def autocor(PSTH,N=None,T=20*br.ms,bin=None):
if bin is None:
bin = br.defaultclock.dt
p = int(T/ bin)
SAC = br.zeros(p)
if N is None:
SAC[0] = br.mean(PSTH * PSTH)
else: # correction to exclude self-coincidences
PSTHnoself = br.clip(PSTH - 1. / (bin * N), 0*br.kHz, br.Inf*br.kHz)
SAC[0] = br.mean(PSTH * PSTHnoself) * N / (N - 1.)
SAC[1:] = [br.mean(PSTH[:-i] * PSTH[i:]) for i in range(1,p)]
SAC = br.hstack((SAC[::-1], SAC[1:]))
out = (br.arange(len(SAC)) - len(SAC) / 2) * bin
return out, SAC
def visualise_connectivity(S):
Ns = len(S.source)
Nt = len(S.target)
b.figure(figsize=(10, 4))
b.subplot(121)
b.plot(b.zeros(Ns), b.arange(Ns), 'ok', ms=10)
b.plot(b.ones(Nt), b.arange(Nt), 'ok', ms=10)
for i, j in zip(S.i, S.j):
b.plot([0, 1], [i, j], '-k')
b.xticks([0, 1], ['Source', 'Target'])
b.ylabel('Neuron index')
b.xlim(-0.1, 1.1)
b.ylim(-1, max(Ns, Nt))
b.subplot(122)
b.plot(S.i, S.j, 'ok')
b.xlim(-1, Ns)
b.ylim(-1, Nt)
b.xlabel('Source neuron index')
b.ylabel('Target neuron index')
import lmfit
except ImportError:
lmfit = None
from numpy.testing import assert_equal, assert_almost_equal
from brian2 import (zeros, Equations, NeuronGroup, StateMonitor, TimedArray,
nS, mV, volt, ms, pA, pF, Quantity, set_device, get_device,
Network, have_same_dimensions, DimensionMismatchError)
from brian2.equations.equations import DIFFERENTIAL_EQUATION, SUBEXPRESSION
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)
'''