def test_poisson(self):
# Check the output types for input rate + n number of neurons
pp = stgen._n_poisson(rate=self.rate, t_stop=self.t_stop, n=self.n)
self.assertIsInstance(pp, list)
self.assertIsInstance(pp[0], neo.core.spiketrain.SpikeTrain)
self.assertEqual(pp[0].simplified.units, 1000*ms)
self.assertEqual(len(pp), self.n)
# Check the output types for input list of rates
pp = stgen._n_poisson(rate=self.rates, t_stop=self.t_stop)
self.assertIsInstance(pp, list)
self.assertIsInstance(pp[0], neo.core.spiketrain.SpikeTrain)
self.assertEqual(pp[0].simplified.units, 1000*ms)
self.assertEqual(len(pp), self.n)
def test_poisson(self):
# Check the output types for input rate + n number of neurons
pp = stgen._n_poisson(rate=self.rate, t_stop=self.t_stop, n=self.n)
self.assertIsInstance(pp, list)
self.assertIsInstance(pp[0], neo.core.spiketrain.SpikeTrain)
self.assertEqual(pp[0].simplified.units, 1000 * ms)
self.assertEqual(len(pp), self.n)
# Check the output types for input list of rates
pp = stgen._n_poisson(rate=self.rates, t_stop=self.t_stop)
self.assertIsInstance(pp, list)
self.assertIsInstance(pp[0], neo.core.spiketrain.SpikeTrain)
self.assertEqual(pp[0].simplified.units, 1000 * ms)
self.assertEqual(len(pp), self.n)
def generate_sts(data_type, N=100):
'''
Generate a list of parallel spike trains with different statistics.
The data are composed of background spiking activity plus possibly
a repeated sequence of synchronous events (SSE).
The background activity depends on the value of data_type.
The size and occurrence count of the SSE is specified by sse_params.
Parameters
----------
data_type : int
An integer specifying the type of background activity.
At the moment the following types of background activity are
supported (note: homog = across neurons; stat = over time):
0 : 100 indep Poisson with rate 25 Hz
1: 100 indep Poisson nonstat-step (10/60/10 Hz)
2: 100 indep Poisson heterog (5->25 Hz), stat
3 : 100 indep Poisson, rate increase with latency variability
N: int
total number of neurons in the model. The default is N=100.
Output
------
sts : list of SpikeTrains
a list of spike trains
params : dict
a dictionary of simulation parameters
'''
T = 1 * pq.s # simulation time
sampl_period = 10 * pq.ms # sampling period of the rate profile
params = {'nr_neurons': N, 'simul_time': T}
# Indep Poisson homog, stat rate 25 Hz
if data_type == 0:
# Define a rate profile
rate = 25 * pq.Hz
# Generate data
sts = stg._n_poisson(rate=rate, t_stop=T, n=N)
# Storing rate parameter
params['rate'] = rate
# Indep Poisson, homog, nonstat-step (10/60/10 Hz)
elif data_type == 1:
a0, a1 = 10 * pq.Hz, 60 * pq.Hz # baseline and transient rates
t1, t2 = 600 * pq.ms, 700 * pq.ms # time segment of transient rate
# Define a rate profile
times = sampl_period.units * np.arange(
0,
T.rescale(sampl_period.units).magnitude, sampl_period.magnitude)
rate_profile = np.zeros(times.shape)
rate_profile[np.any([times < t1, times > t2], axis=0)] = a0.magnitude
rate_profile[np.all([times >= t1, times <= t2], axis=0)] = a1.magnitude
rate_profile = rate_profile * a0.units
rate_profile = neo.AnalogSignal(rate_profile,
sampling_period=sampl_period)
# Generate data
sts = [
stg.inhomogeneous_poisson_process(rate_profile) for i in range(N)
]
# Storing rate parameter
params['rate'] = rate_profile
# Indep Poisson, heterog (5->15 Hz), stat
elif data_type == 2:
rate_min = 5 * pq.Hz # min rate. Ensures that there is >=1 spike
rate_max = 25 * pq.Hz # max rate
rates = np.linspace(rate_min.magnitude, rate_max.magnitude, N) * pq.Hz
# Define a rate profile
# Generate data
sts = [
stg.homogeneous_poisson_process(rate=rate, t_stop=T)
for rate in rates
]
random.shuffle(sts)
# Storing rate parameter
params['rate'] = rates
# Indep Poisson, rate increase sequence
elif data_type == 3:
l = 20 # 20 groups of neurons
w = 5 # of 5 neurons each
t0 = 50 * pq.ms # the first of which increases the rate at time t0
t00 = 500 * pq.ms # and again at time t00
ratechange_dur = 5 * pq.ms # old: 10ms # for a short period
a0, a1 = 14 * pq.Hz, 100 * pq.Hz # from rate a0 to a1
ratechange_delay = 5 * pq.ms # old: 10ms; followed with delay by next group
# Define a rate profile
times = sampl_period.units * np.arange(
0,
T.rescale(sampl_period.units).magnitude, sampl_period.magnitude)
sts = []
rate_profiles = []
for i in range(l * w):
t1 = t0 + (i // w) * ratechange_delay
t2 = t1 + ratechange_dur
t11 = t00 + (i // w) * ratechange_delay
t22 = t11 + ratechange_dur
rate_profile = np.zeros(times.shape)
rate_profile[np.any([times < t1, times > t2], axis=0)] = \
a0.magnitude
rate_profile[np.all([times >= t1, times <= t2], axis=0)] = \
a1.magnitude
rate_profile[np.all([times >= t11, times <= t22], axis=0)] = \
a1.magnitude
rate_profile = rate_profile * a0.units
rate_profile = neo.AnalogSignal(rate_profile,
sampling_period=sampl_period)
rate_profiles.append(rate_profile)
# Generate data
sts.append(stg.inhomogeneous_poisson_process(rate_profile))
# Storing rate parameter
params['rate'] = rate_profiles
else:
raise ValueError(
'data_type %d not supported. Provide int from 0 to 10' % data_type)
return sts, params
# Computation analytical p-values
theo_pvalues = []
for l in lengths:
num_combination_patt = (math.factorial(n) /
math.factorial(n - xi)) * (l)
theo_pvalues.append(
binom.sf(occ - 1,
(t_stop.simplified.magnitude - l.simplified.magnitude) /
binsize.simplified.magnitude, p) * num_combination_patt)
# Generating the data
# Fixing the seed
np.random.seed(0)
# Generating Independent Background
background_sts = stg._n_poisson(rate=rate, t_stop=t_stop, n=n)
# Total number of patterns
num_neu_patt = len(lengths) * xi
sts = []
stps = []
# Raising errors if the number of neurons is smaller than number
# of patterns
if num_neu_patt > n:
raise ValueError('Number of neurons involved in the patterns is '
'larger than total number of patterns')
for l_idx, l in enumerate(lengths):
lag_bins = int(l / (xi - 1))
delays = [i * lag_bins * binsize.magnitude
for i in range(1, xi)] * binsize.units
print(delays)
# Generating patterns