def test_poisson(self, duration=10 * un.s, rate=100 * un.Hz,
print_comparisons=False, dt=0.001,
simulators=['nest', 'neuron'], build_mode='force',
**kwargs): # @UnusedVariable @IgnorePep8
nineml_model = ninemlcatalog.load('input/Poisson', 'Poisson')
build_args = {'neuron': {'build_mode': build_mode,
'external_currents': ['iSyn']},
'nest': {'build_mode': build_mode}}
initial_states = {'t_next': 0.0 * un.ms}
for sim_name in simulators:
meta_class = cell_metaclasses[sim_name]
# Build celltype
celltype = meta_class(
nineml_model, name=nineml_model.name, **build_args[sim_name])
# Initialise simulator
if sim_name == 'neuron':
# Run NEURON simulation
import neuron
simulatorNEURON.clear(rng_seed=NEURON_RNG_SEED)
neuron.h.dt = dt
elif sim_name == 'nest':
# Run NEST simulation
# import nest
# nest.ResetKernel()
# nest.ResetNetwork()
# nest.SetKernelStatus({'resolution': dt})
simulatorNEST.clear(rng_seed=NEST_RNG_SEED, dt=dt)
else:
assert False
# Create and initialise cell
cell = celltype(rate=rate)
cell.record('spike_output')
cell.set_state(initial_states)
# Run simulation
if sim_name == 'neuron':
simulatorNEURON.run(duration.in_units(un.ms))
elif sim_name == 'nest':
simulatorNEST.run(duration.in_units(un.ms))
else:
assert False
# Get recording
spikes = cell.recording('spike_output')
# Calculate the rate of the modelled process
recorded_rate = pq.Quantity(
len(spikes) / (spikes.t_stop - spikes.t_start), 'Hz')
ref_rate = pq.Quantity(UnitHandlerNEST.to_pq_quantity(rate), 'Hz')
rate_difference = abs(ref_rate - recorded_rate)
if print_comparisons:
print "Reference rate: {}".format(ref_rate)
print "{} recorded rate: {}".format(sim_name, recorded_rate)
print "{} difference: {}".format(sim_name, rate_difference)
self.assertLess(
rate_difference, 1.75 * pq.Hz,
("Recorded rate of {} poisson generator ({}) did not match "
"desired ({}) within {}: difference {}".format(
sim_name, recorded_rate, ref_rate, 1.75 * pq.Hz,
recorded_rate - ref_rate)))
def simulate(self, duration, nest_rng_seed=12345, neuron_rng_seed=54321):
"""
Run and the simulation
"""
if self.simulate_nest:
nest.ResetKernel()
simulatorNEST.clear(rng_seed=nest_rng_seed, dt=self.dt)
simulation_controller.set_delays(self.min_delay, self.max_delay,
self.device_delay)
if self.simulate_neuron:
simulatorNEURON.clear(rng_seed=neuron_rng_seed)
neuron.h.dt = self.dt
for simulator in self.simulators:
self._create_9ML(self.nineml_model, self.properties, simulator)
if self.nest_ref is not None:
self._create_NEST(self.nest_ref)
if self.neuron_ref is not None:
self._create_NEURON(self.neuron_ref)
if self.simulate_nest:
simulatorNEST.run(duration)
if self.simulate_neuron:
simulatorNEURON.run(duration)
return self # return self so it can be chained with subsequent methods