def check_rates(self, rates, seconds):
n_neurons = 100
sim.setup(timestep=1.0)
inputs = {}
for rate in rates:
params = {"rate": rate}
input = sim.Population(n_neurons,
sim.SpikeSourcePoisson,
params,
label='inputSpikes_{}'.format(rate))
input.record("spikes")
inputs[rate] = input
sim.run(seconds * 1000)
for rate in rates:
self.check_spikes(inputs[rate], rate * seconds)
sim.end()
def test_get_v_view(self):
sim.setup(timestep=1.0)
pop = sim.Population(4, sim.IF_curr_exp(), label="a label")
pop.record("spikes")
pop._get_spikes = mock_spikes
pop._get_recorded_matrix = mock_v_all
get_simulator().get_current_time = mock_time
view = pop[1:3]
neo = view.get_data("v")
v = neo.segments[0].filter(name='v')[0].magnitude
(target, _, _) = mock_v_one_two("v")
assert v.shape == target.shape
assert numpy.array_equal(v, target)
sim.end()
def do_run(self):
sim.setup(timestep=1.0)
sim.set_number_of_neurons_per_core(sim.IF_curr_exp, neurons_per_core)
input_spikes = list(range(0, simtime - 100, 10))
expected_spikes = len(input_spikes)
input = sim.Population(
1, sim.SpikeSourceArray(spike_times=input_spikes), label="input")
pop_1 = sim.Population(n_neurons, sim.IF_curr_exp(), label="pop_1")
sim.Projection(input, pop_1, sim.AllToAllConnector(),
synapse_type=sim.StaticSynapse(weight=5, delay=1))
pop_1.record(["spikes", "v", "gsyn_exc"])
sim.run(simtime//4*3)
sim.run(simtime//4)
check_data(pop_1, expected_spikes, simtime)
sim.end()
def test_get_spikes_by_view(self):
sim.setup(timestep=1.0)
pop = sim.Population(4, sim.IF_curr_exp(), label="a label")
pop._get_spikes = mock_spikes
get_simulator().get_current_time = mock_time
view = pop[1:3]
view.record("spikes")
neo = view.get_data("spikes", gather=False)
spikes = neo_convertor.convert_spikes(neo)
target = trim_spikes(mock_spikes(), [1, 2])
assert numpy.array_equal(spikes, target)
spiketrains = neo.segments[0].spiketrains
assert 2 == len(spiketrains)
sim.end()
def do_run(nNeurons, timestep):
spike_list = {'spike_times': SPIKE_TIMES}
print(spike_list)
p.setup(timestep=timestep, min_delay=timestep, max_delay=timestep * 10)
pop = p.Population(nNeurons, p.SpikeSourceArray, spike_list, label='input')
pop.record("spikes")
p.run(200)
neo = pop.get_data("spikes")
p.end()
return neo
def test_get_spike_counts(self):
sim.setup(timestep=1.0)
pop = sim.Population(4, sim.IF_curr_exp(), label="a label")
pop.record("spikes")
pop._get_spikes = mock_spikes
get_simulator().get_current_time = mock_time
assert {0: 7, 1: 3, 2: 2, 3: 0} == pop.get_spike_counts()
view = pop[1:4]
assert {1: 3, 2: 2, 3: 0} == view.get_spike_counts()
assert 3 == pop.meanSpikeCount()
assert 5 / 3 == view.mean_spike_count()
sim.end()
def test_get_(self):
sim.setup(timestep=1.0)
pop = sim.Population(4, sim.IF_curr_exp(), label="a label")
pop._get_spikes = mock_spikes
pop._get_recorded_matrix = mock_v_all
get_simulator().get_current_time = mock_time
v = pop.spinnaker_get_data("v")
assert 400 == len(v)
v = pop.spinnaker_get_data(["v"])
assert 400 == len(v)
with pytest.raises(ConfigurationException):
pop.spinnaker_get_data(["v", "spikes"])
sim.end()
def testReset_add(self):
sim.setup(timestep=1.0)
sim.set_number_of_neurons_per_core(sim.IF_curr_exp, 1)
input = sim.Population(1,
sim.SpikeSourceArray(spike_times=[0]),
label="input")
pop_1 = sim.Population(2, sim.IF_curr_exp(), label="pop_1")
sim.Projection(input,
pop_1,
sim.AllToAllConnector(),
synapse_type=sim.StaticSynapse(weight=5, delay=1))
sim.run(10)
sim.Population(2, sim.IF_curr_exp(), label="pop_2")
with self.assertRaises(NotImplementedError):
sim.run(10)
def test_get_v_missing(self):
sim.setup(timestep=1.0)
pop = sim.Population(4, sim.IF_curr_exp(), label="a label")
pop._get_recorded_matrix = mock_v_one_two
get_simulator().get_current_time = mock_time
view = pop[0:3]
neo = view.get_data("v")
v = neo.segments[0].filter(name='v')[0].magnitude
(target, _, _) = mock_v_one_two("v")
assert numpy.array_equal(
[1, 2], neo.segments[0].filter(name='v')[0].channel_index.index)
assert v.shape == target.shape
assert numpy.array_equal(v, target)
sim.end()
def test_using_static_synapse_doubles(self):
sim.setup(timestep=1.0)
input = sim.Population(2, sim.SpikeSourceArray([0]), label="input")
pop = sim.Population(2, sim.IF_curr_exp(), label="pop")
as_list = [(0, 0), (1, 1)]
conn = sim.Projection(
input, pop, sim.FromListConnector(as_list),
sim.StaticSynapse(weight=[0.7, 0.3], delay=[3, 33]))
sim.run(1)
weights = conn.get(['weight', 'delay'], 'list')
target = [(0, 0, 0.7, 3), (1, 1, 0.3, 33)]
for i in range(2):
for j in range(2):
self.assertAlmostEqual(weights[i][j], target[i][j], places=3)
sim.end()
def test_run(self):
sim.setup()
sim.Population(3, sim.SpikeSourcePoisson, {"rate": 100})
p2 = sim.Population(3, sim.SpikeSourceArray,
{"spike_times": [[10.0], [20.0], [30.0]]})
p3 = sim.Population(4, sim.IF_cond_exp, {})
sim.Projection(
p2, p3,
sim.FromListConnector([(0, 0, 0.1, 1.0), (1, 1, 0.1, 1.0),
(2, 2, 0.1, 1.0)]))
sim.run(100.0)
sim.end()
def test_set_spikes_interval(self):
sim.setup(timestep=1)
if_curr = sim.Population(1, sim.IF_curr_exp())
recorder = if_curr._vertex.neuron_recorder
self.assertCountEqual([],
if_curr._recorder.get_all_recording_variables())
ssa = sim.Population(1, sim.SpikeSourceArray(spike_times=[0]))
ssp = sim.Population(2,
sim.SpikeSourcePoisson(rate=100.0),
additional_parameters={"seed": 1})
if_curr.record("spikes", sampling_interval=2)
ssa.record("spikes", sampling_interval=2)
ssp.record("spikes", sampling_interval=2)
self.assertCountEqual(["spikes"],
if_curr._recorder.get_all_recording_variables())
assert recorder.get_neuron_sampling_interval("spikes") == 2
def test_get_spikes_by_index(self):
sim.setup(timestep=1.0)
pop = sim.Population(4, sim.IF_curr_exp(), label="a label")
pop.record("spikes")
Recorder.get_spikes = mock_spikes
get_simulator().get_current_time = mock_time
neo = pop.get_data_by_indexes("spikes", [1, 2])
spikes = neo_convertor.convert_spikes(neo)
target = trim_spikes(mock_spikes(None), [1, 2])
assert numpy.array_equal(spikes, target)
spiketrains = neo.segments[0].spiketrains
assert 2 == len(spiketrains)
sim.end()
def do_run(split, seed=None):
p.setup(1.0)
if split:
p.set_number_of_neurons_per_core(p.SpikeSourcePoisson, 27)
p.set_number_of_neurons_per_core(p.IF_curr_exp, 22)
inp = p.Population(100,
p.SpikeSourcePoisson(rate=100, seed=seed),
label="input")
pop = p.Population(100, p.IF_curr_exp, {}, label="pop")
p.Projection(inp,
pop,
p.OneToOneConnector(),
synapse_type=p.StaticSynapse(weight=5))
pop.record("spikes")
inp.record("spikes")
p.run(100)
inp.set(rate=10)
# pop.set("cm", 0.25)
pop.set(tau_syn_E=1)
p.run(100)
pop_spikes1 = pop.spinnaker_get_data('spikes')
inp_spikes1 = inp.spinnaker_get_data('spikes')
p.reset()
inp.set(rate=0)
pop.set(i_offset=1.0)
vs = p.RandomDistribution("uniform", [-65.0, -55.0],
rng=NumpyRNG(seed=seed))
pop.initialize(v=vs)
p.run(100)
pop_spikes2 = pop.spinnaker_get_data('spikes')
inp_spikes2 = inp.spinnaker_get_data('spikes')
p.end()
return (pop_spikes1, inp_spikes1, pop_spikes2, inp_spikes2)
def do_run(self):
sim.setup(1.0)
pop = sim.Population(1, sim.IF_curr_exp, {}, label="pop")
pop.set(i_offset=1.0)
pop.record(["v"])
initial1 = -64.0
initial2 = -62.0
initial3 = -63.0
initial4 = -61.0
runtime = 10
pop.initialize(v=initial1)
sim.run(runtime)
sim.reset()
pop.initialize(v=initial2)
sim.run(runtime)
sim.reset()
pop.initialize(v=initial3)
pop.set(i_offset=2.0)
sim.run(runtime)
try:
pop.initialize(v=initial4) # this should throw an exception
except Exception:
pass
pop.set(i_offset=2.5)
sim.run(runtime)
v = pop.get_data('v')
sim.end()
# test values at start of each run() call above
self.assertEqual(v.segments[0].filter(name='v')[0][0], initial1)
self.assertEqual(v.segments[1].filter(name='v')[0][0], initial2)
self.assertEqual(v.segments[2].filter(name='v')[0][0], initial3)
self.assertNotEqual(v.segments[2].filter(name='v')[0][runtime],
initial4)
# test the lengths of each segment are correct
self.assertEqual(len(v.segments[0].filter(name='v')[0]), runtime)
self.assertEqual(len(v.segments[0].filter(name='v')[0]),
len(v.segments[1].filter(name='v')[0]))
self.assertEqual(len(v.segments[2].filter(name='v')[0]), 2 * runtime)
def do_run(self):
p.setup(timestep=1.0, min_delay=1.0, max_delay=1.0)
cell_params = {
'i_offset': .1,
'tau_refrac': 3.0,
'v_rest': -65.0,
'v_thresh': -51.0,
'tau_syn_E': 2.0,
'tau_syn_I': 5.0,
'v_reset': -70.0,
'e_rev_E': 0.,
'e_rev_I': -80.
}
# setup test population
if_pop = p.Population(1, p.IF_cond_exp, cell_params)
# setup spike sources
spike_times = [20., 40., 60.]
exc_pop = p.Population(1, p.SpikeSourceArray,
{'spike_times': spike_times})
inh_pop = p.Population(1, p.SpikeSourceArray,
{'spike_times': [120, 140, 160]})
# setup excitatory and inhibitory connections
listcon = p.FromListConnector([(0, 0, 0.05, 1.0)])
p.Projection(exc_pop, if_pop, listcon, receptor_type='excitatory')
p.Projection(inh_pop, if_pop, listcon, receptor_type='inhibitory')
# setup recorder
if_pop.record(["v"])
p.run(100)
p.reset()
if_pop.initialize(v=-65)
exc_pop.set(spike_times=[])
inh_pop.set(spike_times=spike_times)
p.run(100)
# read out voltage and plot
neo = if_pop.get_data("all")
p.end()
v = neo_convertor.convert_data(neo, "v", run=0)
v2 = neo_convertor.convert_data(neo, "v", run=1)
self.assertGreater(v[22][2], v[21][2])
self.assertGreater(v[42][2], v[41][2])
self.assertGreater(v[62][2], v[61][2])
self.assertLess(v2[22][2], v2[21][2])
self.assertLess(v2[42][2], v2[41][2])
self.assertLess(v2[62][2], v2[61][2])
def do_run(nNeurons):
p.setup(timestep=0.1, min_delay=1.0, max_delay=7.5)
p.set_number_of_neurons_per_core(p.IF_curr_exp, 100)
cell_params_lif = {'cm': 0.25, 'i_offset': 0.0, 'tau_m': 20.0,
'tau_refrac': 2.0, 'tau_syn_E': 6, 'tau_syn_I': 6,
'v_reset': -70.0, 'v_rest': -65.0, 'v_thresh': -55.4}
populations = list()
projections = list()
weight_to_spike = 12
injection_delay = 1
delay = 1
spikeArray = {'spike_times': [[0, 10, 20, 30]]}
populations.append(p.Population(1, p.SpikeSourceArray, spikeArray,
label='pop_0'))
populations.append(p.Population(nNeurons, p.IF_curr_exp, cell_params_lif,
label='pop_1'))
populations.append(p.Population(nNeurons, p.IF_curr_exp, cell_params_lif,
label='pop_2'))
connector = p.AllToAllConnector()
synapse_type = p.StaticSynapse(weight=weight_to_spike,
delay=injection_delay)
projections.append(p.Projection(populations[0], populations[1], connector,
synapse_type=synapse_type))
connector = p.OneToOneConnector()
synapse_type = p.StaticSynapse(weight=weight_to_spike, delay=delay)
projections.append(p.Projection(populations[1], populations[2], connector,
synapse_type=synapse_type))
populations[1].record("v")
populations[1].record("spikes")
p.run(100)
neo = populations[1].get_data(["v", "spikes"])
v = neo_convertor.convert_data(neo, name="v")
spikes = neo_convertor.convert_spikes(neo)
p.end()
return (v, spikes)
def structural_eliminate_to_empty():
p.setup(1.0)
stim = p.Population(9, p.SpikeSourceArray(range(10)), label="stim")
# These populations should experience elimination
pop = p.Population(9, p.IF_curr_exp(), label="pop")
# Make a full list
# Elimination with random selection (0 probability formation)
proj = p.Projection(
stim, pop, p.AllToAllConnector(),
p.StructuralMechanismStatic(
partner_selection=p.RandomSelection(),
formation=p.DistanceDependentFormation([3, 3], 0.0),
elimination=p.RandomByWeightElimination(4.0, 1.0, 1.0),
f_rew=1000,
initial_weight=4.0,
initial_delay=3.0,
s_max=9,
seed=0,
weight=0.0,
delay=1.0))
pop.record("rewiring")
p.run(1000)
# Get the final connections
conns = list(proj.get(["weight", "delay"], "list"))
rewiring = pop.get_data("rewiring")
formation_events = rewiring.segments[0].events[0]
elimination_events = rewiring.segments[0].events[1]
num_forms = len(formation_events.times)
num_elims = len(elimination_events.times)
first_elim = elimination_events.labels[0]
p.end()
# These should have no connections since all should be eliminated
assert (len(conns) == 0)
assert (num_elims == 81)
assert (num_forms == 0)
assert (first_elim == "7_5_elimination")
def test_write(self):
sim.setup(timestep=1.0)
pop = sim.Population(4, sim.IF_curr_exp(), label="a label")
pop._get_spikes = mock_spikes
pop._get_recorded_matrix = mock_v_all
get_simulator().get_current_time = mock_time
# Note gather=False will be ignored just testing it can be
pop.write_data("spikes.pkl", "spikes", gather=False)
try:
with open("spikes.pkl") as pkl:
neo = pickle.load(pkl)
spikes = neo_convertor.convert_spikes(neo)
assert numpy.array_equal(spikes, mock_spikes())
except UnicodeDecodeError:
raise SkipTest(
"https://github.com/NeuralEnsemble/python-neo/issues/529")
pop.printSpikes("spikes.pkl")
try:
with open("spikes.pkl") as pkl:
neo = pickle.load(pkl)
spikes = neo_convertor.convert_spikes(neo)
assert numpy.array_equal(spikes, mock_spikes())
except UnicodeDecodeError:
raise SkipTest(
"https://github.com/NeuralEnsemble/python-neo/issues/529")
(target, _, _) = mock_v_all("any")
pop.print_v("v.pkl")
with open("v.pkl") as pkl:
neo = pickle.load(pkl)
v = neo.segments[0].filter(name='v')[0].magnitude
assert v.shape == target.shape
assert numpy.array_equal(v, target)
pop.print_gsyn("gsyn.pkl")
with open("gsyn.pkl") as pkl:
neo = pickle.load(pkl)
exc = neo.segments[0].filter(name='gsyn_exc')[0].magnitude
assert numpy.array_equal(exc, target)
inh = neo.segments[0].filter(name='gsyn_inh')[0].magnitude
assert numpy.array_equal(inh, target)
sim.end()
def test_get_set(self):
sim.setup(timestep=1.0)
pop_1 = sim.Population(N_NEURONS, sim.IF_curr_exp(), label=LABEL)
cells = pop_1.all_cells
p_tau_m = pop_1.get("tau_m")
tau_m_3 = cells[3].tau_m
assert p_tau_m[3] == tau_m_3
cells[2].tau_m = 2
p_tau_m = pop_1.get("tau_m")
assert 2 == p_tau_m[2]
params = cells[1].get_parameters()
p_i_offset = pop_1.get("i_offset")
assert params["i_offset"][0] == p_i_offset[1]
cells[2].set_parameters(tau_m=3, i_offset=13)
params = cells[2].get_parameters()
assert 13 == params["i_offset"][0]
sim.end()
def test_cause_error(self):
with self.assertRaises(ConfigurationException):
sim.setup(timestep=1.0)
sim.set_number_of_neurons_per_core(sim.IF_curr_exp, 100)
pop_1 = sim.Population(1, sim.IF_curr_exp(), label="pop_1")
input = sim.Population(1,
sim.SpikeSourceArray(spike_times=[0]),
label="input")
sim.Projection(input,
pop_1,
sim.OneToOneConnector(),
synapse_type=sim.StaticSynapse(weight=5, delay=1))
simtime = 10
sim.run(simtime)
pop_1.get_data(variables=["v"])
def check_other_connect(self, connections, with_replacement):
sim.setup(1.0)
pop1 = sim.Population(SOURCES, sim.IF_curr_exp(), label="pop1")
pop2 = sim.Population(DESTINATIONS, sim.IF_curr_exp(), label="pop2")
synapse_type = sim.StaticSynapse(weight=5, delay=1)
projection = sim.Projection(pop1,
pop2,
sim.FixedNumberPostConnector(
connections,
with_replacement=with_replacement),
synapse_type=synapse_type)
sim.run(0)
self.check_weights(projection,
connections,
with_replacement,
allow_self_connections=True)
sim.end()
def test_check_connection_estimates(self):
# Test that the estimates for connections per neuron/vertex work
sim.setup(timestep=1.0)
n_neurons = 25
pop1 = sim.Population(n_neurons, sim.IF_curr_exp(), label="pop_1")
pop2 = sim.Population(n_neurons, sim.IF_curr_exp(), label="pop_2")
projection = sim.Projection(pop1,
pop2,
sim.FixedNumberPostConnector(n_neurons //
2),
synapse_type=sim.StaticSynapse(weight=5,
delay=1))
simtime = 10
sim.run(simtime)
weights = projection.get(["weight"], "list")
self.assertEqual(n_neurons * int(n_neurons / 2), len(weights))
sim.end()
def recording_1_element(self):
p.setup(timestep=1.0, min_delay=1.0, max_delay=144.0)
n_neurons = 200 # number of neurons in each population
p.set_number_of_neurons_per_core(p.IF_curr_exp, n_neurons / 2)
cell_params_lif = {
'cm': 0.25,
'i_offset': 0.0,
'tau_m': 20.0,
'tau_refrac': 2.0,
'tau_syn_E': 5.0,
'tau_syn_I': 5.0,
'v_reset': -70.0,
'v_rest': -65.0,
'v_thresh': -50.0
}
populations = list()
projections = list()
spike_array = {'spike_times': [[0]]}
populations.append(
p.Population(n_neurons,
p.IF_curr_exp,
cell_params_lif,
label='pop_1'))
populations.append(
p.Population(1,
p.SpikeSourceArray,
spike_array,
label='inputSpikes_1'))
projections.append(
p.Projection(populations[1], populations[0],
p.AllToAllConnector()))
populations[1].record("spikes")
p.run(5000)
spike_array_spikes = populations[1].spinnaker_get_data("spikes")
boxed_array = numpy.zeros(shape=(0, 2))
boxed_array = numpy.append(boxed_array, [[0, 0]], axis=0)
numpy.testing.assert_array_equal(spike_array_spikes, boxed_array)
p.end()
def check_self_connect(self, connections, with_replacement,
allow_self_connections):
sim.setup(1.0)
pop = sim.Population(DESTINATIONS, sim.IF_curr_exp(), label="pop")
synapse_type = sim.StaticSynapse(weight=5, delay=1)
projection = sim.Projection(
pop,
pop,
sim.FixedNumberPreConnector(
connections,
with_replacement=with_replacement,
allow_self_connections=allow_self_connections),
synapse_type=synapse_type)
sim.run(0)
self.check_weights(projection, connections, with_replacement,
allow_self_connections)
sim.end()
def run_set_run_reset_set(self):
sim.setup(1.0)
pop = sim.Population(1, sim.IF_curr_exp, {}, label="pop")
pop.set(i_offset=1.0)
pop.set(tau_syn_E=1)
pop.record(["v"])
sim.run(2)
pop.set(tau_syn_E=1)
sim.run(3)
v1 = pop.spinnaker_get_data('v')
self.check_from_65(v1)
sim.reset()
pop.set(tau_syn_E=1)
sim.run(5)
v2 = pop.spinnaker_get_data('v')
sim.end()
self.check_from_65(v2)
def test_run(self):
p.setup()
cell_params_lif = {
'cm': 0.25,
'i_offset': 0.0,
'tau_m': 20.0,
'tau_refrac': 2.0,
'tau_syn_E': 5.0,
'tau_syn_I': 5.0,
'v_reset': -70.0,
'v_rest': -65.0,
'v_thresh': -50.0
}
pop = p.Population(10, p.IF_curr_exp(**cell_params_lif), label='test')
p.run(100)
pop.set(cm=0.30)
def do_run(self):
sim.setup(timestep=1.0)
input_pop = sim.Population(1,
sim.SpikeSourceArray(range(
0, run_time, 100)),
label="input")
test_pop = sim.Population(1, MyFullNeuron(), label="my_full_neuron")
test_pop.record(['spikes', 'v'])
sim.Projection(input_pop,
test_pop,
sim.AllToAllConnector(),
receptor_type='excitatory',
synapse_type=sim.StaticSynapse(weight=2.0))
sim.run(run_time)
neo = test_pop.get_data('all')
sim.end()
self.check_results(neo, [501])
def do_run(nNeurons):
p.setup(timestep=1, min_delay=1, max_delay=15)
nNeurons = 1 # number of neurons in each population
neuron_parameters = {
'cm': 0.25,
'i_offset': 2,
'tau_m': 10.0,
'tau_refrac': 2.0,
'tau_syn_E': 0.5,
'tau_syn_I': 0.5,
'v_reset': -65.0,
'v_rest': -65.0,
'v_thresh': -50.0
}
populations = list()
populations.append(
p.Population(nNeurons, p.IF_curr_exp, neuron_parameters,
label='pop_1'))
populations.append(
p.Population(nNeurons, p.IF_curr_exp, neuron_parameters,
label='pop_2'))
populations[1].add_placement_constraint(x=1, y=0)
populations[0].record("v")
populations[0].record("gsyn_exc")
populations[0].record("spikes")
populations[1].record("v")
populations[1].record("gsyn_exc")
populations[1].record("spikes")
p.run(100)
v1 = populations[0].spinnaker_get_data("v")
gsyn1 = populations[0].spinnaker_get_data("gsyn_exc")
spikes1 = populations[0].spinnaker_get_data("spikes")
v2 = populations[1].spinnaker_get_data("v")
gsyn2 = populations[1].spinnaker_get_data("gsyn_exc")
spikes2 = populations[1].spinnaker_get_data("spikes")
p.end()
return (v1, gsyn1, v2, gsyn2, spikes1, spikes2)
def do_run():
CELL_PARAMS_LIF = {
'cm': 0.25,
'i_offset': 0.0,
'tau_m': 20.0,
'tau_refrac': 2.0,
'tau_syn_E': 5.0,
'tau_syn_I': 5.0,
'v_reset': -70.0,
'v_rest': -65.0,
'v_thresh': -50.0
}
p.setup()
p1 = p.Population(5, p.IF_curr_exp(**CELL_PARAMS_LIF), label='pop_1')
p1.set(cm=0.2)
