def test_gap_warning(self):
nio = NeuralynxIO(self.sn, use_cache='never')
with reset_warning_registry():
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
nio.read_block(t_starts=None, t_stops=None)
self.assertGreater(len(w), 0)
self.assertTrue(issubclass(w[0].category, UserWarning))
self.assertEqual('Substituted t_starts and t_stops in order to'
' skip gap in recording session.',
str(w[0].message))
def test_gap_warning(self):
nio = NeuralynxIO(self.sn, use_cache='never')
with reset_warning_registry():
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
nio.read_block(t_starts=None, t_stops=None)
self.assertGreater(len(w), 0)
self.assertTrue(issubclass(w[0].category, UserWarning))
self.assertEqual('Substituted t_starts and t_stops in order to'
' skip gap in recording session.',
str(w[0].message))
def test_read_block(self):
"""Read data in a certain time range into one block"""
t_start, t_stop = 3 * pq.s, 4 * pq.s
nio = NeuralynxIO(self.sn, use_cache='never')
block = nio.read_block(t_starts=[t_start], t_stops=[t_stop])
self.assertEqual(len(nio.parameters_ncs), 5)
self.assertTrue({
'event_id': 19,
'name': 'Starting Recording',
'nttl': 0
} in nio.parameters_nev['Events.nev']['event_types'])
self.assertTrue({
'event_id': 19,
'name': 'Stopping Recording',
'nttl': 0
} in nio.parameters_nev['Events.nev']['event_types'])
# Everything put in one segment
self.assertEqual(len(block.segments), 1)
seg = block.segments[0]
self.assertEqual(len(seg.analogsignals), 1)
self.assertEqual(seg.analogsignals[0].shape[-1], 5)
self.assertEqual(seg.analogsignals[0].sampling_rate.units,
pq.CompoundUnit('32*kHz'))
self.assertAlmostEqual(seg.analogsignals[0].t_start, t_start, places=4)
self.assertAlmostEqual(seg.analogsignals[0].t_stop, t_stop, places=4)
self.assertEqual(len(seg.spiketrains), 0) # no nse files available
# Testing different parameter combinations
block = nio.read_block(lazy=True)
self.assertEqual(len(block.segments[0].analogsignals[0]), 0)
block = nio.read_block(cascade=False)
self.assertEqual(len(block.segments), 0)
block = nio.read_block(electrode_list=[0])
self.assertEqual(len(block.segments[0].analogsignals), 1)
block = nio.read_block(t_starts=None,
t_stops=None,
events=True,
waveforms=True)
self.assertEqual(len(block.segments[0].analogsignals), 1)
self.assertEqual(len(block.segments[0].spiketrains), 0)
self.assertGreater(len(block.segments[0].events), 0)
self.assertEqual(len(block.channel_indexes), 5)
def test_read_block(self):
"""Read data in a certain time range into one block"""
t_start, t_stop = 3 * pq.s, 4 * pq.s
nio = NeuralynxIO(self.sn, use_cache='never')
block = nio.read_block(t_starts=[t_start], t_stops=[t_stop])
self.assertEqual(len(nio.parameters_ncs), 5)
self.assertTrue(
{'event_id': 19, 'name': 'Starting Recording', 'nttl': 0} in
nio.parameters_nev['Events.nev']['event_types'])
self.assertTrue(
{'event_id': 19, 'name': 'Stopping Recording', 'nttl': 0} in
nio.parameters_nev['Events.nev']['event_types'])
# Everything put in one segment
self.assertEqual(len(block.segments), 1)
seg = block.segments[0]
self.assertEqual(len(seg.analogsignals), 1)
self.assertEqual(seg.analogsignals[0].shape[-1], 5)
self.assertEqual(seg.analogsignals[0].sampling_rate.units,
pq.CompoundUnit('32*kHz'))
self.assertAlmostEqual(seg.analogsignals[0].t_start, t_start, places=4)
self.assertAlmostEqual(seg.analogsignals[0].t_stop, t_stop, places=4)
self.assertEqual(len(seg.spiketrains), 0) # no nse files available
# Testing different parameter combinations
block = nio.read_block(lazy=True)
self.assertEqual(len(block.segments[0].analogsignals[0]), 0)
block = nio.read_block(cascade=False)
self.assertEqual(len(block.segments), 0)
block = nio.read_block(electrode_list=[0])
self.assertEqual(len(block.segments[0].analogsignals), 1)
block = nio.read_block(t_starts=None, t_stops=None, events=True,
waveforms=True)
self.assertEqual(len(block.segments[0].analogsignals), 1)
self.assertEqual(len(block.segments[0].spiketrains), 0)
self.assertGreater(len(block.segments[0].events), 0)
self.assertEqual(len(block.channel_indexes), 5)
def test_gap_handling(self):
nio = NeuralynxIO(self.sn, use_cache='never')
block = nio.read_block(t_starts=None, t_stops=None)
# known gap values
n_gaps = 1
self.assertEqual(len(block.segments), n_gaps + 1)
# one channel index for analogsignals for each of the 3 segments and
# one for spiketrains
self.assertEqual(len(block.channel_indexes), len(block.segments) + 1)
self.assertEqual(len(block.channel_indexes[-1].units), 2)
for unit in block.channel_indexes[-1].units:
self.assertEqual(len(unit.spiketrains), n_gaps + 1)
anasig_channels = [i for i in block.channel_indexes
if 'analogsignal' in i.name]
self.assertEqual(len(anasig_channels), n_gaps + 1)
def test_gap_handling(self):
nio = NeuralynxIO(self.sn, use_cache='never')
block = nio.read_block(t_starts=None, t_stops=None)
# known gap values
n_gaps = 1
self.assertEqual(len(block.segments), n_gaps + 1)
# one channel index for analogsignals for each of the 3 segments and
# one for spiketrains
self.assertEqual(len(block.channel_indexes), len(block.segments) + 1)
self.assertEqual(len(block.channel_indexes[-1].units), 2)
for unit in block.channel_indexes[-1].units:
self.assertEqual(len(unit.spiketrains), n_gaps + 1)
anasig_channels = [i for i in block.channel_indexes
if 'analogsignal' in i.name]
self.assertEqual(len(anasig_channels), n_gaps + 1)