def test_spike_neurongroup():
"""
Test dictionary representation of spiking neuron
"""
eqn = ''' dv/dt = (v_th - v) / tau : volt
v_th = 900 * mV :volt
v_rest = -70 * mV :volt
tau :second (constant)'''
tau = 10 * ms
size = 10
grp = NeuronGroup(size, eqn, threshold='v > v_th',
reset='v = v_rest',
refractory=2 * ms)
neuron_dict = collect_NeuronGroup(grp, get_local_namespace(0))
assert neuron_dict['N'] == size
assert neuron_dict['user_method'] is None
eqns = Equations(eqn)
assert neuron_dict['equations']['v']['type'] == DIFFERENTIAL_EQUATION
assert neuron_dict['equations']['v']['unit'] == volt
assert neuron_dict['equations']['v']['var_type'] == FLOAT
assert neuron_dict['equations']['v']['expr'] == eqns['v'].expr.code
assert neuron_dict['equations']['v_th']['type'] == SUBEXPRESSION
assert neuron_dict['equations']['v_th']['unit'] == volt
assert neuron_dict['equations']['v_th']['var_type'] == FLOAT
assert neuron_dict['equations']['v_th']['expr'] == eqns['v_th'].expr.code
assert neuron_dict['equations']['v_rest']['type'] == SUBEXPRESSION
assert neuron_dict['equations']['v_rest']['unit'] == volt
assert neuron_dict['equations']['v_rest']['var_type'] == FLOAT
assert neuron_dict['equations']['tau']['type'] == PARAMETER
assert neuron_dict['equations']['tau']['unit'] == second
assert neuron_dict['equations']['tau']['var_type'] == FLOAT
assert neuron_dict['equations']['tau']['flags'][0] == 'constant'
thresholder = grp.thresholder['spike']
neuron_events = neuron_dict['events']['spike']
assert neuron_events['threshold']['code'] == 'v > v_th'
assert neuron_events['threshold']['when'] == thresholder.when
assert neuron_events['threshold']['order'] == thresholder.order
assert neuron_events['threshold']['dt'] == grp.clock.dt
resetter = grp.resetter['spike']
assert neuron_events['reset']['code'] == 'v = v_rest'
assert neuron_events['reset']['when'] == resetter.when
assert neuron_events['reset']['order'] == resetter.order
assert neuron_events['reset']['dt'] == resetter.clock.dt
assert neuron_dict['events']['spike']['refractory'] == Quantity(2 * ms)
# example 2 with threshold but no reset
start_scope()
grp2 = NeuronGroup(size, '''dv/dt = (100 * mV - v) / tau_n : volt''',
threshold='v > 800 * mV',
method='euler')
tau_n = 10 * ms
neuron_dict2 = collect_NeuronGroup(grp2, get_local_namespace(0))
thresholder = grp2.thresholder['spike']
neuron_events = neuron_dict2['events']['spike']
assert neuron_events['threshold']['code'] == 'v > 800 * mV'
assert neuron_events['threshold']['when'] == thresholder.when
assert neuron_events['threshold']['order'] == thresholder.order
assert neuron_events['threshold']['dt'] == grp2.clock.dt
with pytest.raises(KeyError):
neuron_dict2['events']['spike']['reset']
neuron_dict2['events']['spike']['refractory']
Test the simulation class - runtime
'''
import pytest
import numpy as np
from numpy.testing.utils import assert_equal, assert_raises
from brian2 import (Equations, NeuronGroup, StateMonitor, Network, ms,
start_scope, mV)
from brian2.devices.device import Dummy
from brian2modelfitting.simulator import (initialize_neurons,
initialize_parameter, Simulator,
RuntimeSimulator)
from brian2.devices.device import reinit_devices
model = Equations('''
I = g*(v-E) : amp
v = 10*mvolt :volt
g : siemens (constant)
E : volt (constant)
''')
model2 = Equations(
'''
dv/dt = (gL*(EL-v)+gL*DeltaT*exp((v-VT)/DeltaT) + I)/C : volt
I = 20* nA :amp
gL: siemens (constant)
C: farad (constant)
''',
EL=-70 * mV,
VT=-50 * mV,
DeltaT=2 * mV,
)
def test_construction_errors():
'''
Test that the Equations constructor raises errors correctly
'''
# parse error
assert_raises(EquationError, lambda: Equations('dv/dt = -v / tau volt'))
# Only a single string or a list of SingleEquation objects is allowed
assert_raises(TypeError, lambda: Equations(None))
assert_raises(TypeError, lambda: Equations(42))
assert_raises(TypeError, lambda: Equations(['dv/dt = -v / tau : volt']))
# duplicate variable names
assert_raises(
EquationError, lambda: Equations('''dv/dt = -v / tau : volt
v = 2 * t/second * volt : volt'''
))
eqs = [
SingleEquation(DIFFERENTIAL_EQUATION,
'v',
volt.dim,
expr=Expression('-v / tau')),
SingleEquation(SUBEXPRESSION,
'v',
volt.dim,
expr=Expression('2 * t/second * volt'))
]
assert_raises(EquationError, lambda: Equations(eqs))
# illegal variable names
assert_raises(ValueError, lambda: Equations('ddt/dt = -dt / tau : volt'))
assert_raises(ValueError, lambda: Equations('dt/dt = -t / tau : volt'))
assert_raises(ValueError, lambda: Equations('dxi/dt = -xi / tau : volt'))
assert_raises(ValueError, lambda: Equations('for : volt'))
assert_raises((EquationError, ValueError),
lambda: Equations('d1a/dt = -1a / tau : volt'))
assert_raises(ValueError, lambda: Equations('d_x/dt = -_x / tau : volt'))
# xi in a subexpression
assert_raises(
EquationError, lambda: Equations('''dv/dt = -(v + I) / (5 * ms) : volt
I = second**-1*xi**-2*volt : volt'''))
# more than one xi
assert_raises(
EquationError,
lambda: Equations('''dv/dt = -v / tau + xi/tau**.5 : volt
dx/dt = -x / tau + 2*xi/tau : volt
tau : second'''))
# using not-allowed flags
eqs = Equations('dv/dt = -v / (5 * ms) : volt (flag)')
eqs.check_flags({DIFFERENTIAL_EQUATION: ['flag']}) # allow this flag
assert_raises(ValueError,
lambda: eqs.check_flags({DIFFERENTIAL_EQUATION: []}))
assert_raises(ValueError, lambda: eqs.check_flags({}))
assert_raises(ValueError,
lambda: eqs.check_flags({SUBEXPRESSION: ['flag']}))
assert_raises(
ValueError,
lambda: eqs.check_flags({DIFFERENTIAL_EQUATION: ['otherflag']}))
eqs = Equations('dv/dt = -v / (5 * ms) : volt (flag1, flag2)')
eqs.check_flags({DIFFERENTIAL_EQUATION: ['flag1',
'flag2']}) # allow both flags
# Don't allow the two flags in combination
assert_raises(
ValueError,
lambda: eqs.check_flags({DIFFERENTIAL_EQUATION: ['flag1', 'flag2']},
incompatible_flags=[('flag1', 'flag2')]))
eqs = Equations('''dv/dt = -v / (5 * ms) : volt (flag1)
dw/dt = -w / (5 * ms) : volt (flag2)''')
# They should be allowed when used independently
eqs.check_flags({DIFFERENTIAL_EQUATION: ['flag1', 'flag2']},
incompatible_flags=[('flag1', 'flag2')])
# Circular subexpression
assert_raises(
ValueError, lambda: Equations('''dv/dt = -(v + w) / (10 * ms) : 1
w = 2 * x : 1
x = 3 * w : 1'''))
# Boolean/integer differential equations
assert_raises(TypeError,
lambda: Equations('dv/dt = -v / (10*ms) : boolean'))
assert_raises(TypeError,
lambda: Equations('dv/dt = -v / (10*ms) : integer'))
from brian2modelfitting import (NevergradOptimizer, TraceFitter, MSEMetric,
OnlineTraceFitter, Simulator, Metric,
Optimizer, GammaFactor)
from brian2.devices.device import reinit_devices, reset_device
from brian2modelfitting.fitter import get_param_dic
E = 40*mV
input_traces = zeros((10, 5))*volt
for i in range(5):
input_traces[5:, i] = i*10*mV
output_traces = 10*nS*input_traces
model = Equations('''
I = g*(v-E) : amp
g : siemens (constant)
''')
strmodel = '''
I = g*(v-E) : amp
g : siemens (constant)
'''
constant_model = Equations('''
v = c + x: volt
c : volt (constant)''')
n_opt = NevergradOptimizer()
metric = MSEMetric()
