def test1(self):
def func(m, t, V):
alpha = 0.1 * (V + 40) / (1 - np.exp(-(V + 40) / 10))
beta = 4.0 * np.exp(-(V + 65) / 18)
dmdt = alpha * (1 - m) - beta * m
return dmdt
odeint(method='exponential_euler', show_code=True, f=func)
def test6(self):
with pytest.raises(errors.CodeError):
def func(math, t, exp):
alpha = 0.1 * (exp + 40) / (1 - np.exp(-(exp + 40) / 10))
beta = 4.0 * np.exp(-(exp + 65) / 18)
dmdt = alpha * (1 - math) - beta * math
return dmdt
odeint(method='exponential_euler', show_code=True, f=func)
def test4(self):
with pytest.raises(errors.CodeError):
def func(m, t, m_new):
alpha = 0.1 * (m_new + 40) / (1 - np.exp(-(m_new + 40) / 10))
beta = 4.0 * np.exp(-(m_new + 65) / 18)
dmdt = alpha * (1 - m) - beta * m
return dmdt
odeint(method='exponential_euler', show_code=True, f=func)
def test2(self):
with pytest.raises(errors.CodeError):
def func(f, t, V):
alpha = 0.1 * (V + 40) / (1 - np.exp(-(V + 40) / 10))
beta = 4.0 * np.exp(-(V + 65) / 18)
dmdt = alpha * (1 - f) - beta * f
return dmdt
odeint(method='exponential_euler', show_code=True, f=func)
def __init__(self,
pre,
post,
conn,
g_max=1.,
delay=0.,
tau=8.0,
method='exp_auto',
name=None):
super(ExpCUBA, self).__init__(pre=pre, post=post, conn=conn, name=name)
self.check_pre_attrs('spike')
self.check_post_attrs('input', 'V')
# parameters
self.tau = tau
self.delay = delay
self.g_max = g_max
# connection
assert self.conn is not None
self.pre2post = self.conn.require('pre2post')
# variables
self.g = bm.Variable(bm.zeros(self.post.num))
self.pre_spike = ConstantDelay(self.pre.num,
delay=delay,
dtype=pre.spike.dtype)
# function
self.integral = odeint(lambda g, t: -g / self.tau, method=method)
def __init__(self, size, V_rest=-65., V_reset=-68., V_th=-30., V_T=-59.9, delta_T=3.48, a=1.,
b=1., tau=10., tau_w=30., R=1., method='exp_auto', name=None):
super(AdExIF, self).__init__(size=size, name=name)
# parameters
self.V_rest = V_rest
self.V_reset = V_reset
self.V_th = V_th
self.V_T = V_T
self.delta_T = delta_T
self.a = a
self.b = b
self.tau = tau
self.tau_w = tau_w
self.R = R
# variables
self.w = bm.Variable(bm.zeros(self.num))
self.refractory = bm.Variable(bm.zeros(self.num, dtype=bool))
self.V = bm.Variable(bm.zeros(self.num))
self.input = bm.Variable(bm.zeros(self.num))
self.spike = bm.Variable(bm.zeros(self.num, dtype=bool))
self.t_last_spike = bm.Variable(bm.ones(self.num) * -1e7)
# functions
self.integral = odeint(method=method, f=JointEq([self.dV, self.dw]))
def test_euler(self):
print('Test Euler method:')
print()
odeint(method='euler', show_code=True, f=lambda v, t, p: t)
with pytest.raises(errors.CodeError):
odeint(method='euler', show_code=True, f=lambda f, t, dt: t)
with pytest.raises(errors.CodeError):
odeint(method='euler', show_code=True, f=lambda v, t, dt: t)
with pytest.raises(errors.CodeError):
odeint(method='euler', show_code=True, f=lambda v, t, v_new: t)
with pytest.raises(errors.CodeError):
odeint(method='euler', show_code=True, f=lambda v, t, dv_k1: t)
print('-' * 40)
def __init__(self, size, V_rest=0., V_reset=-5., V_th=20., tau=10.,
tau_ref=1., method='exp_auto', name=None):
# initialization
super(LIF, self).__init__(size=size, name=name)
# parameters
self.V_rest = V_rest
self.V_reset = V_reset
self.V_th = V_th
self.tau = tau
self.tau_ref = tau_ref
# variables
self.V = bm.Variable(bm.zeros(self.num))
self.input = bm.Variable(bm.zeros(self.num))
self.spike = bm.Variable(bm.zeros(self.num, dtype=bool))
self.t_last_spike = bm.Variable(bm.ones(self.num) * -1e7)
self.refractory = bm.Variable(bm.zeros(self.num, dtype=bool))
# integral
self.int_V = odeint(method=method, f=self.dV)
def __init__(self,
pre,
post,
conn,
delay=0.,
g_max=0.42,
E=0.,
alpha=0.98,
beta=0.18,
T=0.5,
T_duration=0.5,
method='exp_auto',
**kwargs):
super(AMPA, self).__init__(pre=pre, post=post, conn=conn, **kwargs)
self.check_pre_attrs('spike')
self.check_post_attrs('input', 'V')
# parameters
self.delay = delay
self.g_max = g_max
self.E = E
self.alpha = alpha
self.beta = beta
self.T = T
self.T_duration = T_duration
# connection
assert self.conn is not None
self.pre_ids, self.post_ids = self.conn.require('pre_ids', 'post_ids')
# variables
self.g = bm.Variable(bm.zeros(self.num))
self.pre_spike = ConstantDelay(self.pre.num,
delay,
dtype=pre.spike.dtype)
self.spike_arrival_time = bm.Variable(bm.ones(self.pre.num) * -1e7)
# functions
self.integral = odeint(method=method, f=self.derivative)
def __init__(self, size, a=0.02, b=0.20, c=-65., d=8., tau_ref=0.,
V_th=30., method='exp_auto', name=None):
# initialization
super(Izhikevich, self).__init__(size=size, name=name)
# params
self.a = a
self.b = b
self.c = c
self.d = d
self.V_th = V_th
self.tau_ref = tau_ref
# variables
self.u = bm.Variable(bm.ones(self.num))
self.refractory = bm.Variable(bm.zeros(self.num, dtype=bool))
self.V = bm.Variable(bm.zeros(self.num))
self.input = bm.Variable(bm.zeros(self.num))
self.spike = bm.Variable(bm.zeros(self.num, dtype=bool))
self.t_last_spike = bm.Variable(bm.ones(self.num) * -1e7)
# functions
self.integral = odeint(method=method, f=JointEq([self.dV, self.du]))
def test_rkf45(self):
method = 'rkf45'
for adaptive in [True, False]:
print(f'Test {"adaptive" if adaptive else ""} {method} method:')
print()
ode.odeint(method=method, show_code=True, adaptive=adaptive, f=lambda v, t, p: t)
with pytest.raises(errors.CodeError):
ode.odeint(method=method, show_code=True, adaptive=adaptive, f=lambda f, t, dt: t)
with pytest.raises(errors.CodeError):
ode.odeint(method=method, show_code=True, adaptive=adaptive, f=lambda v, t, dt: t)
with pytest.raises(errors.CodeError):
ode.odeint(method=method, show_code=True, adaptive=adaptive, f=lambda v, t, v_new: t)
with pytest.raises(errors.CodeError):
ode.odeint(method=method, show_code=True, adaptive=adaptive, f=lambda v, t, dv_k1: t)
with pytest.raises(errors.CodeError):
ode.odeint(method=method, show_code=True, adaptive=adaptive, f=lambda v, t, dv_k2: t)
with pytest.raises(errors.CodeError):
ode.odeint(method=method, show_code=True, adaptive=adaptive, f=lambda v, t, k2_v_arg: t)
with pytest.raises(errors.CodeError):
ode.odeint(method=method, show_code=True, adaptive=adaptive, f=lambda v, t, k2_t_arg: t)
with pytest.raises(errors.CodeError):
ode.odeint(method=method, show_code=True, adaptive=adaptive, f=lambda v, t, k3_v_arg: t)
with pytest.raises(errors.CodeError):
ode.odeint(method=method, show_code=True, adaptive=adaptive, f=lambda v, t, k3_t_arg: t)
with pytest.raises(errors.CodeError):
ode.odeint(method=method, show_code=True, adaptive=adaptive, f=lambda v, t, k4_v_arg: t)
with pytest.raises(errors.CodeError):
ode.odeint(method=method, show_code=True, adaptive=adaptive, f=lambda v, t, k4_t_arg: t)
if adaptive:
with pytest.raises(errors.CodeError):
ode.odeint(method=method, show_code=True, adaptive=adaptive, f=lambda v, t, error: t)
with pytest.raises(errors.CodeError):
ode.odeint(method=method, show_code=True, adaptive=adaptive, f=lambda v, t, v_te: t)
with pytest.raises(errors.CodeError):
ode.odeint(method=method, show_code=True, adaptive=adaptive, f=lambda v, t, dt_new: t)
print('-' * 40)
def test_order3_rk(self):
for method in ['rk3', 'heun3', 'ralston3', 'ssprk3']:
print(f'Test {method} method:')
print()
odeint(method=method, show_code=True, f=lambda v, t, p: t)
with pytest.raises(errors.CodeError):
odeint(method=method, show_code=True, f=lambda f, t, dt: t)
with pytest.raises(errors.CodeError):
odeint(method=method, show_code=True, f=lambda v, t, dt: t)
with pytest.raises(errors.CodeError):
odeint(method=method, show_code=True, f=lambda v, t, v_new: t)
with pytest.raises(errors.CodeError):
odeint(method=method, show_code=True, f=lambda v, t, dv_k1: t)
with pytest.raises(errors.CodeError):
odeint(method=method, show_code=True, f=lambda v, t, dv_k2: t)
with pytest.raises(errors.CodeError):
odeint(method=method, show_code=True, f=lambda v, t, dv_k3: t)
with pytest.raises(errors.CodeError):
odeint(method=method,
show_code=True,
f=lambda v, t, k2_v_arg: t)
with pytest.raises(errors.CodeError):
odeint(method=method,
show_code=True,
f=lambda v, t, k2_t_arg: t)
with pytest.raises(errors.CodeError):
odeint(method=method,
show_code=True,
f=lambda v, t, k3_v_arg: t)
with pytest.raises(errors.CodeError):
odeint(method=method,
show_code=True,
f=lambda v, t, k3_t_arg: t)
print('-' * 40)
def test_rk2(self):
method = 'rk2'
print(f'Test {method} method:')
print()
odeint(method=method, show_code=True, f=lambda v, t, p: t)
with pytest.raises(errors.CodeError):
odeint(method=method, show_code=True, f=lambda f, t, dt: t)
with pytest.raises(errors.CodeError):
odeint(method=method, show_code=True, f=lambda v, t, dt: t)
with pytest.raises(errors.CodeError):
odeint(method=method, show_code=True, f=lambda v, t, v_new: t)
with pytest.raises(errors.CodeError):
odeint(method=method, show_code=True, f=lambda v, t, dv_k1: t)
with pytest.raises(errors.CodeError):
odeint(method=method, show_code=True, f=lambda v, t, dv_k2: t)
with pytest.raises(errors.CodeError):
odeint(method=method, show_code=True, f=lambda v, t, k2_v_arg: t)
with pytest.raises(errors.CodeError):
odeint(method=method, show_code=True, f=lambda v, t, k2_t_arg: t)
print('-' * 40)