def test_joint_isi_dithering_format(self):
rate = 100. * pq.Hz
t_stop = 1. * pq.s
spiketrain = stg.homogeneous_poisson_process(rate, t_stop=t_stop)
n_surrogates = 2
dither = 10 * pq.ms
# Test fast version
joint_isi_instance = surr.JointISI(spiketrain, dither=dither)
surrogate_trains = joint_isi_instance.dithering(
n_surrogates=n_surrogates)
self.assertIsInstance(surrogate_trains, list)
self.assertEqual(len(surrogate_trains), n_surrogates)
self.assertEqual(joint_isi_instance.method, 'fast')
for surrogate_train in surrogate_trains:
self.assertIsInstance(surrogate_train, neo.SpikeTrain)
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))
# Test window_version
joint_isi_instance = surr.JointISI(spiketrain,
method='window',
dither=2 * dither,
num_bins=50)
surrogate_trains = joint_isi_instance.dithering(
n_surrogates=n_surrogates)
self.assertIsInstance(surrogate_trains, list)
self.assertEqual(len(surrogate_trains), n_surrogates)
self.assertEqual(joint_isi_instance.method, 'window')
for surrogate_train in surrogate_trains:
self.assertIsInstance(surrogate_train, neo.SpikeTrain)
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))
# Test surrogate methods wrapper
surrogate_trains = surr.surrogates(spiketrain,
n=n_surrogates,
surr_method='joint_isi_dithering')
self.assertIsInstance(surrogate_trains, list)
self.assertEqual(len(surrogate_trains), n_surrogates)
for surrogate_train in surrogate_trains:
self.assertIsInstance(surrogate_train, neo.SpikeTrain)
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 test_joint_isi_dithering_output(self):
process = stg.StationaryPoissonProcess(
rate=100. * pq.Hz, refractory_period=3 * pq.ms, t_stop=0.1 * pq.s)
spiketrain = process.generate_spiketrain()
surrogate_train = surr.JointISI(spiketrain).dithering()[0]
ground_truth = [0.0060744, 0.01886591, 0.02732847, 0.03683888,
0.04569622, 0.05196334, 0.05899197, 0.07855664]
assert_array_almost_equal(surrogate_train.magnitude, ground_truth)
def test_joint_isi_dithering_output(self):
spiketrain = stg.homogeneous_poisson_process(
rate=100. * pq.Hz,
refractory_period=3 * pq.ms,
t_stop=0.1 * pq.s)
surrogate_train = surr.JointISI(spiketrain).dithering()[0]
ground_truth = [0.005571, 0.018363, 0.026825, 0.036336, 0.045193,
0.05146, 0.058489, 0.078053]
assert_array_almost_equal(surrogate_train.magnitude, ground_truth)
def test_joint_isi_dithering_empty_train(self):
spiketrain = neo.SpikeTrain([] * pq.ms, t_stop=500 * pq.ms)
surrogate_train = surr.JointISI(spiketrain).dithering()[0]
self.assertEqual(len(surrogate_train), 0)
def test_joint_isi_dithering_format(self):
rate = 100. * pq.Hz
t_stop = 1. * pq.s
spiketrain = stg.homogeneous_poisson_process(rate, t_stop=t_stop)
n_surrogates = 2
dither = 10 * pq.ms
# Test fast version
joint_isi_instance = surr.JointISI(spiketrain,
dither=dither,
method='fast')
surrogate_trains = joint_isi_instance.dithering(
n_surrogates=n_surrogates)
self.assertIsInstance(surrogate_trains, list)
self.assertEqual(len(surrogate_trains), n_surrogates)
self.assertEqual(joint_isi_instance.method, 'fast')
for surrogate_train in surrogate_trains:
self.assertIsInstance(surrogate_train, neo.SpikeTrain)
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))
# Test window_version
joint_isi_instance = surr.JointISI(spiketrain,
method='window',
dither=2 * dither,
n_bins=50)
surrogate_trains = joint_isi_instance.dithering(
n_surrogates=n_surrogates)
self.assertIsInstance(surrogate_trains, list)
self.assertEqual(len(surrogate_trains), n_surrogates)
self.assertEqual(joint_isi_instance.method, 'window')
for surrogate_train in surrogate_trains:
self.assertIsInstance(surrogate_train, neo.SpikeTrain)
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))
# Test isi_dithering
joint_isi_instance = surr.JointISI(spiketrain,
method='window',
dither=2 * dither,
n_bins=50,
isi_dithering=True,
use_sqrt=True,
cutoff=False)
surrogate_trains = joint_isi_instance.dithering(
n_surrogates=n_surrogates)
self.assertIsInstance(surrogate_trains, list)
self.assertEqual(len(surrogate_trains), n_surrogates)
self.assertEqual(joint_isi_instance.method, 'window')
for surrogate_train in surrogate_trains:
self.assertIsInstance(surrogate_train, neo.SpikeTrain)
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))
# Test surrogate methods wrapper
surrogate_trains = surr.surrogates(spiketrain,
dt=15 * pq.ms,
n_surrogates=n_surrogates,
method='joint_isi_dithering')
self.assertIsInstance(surrogate_trains, list)
self.assertEqual(len(surrogate_trains), n_surrogates)
for surrogate_train in surrogate_trains:
self.assertIsInstance(surrogate_train, neo.SpikeTrain)
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))
with self.assertRaises(ValueError):
joint_isi_instance = surr.JointISI(spiketrain,
method='wrong method',
dither=2 * dither,
n_bins=50)
