, self.B), sqrt(3))
self.assertEqual(s.distances(self.A, self.D), sqrt(4 + 4 + 1))
self.assertEqual(s.distances(self.C, self.D), sqrt(4 + 1 + 0))
self.assertArraysEqual(
s.distances(self.A, self.ABCD),
numpy.array([0.0, sqrt(3), sqrt(3),
sqrt(4 + 4 + 1)]))
self.assertArraysEqual(s.distances(self.A, self.ABCD),
s.distances(self.ABCD, self.A).T)
self.assertArraysEqual(
s.distances(self.C, self.ABCD),
numpy.array([sqrt(3),
sqrt(4 + 4 + 4), 0.0,
sqrt(4 + 1 + 0)]))
def create_local_inhibition(layers_dict):
"""
Creates local inhibitory connections from a neuron to its neighbors in an
area of a fixed distance. The latency of its neighboring neurons decreases
linearly with the distance from the spike from 15% to 5%, as described in
Masquelier's paper. Here we assumed that a weight of -10 inhibits the
neuron completely and took that as a starting point.
"""
for size, layers in layers_dict.items():
print('Create local inhibition for size', size)
for layer in layers:
sim.Projection(layer.population,
layer.population,
sim.DistanceDependentProbabilityConnector(
'd < 5', allow_self_connections=False),
sim.StaticSynapse(weight='.25 * d - 1.75'),
space=space.Space(axes='xy'))
def _connect(self):
method = self.sim.FixedProbabilityConnector(
self.parameters.connection_probability,
allow_self_connections=False,
safe=True,
rng=mozaik.pynn_rng)
self.proj = self.sim.Projection(
self.source.pop,
self.target.pop,
method,
synapse_type=self.init_synaptic_mechanisms(
weight=self.parameters.weights * self.weight_scaler,
delay=self.parameters.delay),
label=self.name,
space=space.Space(axes='xy'),
receptor_type=self.parameters.target_synapses)
def _connect(self):
method = self.sim.FixedNumberPreConnector(self.parameters.k,
allow_self_connections=False,
safe=True,
rng=mozaik.pynn_rng)
print("connectors fast FixedKConnector ", method)
print("connectors fast FixedKConnector ", self.source.pop)
print("connectors fast FixedKConnector ", self.target.pop)
self.proj = self.sim.Projection(
self.source.pop,
self.target.pop,
method,
synapse_type=self.init_synaptic_mechanisms(
weight=self.parameters.weights * self.weight_scaler,
delay=self.parameters.delay),
label=self.name,
space=space.Space(axes="xy"),
receptor_type=self.parameters.target_synapses)
def test_generator_for_infinite_space_with_3D_distances(self):
s = space.Space()
def f(i):
return self.ABCD[i]
def g(j):
return self.ABCD[j]
self.assertArraysEqual(
s.distance_generator(f, g)(0, np.arange(4)),
np.array([0.0, sqrt(3), sqrt(3), sqrt(29)]))
assert_array_equal(
np.fromfunction(s.distance_generator(f, g),
shape=(4, 4),
dtype=int),
np.array([(0.0, sqrt(3), sqrt(3), sqrt(29)),
(sqrt(3), 0.0, sqrt(12), sqrt(14)),
(sqrt(3), sqrt(12), 0.0, sqrt(50.0)),
(sqrt(29), sqrt(14), sqrt(50.0), 0.0)]))
def _connect(self):
# JAHACK, 0.1 as minimal delay should be replaced with the simulations time_step
if isinstance(self.target, SheetWithMagnificationFactor):
self.arborization_expression = lambda d: self.arborization_function(
self.target.dvf_2_dcs(d))
self.delay_expression = lambda d: self.delay_function(
self.target.dvf_2_dcs(d))
else:
self.arborization_expression = lambda d: self.arborization_function(
d)
self.delay_expression = lambda d: self.delay_function(d)
method = self.sim.DistanceDependentProbabilityConnector(
self.arborization_expression,
allow_self_connections=False,
weights=self.parameters.weights * self.weight_scaler,
delays=self.delay_expression,
space=space.Space(axes="xy"),
safe=True,
verbose=False,
n_connections=None,
rng=mozaik.pynn_rng)
print("connectors fast DistanceDependentProbabilisticArborization ",
method)
print("connectors fast DistanceDependentProbabilisticArborization ",
self.source.pop)
print("connectors fast DistanceDependentProbabilisticArborization ",
self.target.pop)
self.proj = self.sim.Projection(
self.source.pop,
self.target.pop,
method,
synapse_type=self.init_synaptic_mechanisms(),
label=self.name,
receptor_type=self.parameters.target_synapses)
v_random = np.random.rand(N_lgn) * (v_thresh - v_rest) + v_rest
lgn_neurons.initialize(v=v_random)
# Synapses, Connections and Projections
# Synapses
exc_synapse = simulator.StaticSynapse(weight=20.0, delay=0.1) # The synapses
inh_synapse = simulator.StaticSynapse(weight=10.0, delay=0.1) # The synapses
# Connectors
# Position dependent probability connector
DDPC = simulator.DistanceDependentProbabilityConnector
exc_connector = DDPC('d < 3')
inh_connector = DDPC('d < 7 and 3 < d')
# Projections
space = space.Space(axes=None,
periodic_boundaries=((0, N_retina), (0, N_retina), None))
exc_projection = simulator.Projection(retinal_neurons,
lgn_neurons,
connector=exc_connector,
synapse_type=exc_synapse,
receptor_type='excitatory',
space=space,
label='excitatory connections')
inh_projection = simulator.Projection(retinal_neurons,
lgn_neurons,
connector=inh_connector,
synapse_type=inh_synapse,
receptor_type='inhibitory',
space=space,
# Use CVode to calculate i_membrane_ for fast LFP calculation
cvode = h.CVode()
cvode.active(0)
# Get the second spatial derivative (the segment current) for the collateral
cvode.use_fast_imem(1)
# Set initial values for cell membrane voltages
v_init = -68
# Create random distribution for cell membrane noise current
r_init = RandomDistribution('uniform', (0, Pop_size))
# Create Spaces for STN Population
STN_Electrode_space = space.Space(axes='xy')
STN_space = space.RandomStructure(
boundary=space.Sphere(2000)) # Sphere with radius 2000um
# Generate poisson distributed spike time striatal input
striatal_spike_times = np.load(
'Striatal_Spike_Times.npy') # Load spike times from file
# Generate the cortico-basal ganglia neuron populations
Cortical_Pop = Population(
Pop_size,
Cortical_Neuron_Type(soma_bias_current_amp=0.245),
structure=STN_space,
label='Cortical Neurons') # Better than above (ibias=0.2575)
Interneuron_Pop = Population(Pop_size,
Interneuron_Type(bias_current_amp=0.070),
def test_really_simple0(self):
A = numpy.zeros((3, ))
B = numpy.zeros((3, 5))
D = connectors.DistanceMatrix(B, space.Space())
D.set_source(A)
assert_arrays_equal(D.as_array(), numpy.zeros((5, ), float))