def test_surr_method(self):
st = neo.SpikeTrain([90, 150, 180, 350] * pq.ms, t_stop=500 * pq.ms)
nr_surr = 2
surrs = surr.surrogates(st, dt=3 * pq.ms, n=nr_surr,
surr_method='shuffle_isis', edges=False)
self.assertRaises(ValueError, surr.surrogates, st, n=1,
surr_method='spike_shifting',
dt=None, decimals=None, edges=True)
self.assertTrue(len(surrs) == nr_surr)
nr_surr2 = 4
surrs2 = surr.surrogates(st, dt=5 * pq.ms, n=nr_surr2,
surr_method='dither_spike_train', edges=True)
for surrog in surrs:
self.assertTrue(isinstance(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))
self.assertTrue(len(surrs) == nr_surr)
for surrog in surrs2:
self.assertTrue(isinstance(surrs2[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))
self.assertTrue(len(surrs2) == nr_surr2)
def test_joint_isi_spikes_at_border(self):
surr_method = 'joint_isi_dithering'
n_surr = 30
dither = 15 * pq.ms
spiketrain = neo.SpikeTrain(
[4., 28., 45., 51., 83., 87., 96., 111., 126., 131.,
138., 150.,
209., 232., 253., 275., 279., 303., 320., 371., 396.,
401., 429., 447.,
479., 511., 535., 549., 581., 585., 605., 607., 626.,
630., 644., 714.,
832., 835., 853., 858., 878., 905., 909., 932., 950.,
961., 999., 1000.],
t_start=0.*pq.ms, t_stop=1000.*pq.ms, units=pq.ms)
surr.surrogates(
spiketrain, n_surrogates=n_surr, method=surr_method, dt=dither)
def test_joint_isi_with_wrongly_ordered_spikes(self):
surr_method = 'joint_isi_dithering'
n_surr = 30
dither = 15 * pq.ms
spiketrain = neo.SpikeTrain(
[39.65696411, 98.93868274, 120.2417674, 134.70971166,
154.20788924,
160.29077989, 179.19884034, 212.86773029, 247.59488061,
273.04095041,
297.56437605, 344.99204215, 418.55696486, 460.54298334,
482.82299125,
524.236052, 566.38966742, 597.87562722, 651.26965293,
692.39802855,
740.90285815, 849.45874695, 974.57724848, 8.79247605],
t_start=0.*pq.ms, t_stop=1000.*pq.ms, units=pq.ms)
surr.surrogates(spiketrain, n_surrogates=n_surr, method=surr_method,
dt=dither)
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_surr_method(self):
surr_methods = \
('dither_spike_train', 'dither_spikes', 'jitter_spikes',
'randomise_spikes', 'shuffle_isis', 'joint_isi_dithering',
'dither_spikes_with_refractory_period', 'trial_shifting',
'bin_shuffling', 'isi_dithering')
surr_method_kwargs = \
{'dither_spikes': {},
'dither_spikes_with_refractory_period': {'refractory_period':
3*pq.ms},
'randomise_spikes': {},
'shuffle_isis': {},
'dither_spike_train': {},
'jitter_spikes': {},
'bin_shuffling': {'bin_size': 3*pq.ms},
'joint_isi_dithering': {},
'isi_dithering': {},
'trial_shifting': {'trial_length': 200*pq.ms,
'trial_separation': 50*pq.ms}}
dt = 15 * pq.ms
spiketrain = neo.SpikeTrain(
[90, 150, 180, 350] * pq.ms, t_stop=500 * pq.ms)
n_surrogates = 3
for method in surr_methods:
surrogates = surr.surrogates(
spiketrain,
dt=dt,
n_surrogates=n_surrogates,
method=method,
**surr_method_kwargs[method]
)
self.assertTrue(len(surrogates) == n_surrogates)
for surrogate_train in surrogates:
self.assertTrue(
isinstance(surrogates[0], 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))
self.assertTrue(len(surrogates) == n_surrogates)
self.assertRaises(ValueError, surr.surrogates, spiketrain,
n_surrogates=1,
method='spike_shifting',
dt=None, decimals=None, edges=True)
self.assertRaises(ValueError, surr.surrogates, spiketrain,
method='dither_spikes', dt=None)
self.assertRaises(TypeError, surr.surrogates, spiketrain.magnitude,
method='dither_spikes', dt=10*pq.ms)
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)
