def test_dither_spike_train_empty_train(self):
st = neo.SpikeTrain([] * pq.ms, t_stop=500 * pq.ms)
shift = 10 * pq.ms
surrog = surr.dither_spike_train(st, shift=shift, n=1)[0]
self.assertEqual(len(surrog), 0)
def test_dither_spike_train_empty_train(self):
spiketrain = neo.SpikeTrain([] * pq.ms, t_stop=500 * pq.ms)
shift = 10 * pq.ms
surrogate_train = surr.dither_spike_train(
spiketrain, shift=shift, n_surrogates=1)[0]
self.assertEqual(len(surrogate_train), 0)
def test_dither_spike_train_output_decimals(self):
st = neo.SpikeTrain([90, 150, 180, 350] * pq.ms, t_stop=500 * pq.ms)
nr_surr = 2
shift = 10 * pq.ms
surrs = surr.dither_spike_train(st, shift=shift, n=nr_surr, decimals=3)
for surrog in surrs:
for i in range(len(surrog)):
self.assertNotEqual(surrog[i] - int(surrog[i]) * pq.ms,
surrog[i] - surrog[i])
def test_dither_spike_train_false_edges(self):
st = neo.SpikeTrain([90, 150, 180, 350] * pq.ms, t_stop=500 * pq.ms)
nr_surr = 2
shift = 10 * pq.ms
surrs = surr.dither_spike_train(st, shift=shift, n=nr_surr, edges=False)
for surrog in surrs:
for i in range(len(surrog)):
self.assertLessEqual(surrog[i], st.t_stop)
def test_dither_spike_train_false_edges(self):
spiketrain = neo.SpikeTrain(
[90, 150, 180, 350] * pq.ms, t_stop=500 * pq.ms)
n_surrogates = 2
shift = 10 * pq.ms
surrogate_trains = surr.dither_spike_train(
spiketrain, shift=shift, n_surrogates=n_surrogates, edges=False)
for surrogate_train in surrogate_trains:
for i in range(len(surrogate_train)):
self.assertLessEqual(surrogate_train[i], spiketrain.t_stop)
def test_dither_spike_train_output_format(self):
st = neo.SpikeTrain([90, 150, 180, 350] * pq.ms, t_stop=500 * pq.ms)
nr_surr = 2
shift = 10 * pq.ms
surrs = surr.dither_spike_train(st, shift=shift, n=nr_surr)
self.assertIsInstance(surrs, list)
self.assertEqual(len(surrs), nr_surr)
for surrog in surrs:
self.assertIsInstance(surrs[0], neo.SpikeTrain)
self.assertEqual(surrog.units, st.units)
self.assertEqual(surrog.t_start, st.t_start)
self.assertEqual(surrog.t_stop, st.t_stop)
self.assertEqual(len(surrog), len(st))
def test_dither_spike_train_output_format(self):
spiketrain = neo.SpikeTrain(
[90, 150, 180, 350] * pq.ms, t_stop=500 * pq.ms)
n_surrogates = 2
shift = 10 * pq.ms
surrogate_trains = surr.dither_spike_train(
spiketrain, shift=shift, n_surrogates=n_surrogates)
self.assertIsInstance(surrogate_trains, list)
self.assertEqual(len(surrogate_trains), n_surrogates)
self.assertIsInstance(surrogate_trains[0], neo.SpikeTrain)
for surrogate_train in surrogate_trains:
self.assertEqual(surrogate_train.units, spiketrain.units)
self.assertEqual(surrogate_train.t_start, spiketrain.t_start)
self.assertEqual(surrogate_train.t_stop, spiketrain.t_stop)
self.assertEqual(len(surrogate_train), len(spiketrain))
def compound_poisson_process(rate, A, t_stop, shift=None, t_start=0 * ms):
"""
Generate a Compound Poisson Process (CPP; see [1]) with a given amplitude
distribution A and stationary marginal rates r.
The CPP process is a model for parallel, correlated processes with Poisson
spiking statistics at pre-defined firing rates. It is composed of len(A)-1
spike trains with a correlation structure determined by the amplitude
distribution A: A[j] is the probability that a spike occurs synchronously
in any j spike trains.
The CPP is generated by creating a hidden mother Poisson process, and then
copying spikes of the mother process to j of the output spike trains with
probability A[j].
Note that this function decorrelates the firing rate of each SpikeTrain
from the probability for that SpikeTrain to participate in a synchronous
event (which is uniform across SpikeTrains).
Parameters
----------
rate : quantities.Quantity
Average rate of each spike train generated. Can be:
- a single value, all spike trains will have same rate rate
- an array of values (of length len(A)-1), each indicating the
firing rate of one process in output
A : array
CPP's amplitude distribution. A[j] represents the probability of
a synchronous event of size j among the generated spike trains.
The sum over all entries of A must be equal to one.
t_stop : quantities.Quantity
The end time of the output spike trains.
shift : None or quantities.Quantity, optional
If None, the injected synchrony is exact. If shift is a Quantity, all
the spike trains are shifted independently by a random amount in
the interval [-shift, +shift].
Default: None
t_start : quantities.Quantity, optional
The t_start time of the output spike trains.
Default: 0 s
Returns
-------
List of neo.SpikeTrains
SpikeTrains with specified firing rates forming the CPP with amplitude
distribution A.
References
----------
[1] Staude, Rotter, Gruen (2010) J Comput Neurosci 29:327-350.
"""
# Check A is a probability distribution (it sums to 1 and is positive)
if abs(sum(A) - 1) > np.finfo('float').eps:
raise ValueError('A must be a probability vector, sum(A)= %f !=1' %
(sum(A)))
if any([a < 0 for a in A]):
raise ValueError(
'A must be a probability vector, all the elements of must be >0')
# Check that the rate is not an empty Quantity
if rate.ndim == 1 and len(rate.magnitude) == 0:
raise ValueError('Rate is an empty Quantity array')
# Return empty spike trains for specific parameters
elif A[0] == 1 or np.sum(np.abs(rate.magnitude)) == 0:
return [
SpikeTrain([] * t_stop.units, t_stop=t_stop, t_start=t_start)
for i in range(len(A) - 1)
]
else:
# Homogeneous rates
if rate.ndim == 0:
cpp = _cpp_hom_stat(A=A, t_stop=t_stop, rate=rate, t_start=t_start)
# Heterogeneous rates
else:
cpp = _cpp_het_stat(A=A, t_stop=t_stop, rate=rate, t_start=t_start)
if shift is None:
return cpp
# Dither the output spiketrains
else:
cpp = [
dither_spike_train(cp, shift=shift, edges=True)[0]
for cp in cpp
]
return cpp
def compound_poisson_process(rate, A, t_stop, shift=None, t_start=0 * ms):
"""
Generate a Compound Poisson Process (CPP; see [1]) with a given amplitude
distribution A and stationary marginal rates r.
The CPP process is a model for parallel, correlated processes with Poisson
spiking statistics at pre-defined firing rates. It is composed of len(A)-1
spike trains with a correlation structure determined by the amplitude
distribution A: A[j] is the probability that a spike occurs synchronously
in any j spike trains.
The CPP is generated by creating a hidden mother Poisson process, and then
copying spikes of the mother process to j of the output spike trains with
probability A[j].
Note that this function decorrelates the firing rate of each SpikeTrain
from the probability for that SpikeTrain to participate in a synchronous
event (which is uniform across SpikeTrains).
Parameters
----------
rate : quantities.Quantity
Average rate of each spike train generated. Can be:
- a single value, all spike trains will have same rate rate
- an array of values (of length len(A)-1), each indicating the
firing rate of one process in output
A : array
CPP's amplitude distribution. A[j] represents the probability of
a synchronous event of size j among the generated spike trains.
The sum over all entries of A must be equal to one.
t_stop : quantities.Quantity
The end time of the output spike trains.
shift : None or quantities.Quantity, optional
If None, the injected synchrony is exact. If shift is a Quantity, all
the spike trains are shifted independently by a random amount in
the interval [-shift, +shift].
Default: None
t_start : quantities.Quantity, optional
The t_start time of the output spike trains.
Default: 0 s
Returns
-------
List of neo.SpikeTrains
SpikeTrains with specified firing rates forming the CPP with amplitude
distribution A.
References
----------
[1] Staude, Rotter, Gruen (2010) J Comput Neurosci 29:327-350.
"""
# Check A is a probability distribution (it sums to 1 and is positive)
if abs(sum(A) - 1) > np.finfo('float').eps:
raise ValueError(
'A must be a probability vector, sum(A)= %f !=1' % (sum(A)))
if any([a < 0 for a in A]):
raise ValueError(
'A must be a probability vector, all the elements of must be >0')
# Check that the rate is not an empty Quantity
if rate.ndim == 1 and len(rate.magnitude) == 0:
raise ValueError('Rate is an empty Quantity array')
# Return empty spike trains for specific parameters
elif A[0] == 1 or np.sum(np.abs(rate.magnitude)) == 0:
return [
SpikeTrain([] * t_stop.units, t_stop=t_stop,
t_start=t_start) for i in range(len(A) - 1)]
else:
# Homogeneous rates
if rate.ndim == 0:
cpp = _cpp_hom_stat(A=A, t_stop=t_stop, rate=rate, t_start=t_start)
# Heterogeneous rates
else:
cpp = _cpp_het_stat(A=A, t_stop=t_stop, rate=rate, t_start=t_start)
if shift is None:
return cpp
# Dither the output spiketrains
else:
cpp = [
dither_spike_train(cp, shift=shift, edges=True)[0]
for cp in cpp]
return cpp