def backward_Euler(f, dt=None, epsilon=1e-12):
"""Backward Euler method. Also named as ``implicit_Euler``.
Parameters
----------
f : callable
The function at the right hand of the differential equation.
dt : None, float
Precision of numerical integration.
Returns
-------
func : callable
The one-step numerical integration function.
"""
f = autojit(f)
if dt is None:
dt = profile.get_dt()
def int_f(y0, t, *args):
y1 = y0 + dt * f(y0, t, *args)
y2 = y0 + dt * f(y1, t, *args)
while not np.all(np.abs(y1 - y2) < epsilon):
y1 = y2
y2 = y0 + dt * f(y1, t, *args)
return y2
return autojit(int_f)
def trapezoidal_rule(f, dt=None, epsilon=1e-12):
"""Trapezoidal rule.
The trapezoidal rule is an implicit second-order method, which can
be considered as both a Runge–Kutta method and a linear multistep method.
Parameters
----------
f : callable
The function at the right hand of the differential equation.
dt : None, float
Precision of numerical integration.
Returns
-------
func : callable
The one-step numerical integration function.
"""
f = autojit(f)
if dt is None:
dt = profile.get_dt()
def int_f(y0, t, *args):
dy0 = f(y0, t, *args)
y1 = y0 + dt * dy0
y2 = y0 + dt / 2 * (dy0 + f(y1, t + dt, *args))
while not np.all(np.abs(y1 - y2) < epsilon):
y1 = y2
y2 = y0 + dt / 2 * (dy0 + f(y1, t + dt, *args))
return y2
return autojit(int_f)
def rk3(f, dt=None):
"""Kutta's third-order method (commonly known as RK3).
Also named as ``RK3``.
Parameters
----------
f : callable
The function at the right hand of the differential equation.
dt : None, float
Precision of numerical integration.
Returns
-------
func : callable
The one-step numerical integration function.
"""
f = autojit(f)
if dt is None:
dt = profile.get_dt()
def int_f(y0, t, *args):
k1 = f(y0, t, *args)
k2 = f(y0 + dt / 2 * k1, t + dt / 2, *args)
k3 = f(y0 - dt * k1 + 2 * dt * k2, t + dt, *args)
return y0 + dt / 6 * (k1 + 4 * k2 + k3)
return autojit(int_f)
def rk4_alternative(f, dt=None):
"""An alternative of fourth-order Runge-Kutta method.
Also named as ``RK4_alternative``.
Parameters
----------
f : callable
The function at the right hand of the differential equation.
dt : None, float
Precision of numerical integration.
Returns
-------
func : callable
The one-step numerical integration function.
"""
f = autojit(f)
if dt is None:
dt = profile.get_dt()
def int_f(y0, t, *args):
k1 = f(y0, t, *args)
k2 = f(y0 + dt / 3 * k1, t + dt / 3, *args)
k3 = f(y0 - dt / 3 * k1 + dt * k2, t + 2 * dt / 3, *args)
k4 = f(y0 + dt * k1 - dt * k2 + dt * k3, t + dt, *args)
return y0 + dt / 8 * (k1 + 3 * k2 + 3 * k3 + k4)
return autojit(int_f)
def rk2(f, dt=None, beta=2 / 3):
"""Parametric second-order Runge-Kutta (RK2).
Also named as ``RK2``.
Popular choices for 'beta':
1/2 :
explicit midpoint method
2/3 :
Ralston's method
1 :
Heun's method, also known as the explicit trapezoid rule
Parameters
----------
f : callable
The function at the right hand of the differential equation.
dt : None, float
Precision of numerical integration.
Returns
-------
func : callable
The one-step numerical integration function.
"""
f = autojit(f)
if dt is None:
dt = profile.get_dt()
def int_f(y0, t, *args):
k1 = f(y0, t, *args)
k2 = f(y0 + beta * dt * k1, t + beta * dt, *args)
return y0 + dt * ((1 - 1 / (2 * beta)) * k1 + 1 / (2 * beta) * k2)
return autojit(int_f)
def forward_Euler(f, dt=None):
"""Forward Euler method. Also named as ``explicit_Euler``.
The most unstable integrator known. Requires a very small timestep.
Accuracy is O(dt).
Parameters
----------
f : callable
The function at the right hand of the differential equation.
dt : None, float
Precision of numerical integration.
Returns
-------
func : callable
The one-step numerical integration function.
"""
f = autojit(f)
if dt is None:
dt = profile.get_dt()
def int_f(y0, t, *args):
return y0 + dt * f(y0, t, *args)
return autojit(int_f)
def Heun_method(f, g, dt=None):
"""Stratonovich stochastic integral.
Use the Stratonovich Heun algorithm
to integrate Stratonovich equation,
according to paper [2]_, [3]_.
Parameters
----------
f : callable
The drift coefficient, the deterministic part of the SDE.
g : callable, float
The diffusion coefficient, the stochastic part.
dt : None, float
Precision of numerical integration.
Returns
-------
func : callable
The one-step numerical integration function.
References
----------
.. [2] H. Gilsing and T. Shardlow, SDELab: A package for solving stochastic differential
equations in MATLAB, Journal of Computational and Applied Mathematics 205 (2007),
no. 2, 1002{1018.
.. [3] P.E. Kloeden, E. Platen, and H. Schurz, Numerical solution of SDE through computer
experiments, Springer, 1994.
"""
dt = profile.get_dt() if dt is None else dt
dt_sqrt = np.sqrt(dt)
f = autojit(f)
if callable(g):
g = autojit(g)
def int_fg(y0, t, *args):
dW = np.random.normal(0.0, 1.0, y0.shape)
df = f(y0, t - dt, *args) * dt
gn = g(y0, t - dt, *args)
y_bar = y0 + gn * dW * dt_sqrt
gn_bar = g(y_bar, t, *args)
dg = 0.5 * (gn + gn_bar) * dW * dt_sqrt
y1 = y0 + df + dg
return y1
else:
assert isinstance(g, (int, float, np.ndarray))
def int_fg(y0, t, *args):
dW = np.random.normal(0.0, 1.0, y0.shape)
df = f(y0, t - dt, *args) * dt
dg = g * dW * dt_sqrt
y1 = y0 + df + dg
return y1
return autojit(int_fg)
def run_time(self):
"""Get the time points of the network.
Returns
-------
times : numpy.ndarray
The running time-steps of the network.
"""
return np.arange(0, self.current_time, profile.get_dt())
def firing_rate(mon, width, window='gaussian'):
"""Calculate the mean firing rate over in a neuron group.
This method is adopted from Brian2.
The firing rate in trial :math:`k` is the spike count :math:`n_{k}^{sp}`
in an interval of duration :math:`T` divided by :math:`T`:
.. math::
v_k = {n_k^{sp} \\over T}
Parameters
----------
mon : StateMonitor
The monitor which record spiking activities.
width : int, float
The width of the ``window`` in millisecond.
window : str
The window to use for smoothing. It can be a string to chose a
predefined window:
- `flat`: a rectangular,
- `gaussian`: a Gaussian-shaped window.
For the `Gaussian` window, the `width` parameter specifies the
standard deviation of the Gaussian, the width of the actual window
is `4 * width + dt`.
For the `flat` window, the width of the actual window
is `2 * width/2 + dt`.
Returns
-------
rate : numpy.ndarray
The population rate in Hz, smoothed with the given window.
"""
# rate
assert hasattr(
mon, 'spike'
), 'Must record the "spike" of the neuron group to get firing rate.'
rate = np.sum(mon.spike, axis=1)
# window
dt = profile.get_dt()
if window == 'gaussian':
width1 = 2 * width / dt
width2 = int(np.round(width1))
window = np.exp(-np.arange(-width2, width2 + 1)**2 / (width1**2 / 2))
elif window == 'flat':
width1 = int(width / 2 / dt) * 2 + 1
window = np.ones(width1)
else:
raise ValueError('Unknown window type "{}".'.format(window))
window = np.float_(window)
return np.convolve(rate, window / sum(window), mode='same')
def Milstein_dfree_Stra(f, g, dt=None):
"""Stratonovich stochastic integral. The derivative-free Milstein
method is an order 1.0 strong Taylor schema.
Parameters
----------
f : callable
The drift coefficient, the deterministic part of the SDE.
g : callable, float
The diffusion coefficient, the stochastic part.
dt : None, float
Precision of numerical integration.
Returns
-------
func : callable
The one-step numerical integration function.
"""
dt = profile.get_dt() if dt is None else dt
dt_sqrt = np.sqrt(dt)
f = autojit(f)
if callable(g):
g = autojit(g)
def int_fg(y0, t, *args):
dW = np.random.normal(0.0, 1.0, y0.shape)
df = f(y0, t - dt, *args) * dt
g_n = g(y0, t - dt, *args)
dg = g_n * dW * dt_sqrt
y_n_bar = y0 + df + g_n * dt_sqrt
g_n_bar = g(y_n_bar, t, *args)
extra_term = 0.5 * (g_n_bar - g_n) * (dW * dW * dt_sqrt)
y1 = y0 + df + dg + extra_term
return y1
else:
assert isinstance(g, (int, float, np.ndarray))
def int_fg(y0, t, *args):
dW = np.random.normal(0.0, 1.0, y0.shape)
df = f(y0, t - dt, *args) * dt
dg = g * dW * dt_sqrt
y1 = y0 + df + dg
return y1
return autojit(int_fg)
def Euler_method(f, g, dt=None):
"""Itô stochastic integral. The simplest stochastic numerical approximation
is the Euler-Maruyama method. Its is an order 0.5 strong Taylor schema.
Also named as ``EM``, ``EM_method``, ``Euler``, ``Euler_Maruyama_method``.
Parameters
----------
f : callable
The drift coefficient, the deterministic part of the SDE.
g : callable, float
The diffusion coefficient, the stochastic part.
dt : None, float
Precision of numerical integration.
Returns
-------
func : callable
The one-step numerical integration function.
"""
dt = profile.get_dt() if dt is None else dt
dt_sqrt = np.sqrt(dt)
f = autojit(f)
if callable(g):
g = autojit(g)
def int_fg(y0, t, *args):
dW = np.random.normal(0.0, 1.0, y0.shape)
df = f(y0, t, *args) * dt
dg = dt_sqrt * g(y0, t, *args) * dW
return y0 + df + dg
else:
assert isinstance(g, (int, float, np.ndarray))
def int_fg(y0, t, *args):
dW = np.random.normal(0.0, 1.0, y0.shape)
df = f(y0, t, *args) * dt
dg = dt_sqrt * g * dW
return y0 + df + dg
return autojit(int_fg)
def format_delay(delay, dt=None):
"""Format the given delay and get the delay length.
Parameters
----------
delay : None, int, float, np.ndarray
The delay.
dt : float, None
The precision of the numerical integration.
Returns
-------
delay_len : int
Delay length.
"""
if delay is None:
delay_len = 1
elif isinstance(delay, (int, float)):
dt = profile.get_dt() if dt is None else dt
delay_len = int(np.ceil(delay / dt)) + 1
else:
raise ValueError()
return delay_len
def __init__(self, **kwargs):
if 'kwargs' in kwargs:
kwargs.pop('kwargs')
for k, v in kwargs.items():
setattr(self, k, v)
self.post.pre_synapses.append(self)
self.pre.post_synapses.append(self)
# check functions
assert 'update_state' in kwargs, 'Must provide "update_state" function.'
if 'output_synapse' not in kwargs:
def f1(syn_state, var_index, neu_state):
output_idx = var_index[-2]
neu_state[-1] += syn_state[output_idx[0]][output_idx[1]]
self.output_synapse = f1
if 'collect_spike' not in kwargs:
def f2(syn_state, pre_neu_state, post_neu_state):
syn_state[0][-1] = pre_neu_state[-3]
self.collect_spike = f2
self.update_state = helper.autojit(self.update_state)
self.output_synapse = helper.autojit(self.output_synapse)
self.collect_spike = helper.autojit(self.collect_spike)
# check `name`
if 'name' not in kwargs:
global synapse_no
self.name = "Synapses-{}".format(synapse_no)
synapse_no += 1
# check `num`, `num_pre` and `num_post`
assert 'num' in kwargs, 'Must provide "num" attribute.'
if 'num_pre' not in kwargs:
self.num_pre = self.pre.num
if 'num_post' not in kwargs:
self.num_post = self.post.num
# check `delay_len`
if 'delay_len' not in kwargs:
if 'delay' not in kwargs:
raise ValueError('Must define "delay".')
else:
dt = kwargs.get('dt', profile.get_dt())
self.delay_len = format_delay(self.delay, dt)
# check `var2index`
if 'var2index' not in kwargs:
raise ValueError('Must define "var2index".')
assert isinstance(self.var2index, dict), '"var2index" must be a dict.'
# "g" is the "delay_idx"
# 'g_post' is the "output_idx"
default_variables = [('pre_spike', (0, -1)),
('g', (1, self.delay_len - 1)),
('g_post', (1, 0)), ]
self.default_variables = default_variables
for k, _ in default_variables:
if k in self.var2index:
raise ValueError('"{}" is a pre-defined variable, '
'cannot be defined in "var2index".'.format(k))
user_defined_variables = sorted(list(self.var2index.items()), key=lambda a: a[1])
syn_variables = user_defined_variables + default_variables
var2index_array = np.zeros((len(syn_variables) + 1, 2), dtype=np.int32)
var2index_array[-1, 0] = self.delay_len
vars = dict(delay_len=-1)
for i, (var, index) in enumerate(syn_variables):
var2index_array[i] = list(index)
vars[var] = i
self.var2index = vars
self.var2index_array = var2index_array
def run(self, duration, report=False, inputs=(), repeat=False):
"""Run the simulation for the given duration.
This function provides the most convenient way to run the network.
For example:
>>> # first of all, define the network we want.
>>> import npbrain as nn
>>> lif1 = nn.LIF(10, noise=0.2)
>>> lif2 = nn.LIF(10, noise=0.5)
>>> syn = nn.VoltageJumpSynapse(lif1, lif2, 1.0, nn.conn.all2all(lif1.num, lif2.num))
>>> net = Network(syn, lif1, lif2)
>>> # next, run the network.
>>> net.run(100.) # run 100. ms
>>>
>>> # if you want to provide input to `lif1`
>>> # for example, a constant input `11` (more complex inputs please use `input_factory.py`)
>>> net.run(100., inputs=(lif1, 11.))
>>>
>>> # if you want to provide input to `lif1` in the period of 30-50 ms.
>>> net.run(100., inputs=(lif1, 11., (30., 50.)))
>>>
>>> # moreover, if you want to provide input to `lif1` in the period of 30-50 ms,
>>> # and provide input to `lif2` in the period of 10-100 ms.
>>> net.run(100., inputs=[(lif1, 11., (30., 50.)), (lif2, -1., (10., 100.))])
>>>
>>> # if you want to known the running status in real-time.
>>> net.run(100., report=True)
>>>
Parameters
----------
duration : int, float
The amount of simulation time to run for.
report : bool
Report the progress of the simulation.
repeat : bool
Whether repeat run this model. If `repeat=True`, every time
call this method will initialize the object state.
inputs : list, tuple
The receivers, external inputs and durations.
"""
# 1. checking
# ------------
self._check_run_order()
# 2. initialization
# ------------------
# time
dt = profile.get_dt()
ts = np.arange(self.current_time, self.current_time + duration, dt)
run_length = len(ts)
# monitors
for mon in self.monitors:
mon.init_state(run_length)
# neurons
if repeat:
if self._neuron_states is None:
self._neuron_states = [
neu.state.copy() for neu in self.neurons
]
else:
for neu, state in zip(self.neurons, self._neuron_states):
neu.state = state.copy()
# synapses
if repeat:
if self._synapse_states is None:
self._synapse_states = []
for syn in self.synapses:
state = tuple(st.copy() for st in syn.state)
self._synapse_states.append(
[state, syn.var2index_array.copy()])
else:
for syn, (state, var_index) in zip(self.synapses,
self._synapse_states):
syn.state = tuple(st.copy() for st in state)
syn.var2index_array = var_index.copy()
# 3. format external inputs
# --------------------------
iterable_inputs, fixed_inputs, no_inputs = self._format_inputs_and_receiver(
inputs, duration)
# 4. run
# ---------
# initialize
if report:
t0 = time.time()
self._input(0, iterable_inputs, fixed_inputs, no_inputs)
self._step(ts[0], 0)
# record time
if report:
print('Compilation used {:.4f} ms.'.format(time.time() - t0))
print("Start running ...")
report_gap = int(run_length / 10)
t0 = time.time()
# run
for run_idx in range(1, run_length):
t = ts[run_idx]
self._input(run_idx, iterable_inputs, fixed_inputs, no_inputs)
self._step(t, run_idx)
if report and ((run_idx + 1) % report_gap == 0):
percent = (run_idx + 1) / run_length * 100
print('Run {:.1f}% using {:.3f} s.'.format(
percent,
time.time() - t0))
if report:
print('Simulation is done. ')
# 5. Finally
# -----------
self.current_time = duration
def _format_inputs_and_receiver(self, inputs, duration):
dt = profile.get_dt()
# format inputs and receivers
if len(inputs) > 1 and not isinstance(inputs[0], (list, tuple)):
if isinstance(inputs[0], Neurons):
inputs = [inputs]
else:
raise ValueError('Unknown input structure.')
# ---------------------
# classify input types
# ---------------------
# 1. iterable inputs
# 2. fixed inputs
iterable_inputs = []
fixed_inputs = []
neuron_with_inputs = []
for input_ in inputs:
# get "receiver", "input", "duration"
if len(input_) == 2:
obj, Iext = input_
dur = (0, duration)
elif len(input_) == 3:
obj, Iext, dur = input_
else:
raise ValueError
err = 'You can assign inputs only for added object. "{}" is not in the network.'
if isinstance(obj, str):
try:
obj = self._objsets[obj]
except:
raise ValueError(err.format(obj))
assert isinstance(
obj, Neurons), "You can assign inputs only for Neurons."
assert obj in self.objects, err.format(obj)
assert len(
dur
) == 2, "Must provide the start and the end simulation time."
assert 0 <= dur[0] < dur[1] <= duration
dur = (int(dur[0] / dt), int(dur[1] / dt))
neuron_with_inputs.append(obj)
# judge the type of the inputs.
if isinstance(Iext, (int, float)):
Iext = np.ones(obj.num) * Iext
fixed_inputs.append([obj, Iext, dur])
continue
size = np.shape(Iext)[0]
run_length = dur[1] - dur[0]
if size != run_length:
if size == 1:
Iext = np.ones(obj.num) * Iext
elif size == obj.num:
Iext = Iext
else:
raise ValueError('Wrong size of inputs for', obj)
fixed_inputs.append([obj, Iext, dur])
else:
input_size = np.size(Iext[0])
err = 'The input size "{}" do not match with neuron ' \
'group size "{}".'.format(input_size, obj.num)
assert input_size == 1 or input_size == obj.num, err
iterable_inputs.append([obj, Iext, dur])
# 3. no inputs
no_inputs = []
for neu in self.neurons:
if neu not in neuron_with_inputs:
no_inputs.append(neu)
return iterable_inputs, fixed_inputs, no_inputs
