def __init__(self, tau=10.0, B=0.0, T=0.0, sum='sum(exc) - sum(inh)', noise=None):
# Create the arguments
parameters = """
tau = %(tau)s : population
B = %(B)s
T = %(T)s : population
""" % {'tau': tau, 'B': B, 'T': T}
# Equations for the variables
if not noise:
noise_def = ''
else:
noise_def = '+ ' + noise
equations="""
tau * dv/dt + v = %(sum)s + B %(noise)s : exponential
r = pos(v - T)
""" % { 'sum' : sum, 'noise': noise_def}
Neuron.__init__(self, parameters=parameters, equations=equations,
name="Leaky-Integrator", description="Leaky-Integrator with positive transfer function and additive noise.")
# For reporting
self._instantiated.append(True)
def __init__(self,
parameters,
equations,
inputs,
output=["BOLD"],
name="Custom BOLD model",
description=""):
"""
See ANNarchy.extensions.bold.PredefinedModels.py for some example models.
:param parameters: parameters of the model and their initial value.
:param equations: equations defining the temporal evolution of variables.
:param inputs: single variable or list of input signals (e.g. 'I_CBF' or ['I_CBF', 'I_CMRO2']).
:param output: output variable of the model (default is 'BOLD').
:param name: optional model name.
:param description: optional model description.
"""
# The processing in BoldMonitor expects lists, but the interface
# should allow also single strings (if only one variable is considered)
self._inputs = [inputs] if isinstance(inputs, str) else inputs
self._output = [output] if isinstance(output, str) else output
Neuron.__init__(self,
parameters=parameters,
equations=equations,
name=name,
description=description)
self._model_instantiated = False # activated by BoldMonitor
def __init__(self, v_rest=-65.0, cm=1.0, tau_m=20.0, tau_refrac=0.0, tau_syn_E=5.0, tau_syn_I=5.0, v_thresh=-50.0, v_reset=-65.0, i_offset=0.0):
# Create the arguments
parameters = """
v_rest = %(v_rest)s
cm = %(cm)s
tau_m = %(tau_m)s
tau_refrac = %(tau_refrac)s
tau_syn_E = %(tau_syn_E)s
tau_syn_I = %(tau_syn_I)s
v_thresh = %(v_thresh)s
v_reset = %(v_reset)s
i_offset = %(i_offset)s
""" % {'v_rest':v_rest, 'cm':cm, 'tau_m':tau_m, 'tau_refrac':tau_refrac, 'tau_syn_E':tau_syn_E, 'tau_syn_I':tau_syn_I, 'v_thresh':v_thresh, 'v_reset':v_reset, 'i_offset':i_offset}
# Equations for the variables
equations="""
gmax_exc = exp((tau_syn_E - dt/2.0)/tau_syn_E)
gmax_inh = exp((tau_syn_I - dt/2.0)/tau_syn_I)
cm * dv/dt = cm/tau_m*(v_rest -v) + alpha_exc - alpha_inh + i_offset : exponential, init=%(v_reset)s
tau_syn_E * dg_exc/dt = - g_exc : exponential
tau_syn_I * dg_inh/dt = - g_inh : exponential
tau_syn_E * dalpha_exc/dt = gmax_exc * g_exc - alpha_exc : exponential
tau_syn_I * dalpha_inh/dt = gmax_inh * g_inh - alpha_inh : exponential
""" % {'v_reset':v_reset}
spike = """
v > v_thresh
"""
reset = """
v = v_reset
"""
Neuron.__init__(self, parameters=parameters, equations=equations, spike=spike, reset=reset, refractory='tau_refrac',
name="Integrate-and-Fire", description="Leaky integrate-and-fire model with fixed threshold and alpha post-synaptic currents.")
# For reporting
self._instantiated.append(True)
def __init__(self, spike_times, name=None, copied=False):
if not isinstance(spike_times, list):
Global._error(
'In a SpikeSourceArray, spike_times must be a Python list.')
if isinstance(spike_times[0], list): # several neurons
nb_neurons = len(spike_times)
else: # a single Neuron
nb_neurons = 1
spike_times = [spike_times]
# Create a fake neuron just to be sure the description has the correct parameters
neuron = Neuron(parameters="",
equations="",
spike=" t == 0",
reset="",
name="Spike source",
description="Spike source array.")
SpecificPopulation.__init__(self,
geometry=nb_neurons,
neuron=neuron,
name=name,
copied=copied)
self.init['spike_times'] = spike_times
def __init__(self, geometry, name=None, copied=False):
"""
:param geometry: population geometry as tuple. It must correspond to the image size and be fixed through the whole simulation.
:param name: unique name of the population (optional).
"""
# Check geometry
if isinstance(geometry, int) or len(geometry) == 1:
Global._error(
'The geometry of an ImagePopulation should be 2D (grayscale) or 3D (color).'
)
if len(geometry) == 3 and (geometry[2] != 3 and geometry[2] != 1):
Global._error(
'The third dimension of an ImagePopulation should be either 1 (grayscale) or 3 (color).'
)
if len(geometry) == 3 and geometry[2] == 1:
geometry = (int(geometry[0]), int(geometry[1]))
# Create the population
Population.__init__(self,
geometry=geometry,
name=name,
neuron=Neuron(parameters="r = 0.0"),
copied=copied)
def __init__(self, spike_times, name=None):
if not isinstance(spike_times, list):
Global._error('in SpikeSourceArray, spike_times must be a Python list.')
exit(0)
if isinstance(spike_times[0], list): # several neurons
nb_neurons = len(spike_times)
else: # a single Neuron
nb_neurons = 1
spike_times = [ spike_times ]
# Create a fake neuron just to be sure the description has the correct parameters
neuron = Neuron(
parameters="""
spike_times = 0.0
""",
equations="",
spike=" t == spike_times",
reset="",
name="Spike source",
description="Spikes source array."
)
Population.__init__(self, geometry=nb_neurons, neuron=neuron, name=name)
# Do some sorting to save C++ complexity
times = []
for neur_times in spike_times:
times.append(sorted(list(set(neur_times)))) # suppress doublons and sort
self.init['spike_times'] = times
def __init__(self, geometry, name=None, copied=False):
"""
*Parameters*:
* *geometry*: population geometry as tuple. It must correspond to the image size and be fixed through the whole simulation.
* *name*: unique name of the population (optional).
About the geometry:
* If the geometry is 2D, it corresponds to the (height, width) of the image. Only the luminance of the pixels will be represented (grayscale image).
* If the geometry is 3D, the third dimension can be either 1 (grayscale) or 3 (color).
If the third dimension is 3, each will correspond to the RGB values of the pixels.
.. warning::
Due to the indexing system of Numpy, a 640*480 image should be fed into a (480, 640) or (480, 640, 3) population.
"""
# Check geometry
if isinstance(geometry, int) or len(geometry)==1:
Global._error('The geometry of an ImagePopulation should be 2D (grayscale) or 3D (color).')
if len(geometry)==3 and (geometry[2]!=3 and geometry[2]!=1):
Global._error('The third dimension of an ImagePopulation should be either 1 (grayscale) or 3 (color).')
if len(geometry)==3 and geometry[2]==1:
geometry = (int(geometry[0]), int(geometry[1]))
# Create the population
Population.__init__(self, geometry = geometry, name=name, neuron = Neuron(parameters="r = 0.0"), copied=copied)
def __init__(self, population, name=None, scaling=1.0, refractory=None, copied=False):
"""
:param population: the Population to convert. Its neuron type must be spiking.
:param name: the (optional) name of the hybrid population.
:param scaling: the scaling of the firing rate. Defines what a rate ``r`` of 1.0 means in Hz (default: 1.0).
:param refractory: a refractory period in ms to ensure the ISI is not too high (default: None)
"""
self.population = population
self.refractory_init = refractory
if not self.population.neuron_type.description['type'] == 'rate':
Global._error('the population ' + self.population.name + ' must contain rate-coded neurons.')
# Create the description, but it will not be used for generation
Population.__init__(
self,
geometry = self.population.geometry,
name=name,
neuron = Neuron(
parameters="""
scaling = %(scaling)s : population
""" % {'scaling': scaling} ,
equations="""
p = Uniform(0.0, 1.0)
rates = p
""",
spike="rates>p",
refractory=refractory
) ,
copied=self.copied
)
self._specific = True
def __init__(self,
geometry,
rates,
corr,
tau,
name=None,
refractory=None,
copied=False):
"""
*Parameters*:
* **geometry**: population geometry as tuple.
* **rates**: rate in Hz of the population (must be a positive float)
* **corr**: total correlation strength (float in [0, 1])
* **tau**: correlation time constant in ms.
* **name**: unique name of the population (optional).
* **refractory**: refractory period in ms (careful: may break the correlation)
"""
# Store parameters
self.rates = float(rates)
self.corr = corr
self.tau = tau
self.refractory_init = refractory
# Correction of mu and sigma
mu, sigma = self._rectify(self.rates, self.corr, tau)
# Create the neuron
corr_neuron = Neuron(
parameters="""
tau = %(tau)s : population
mu = %(mu)s : population
sigma = %(sigma)s : population
""" % {
'tau': tau,
'mu': mu,
'sigma': sigma
},
equations="""
x += dt*(mu - x)/tau + sqrt(dt/tau) * sigma * Normal(0., 1.) : population, init=%(mu)s
p = Uniform(0.0, 1.0) * 1000.0 / dt
""" % {'mu': mu},
spike="p < x",
refractory=refractory,
name="HomogeneousCorrelated",
description="Homogeneous correlated spike trains.")
SpecificPopulation.__init__(self,
geometry=geometry,
neuron=corr_neuron,
name=name,
copied=copied)
def __init__(self, a=0.2, b=0.2, c=-65.0, d=2.0, v_thresh=30.0, i_offset=0.0, noise=0.0, tau_refrac=0.0, conductance="g_exc - g_inh"):
# Extract which targets are defined in the conductance
import re
targets = re.findall(r'g_([\w]+)', conductance)
# Create the arguments
parameters = """
noise = %(noise)s
a = %(a)s
b = %(b)s
c = %(c)s
d = %(d)s
v_thresh = %(v_thresh)s
i_offset = %(i_offset)s
tau_refrac = %(tau_refrac)s
""" % {'a': a, 'b':b, 'c':c, 'd':d, 'v_thresh':v_thresh, 'i_offset':i_offset, 'noise':noise, 'tau_refrac':tau_refrac}
# Equations for the variables
equations="""
I = %(conductance)s + noise * Normal(0.0, 1.0) + i_offset
dv/dt = 0.04 * v^2 + 5.0 * v + 140.0 - u + I : init = %(c)s
du/dt = a * (b*v - u) : init= %(u)s
""" % { 'conductance' : conductance, 'c':c , 'u': b*c}
# # Default behavior for the conductances (avoid warning)
# for target in targets:
# equations += """
# g_%(target)s = 0.0""" % {'target' : target}
spike = """
v > v_thresh
"""
reset = """
v = c
u += d
"""
Neuron.__init__(self, parameters=parameters, equations=equations, spike=spike, reset=reset, refractory='tau_refrac',
name="Izhikevich", description="Quadratic integrate-and-fire spiking neuron with adaptation.")
# For reporting
self._instantiated.append(True)
def __init__(self,
rates,
schedule=0.,
period=-1.,
name=None,
copied=False):
neuron = Neuron(parameters="",
equations=" r = 0.0",
name="Timed Array",
description="Timed array source.")
# Geometry of the population
geometry = rates.shape[1:]
# Check the schedule
if isinstance(schedule, (int, float)):
if float(schedule) <= 0.0:
schedule = Global.config['dt']
schedule = [float(schedule * i) for i in range(rates.shape[0])]
if len(schedule) > rates.shape[0]:
Global._error(
'TimedArray: the length of the schedule parameter cannot exceed the first dimension of the rates parameter.'
)
if len(schedule) < rates.shape[0]:
Global._warning(
'TimedArray: the length of the schedule parameter is smaller than the first dimension of the rates parameter (more data than time points). Make sure it is what you expect.'
)
SpecificPopulation.__init__(self,
geometry=geometry,
neuron=neuron,
name=name,
copied=copied)
self.init['schedule'] = schedule
self.init['rates'] = rates
self.init['period'] = period
def _create_adaptive(self):
# Create the description, but it will not be used for generation
Population.__init__(self,
geometry=self.population.geometry,
name=self.name,
neuron=Neuron(parameters="""
window = %(window)s : population
scaling = %(scaling)s : population
smooth = %(smooth)s : population
""" % {
'window': self.window,
'scaling': self.scaling,
'smooth': self.smooth
},
equations="r = 0.0"),
copied=self.copied)
# Generate specific code
omp_code = "#pragma omp parallel for private(pop%(id)s_nb, pop%(id)s_out)" if Global.config[
'num_threads'] > 1 else ""
code = """#pragma once
#include "pop%(id_pre)s.hpp"
extern PopStruct%(id_pre)s pop%(id_pre)s;
struct PopStruct%(id)s{
// Number of neurons
int size;
bool _active;
// Local parameter window
%(float_prec)s window ;
std::vector< %(float_prec)s > ad_window ;
// Global parameter scaling
%(float_prec)s scaling ;
// Global parameter smooth
%(float_prec)s smooth ;
// Local variable r
std::vector< %(float_prec)s > r ;
std::vector< std::vector< %(float_prec)s > > recorded_r ;
bool record_r ;
// Store the last spikes
std::vector< std::vector<long int> > last_spikes;
std::vector< %(float_prec)s > isi;
int get_size() { return size; }
void set_size(int value) { size = value; }
bool is_active() { return _active; }
void set_active(bool value) { _active = value; }
%(float_prec)s get_window() { return window; }
void set_window(%(float_prec)s value) { window = value; }
%(float_prec)s get_scaling() { return scaling; }
void set_scaling(%(float_prec)s value) { scaling = value; }
%(float_prec)s get_smooth() { return smooth; }
void set_smooth(%(float_prec)s value) { smooth = value; }
std::vector< %(float_prec)s > get_r() { return r; }
void set_r(std::vector< %(float_prec)s > value) { r = value; }
%(float_prec)s get_single_r(int rk) { return r[rk]; }
void set_single_r(int rk, %(float_prec)s value) { r[rk] = value; }
void init_population() {
size = %(size)s;
_active = true;
last_spikes = std::vector< std::vector<long int> >(size, std::vector<long int>());
ad_window = std::vector< %(float_prec)s >(size, window);
isi = std::vector< %(float_prec)s >(size, 10000.0);
}
void update_rng() {
}
void update() {
// Updating the local variables of Spike2Rate population %(id)s
if(_active){
int pop%(id)s_nb, pop%(id)s_out;
%(omp_code)s
for(int i = 0; i < size; i++){
// Increase when spiking
if (pop%(id_pre)s.last_spike[i] == t-1){
if(last_spikes[i].size() > 0)
isi[i] = %(float_prec)s(t-1 - last_spikes[i][last_spikes[i].size()-1]);
else
isi[i] = 10000.0;
last_spikes[i].push_back(t-1);
}
pop%(id)s_nb = 0;
pop%(id)s_out = -1;
for(int j=0; j < last_spikes[i].size(); j++){
if(last_spikes[i][j] >= t -1 - (long int)(ad_window[i]/dt) ){
pop%(id)s_nb++;
}
else{
pop%(id)s_out = j;
}
}
if (pop%(id)s_out > -1){
last_spikes[i].erase(last_spikes[i].begin(), last_spikes[i].begin()+pop%(id)s_out);
}
r[i] += dt*(1000.0/scaling / ad_window[i] * %(float_prec)s(pop%(id)s_nb) - r[i] ) / smooth;
//ad_window[i] = clip(5.0*isi[i], 20.0*dt, window) ;
ad_window[i] += dt * (clip(5.0*isi[i], 20.0*dt, window) - ad_window[i])/100.0;
if (i==0)
std::cout << ad_window[i] << " " << isi[i] << std::endl;
}
}
}
};
""" % {
'id': self.id,
'id_pre': self.population.id,
'omp_code': omp_code,
'size': self.size,
'float_prec': Global.config['precision']
}
return code
def __init__(self,
geometry,
name=None,
rates=None,
target=None,
parameters=None,
refractory=None,
copied=False):
"""
*Parameters*:
* **geometry**: population geometry as tuple.
* **name**: unique name of the population (optional).
* **rates**: mean firing rate of each neuron. It can be a single value (e.g. 10.0) or an equation (as string).
* **target**: the mean firing rate will be the weighted sum of inputs having this target name (e.g. "exc").
* **parameters**: additional parameters which can be used in the *rates* equation.
* **refractory**: refractory period in ms.
"""
if rates is None and target is None:
Global._error(
'A PoissonPopulation must define either rates or target.')
self.target = target
self.parameters = parameters
self.refractory_init = refractory
self.rates_init = rates
if target is not None: # hybrid population
# Create the neuron
poisson_neuron = Neuron(
parameters="""
%(params)s
""" % {'params': parameters if parameters else ''},
equations="""
rates = sum(%(target)s)
p = Uniform(0.0, 1.0) * 1000.0 / dt
_sum_%(target)s = 0.0
""" % {'target': target},
spike="""
p < rates
""",
refractory=refractory,
name="Hybrid",
description=
"Hybrid spiking neuron emitting spikes according to a Poisson distribution at a frequency determined by the weighted sum of inputs."
)
elif isinstance(rates, str):
# Create the neuron
poisson_neuron = Neuron(
parameters="""
%(params)s
""" % {'params': parameters if parameters else ''},
equations="""
rates = %(rates)s
p = Uniform(0.0, 1.0) * 1000.0 / dt
_sum_exc = 0.0
""" % {'rates': rates},
spike="""
p < rates
""",
refractory=refractory,
name="Poisson",
description=
"Spiking neuron with spikes emitted according to a Poisson distribution."
)
elif isinstance(rates, np.ndarray):
poisson_neuron = Neuron(
parameters="""
rates = 10.0
""",
equations="""
p = Uniform(0.0, 1.0) * 1000.0 / dt
""",
spike="""
p < rates
""",
refractory=refractory,
name="Poisson",
description=
"Spiking neuron with spikes emitted according to a Poisson distribution."
)
else:
poisson_neuron = Neuron(
parameters="""
rates = %(rates)s
""" % {'rates': rates},
equations="""
p = Uniform(0.0, 1.0) * 1000.0 / dt
""",
spike="""
p < rates
""",
refractory=refractory,
name="Poisson",
description=
"Spiking neuron with spikes emitted according to a Poisson distribution."
)
SpecificPopulation.__init__(self,
geometry=geometry,
neuron=poisson_neuron,
name=name,
copied=copied)
if isinstance(rates, np.ndarray):
self.rates = rates