def test__get_epochs(self):
a = Epoch([0.5, 10.0, 25.2] * pq.s, durations=[5.1, 4.8, 5.0] * pq.s)
a.annotate(epoch_type='a', pick='me')
a.array_annotate(trial_id=[1, 2, 3])
b = Epoch([5.5, 14.9, 30.1] * pq.s, durations=[4.7, 4.9, 5.2] * pq.s)
b.annotate(epoch_type='b')
b.array_annotate(trial_id=[1, 2, 3])
proxy_epoch = EpochProxy(rawio=self.reader,
event_channel_index=1,
block_index=0,
seg_index=0)
proxy_epoch.annotate(epoch_type='a')
seg = Segment()
seg.epochs = [a, b, proxy_epoch]
# test getting multiple epochs including a proxy
extracted_epochs = get_epochs(seg, epoch_type='a')
self.assertEqual(len(extracted_epochs), 2)
# make sure the epoch is loaded and a neo.Epoch object is returned
self.assertTrue(isinstance(extracted_epochs[0], Epoch))
self.assertTrue(isinstance(extracted_epochs[1], Epoch))
def test__cut_block_by_epochs(self):
seg = Segment()
proxy_anasig = AnalogSignalProxy(rawio=self.reader,
global_channel_indexes=None,
block_index=0,
seg_index=0)
seg.analogsignals.append(proxy_anasig)
proxy_st = SpikeTrainProxy(rawio=self.reader,
unit_index=0,
block_index=0,
seg_index=0)
seg.spiketrains.append(proxy_st)
proxy_event = EventProxy(rawio=self.reader,
event_channel_index=0,
block_index=0,
seg_index=0)
seg.events.append(proxy_event)
proxy_epoch = EpochProxy(rawio=self.reader,
event_channel_index=1,
block_index=0,
seg_index=0)
proxy_epoch.annotate(pick='me')
seg.epochs.append(proxy_epoch)
loaded_epoch = proxy_epoch.load()
loaded_event = proxy_event.load()
loaded_st = proxy_st.load()
loaded_anasig = proxy_anasig.load()
block = Block()
block.segments = [seg]
block.create_many_to_one_relationship()
cut_block_by_epochs(block, properties={'pick': 'me'})
assert_neo_object_is_compliant(block)
self.assertEqual(len(block.segments), proxy_epoch.shape[0])
for epoch_idx in range(len(loaded_epoch)):
sliced_event = loaded_event.time_slice(
t_start=loaded_epoch.times[epoch_idx],
t_stop=loaded_epoch.times[epoch_idx] +
loaded_epoch.durations[epoch_idx])
has_event = len(sliced_event) > 0
sliced_anasig = loaded_anasig.time_slice(
t_start=loaded_epoch.times[epoch_idx],
t_stop=loaded_epoch.times[epoch_idx] +
loaded_epoch.durations[epoch_idx])
sliced_st = loaded_st.time_slice(
t_start=loaded_epoch.times[epoch_idx],
t_stop=loaded_epoch.times[epoch_idx] +
loaded_epoch.durations[epoch_idx])
self.assertEqual(len(block.segments[epoch_idx].events),
int(has_event))
self.assertEqual(len(block.segments[epoch_idx].spiketrains), 1)
self.assertEqual(len(block.segments[epoch_idx].analogsignals), 1)
self.assertTrue(
isinstance(block.segments[epoch_idx].spiketrains[0],
SpikeTrain))
assert_same_attributes(block.segments[epoch_idx].spiketrains[0],
sliced_st)
self.assertTrue(
isinstance(block.segments[epoch_idx].analogsignals[0],
AnalogSignal))
assert_same_attributes(block.segments[epoch_idx].analogsignals[0],
sliced_anasig)
if has_event:
self.assertTrue(
isinstance(block.segments[epoch_idx].events[0], Event))
assert_same_attributes(block.segments[epoch_idx].events[0],
sliced_event)
block2 = Block()
seg2 = Segment()
epoch = Epoch(np.arange(10) * pq.s, durations=np.ones((10)) * pq.s)
epoch.annotate(pick='me instead')
seg2.epochs = [proxy_epoch, epoch]
block2.segments = [seg2]
block2.create_many_to_one_relationship()
# test correct loading and slicing of EpochProxy objects
# (not tested above since we used the EpochProxy to cut the block)
cut_block_by_epochs(block2, properties={'pick': 'me instead'})
for epoch_idx in range(len(epoch)):
sliced_epoch = loaded_epoch.time_slice(
t_start=epoch.times[epoch_idx],
t_stop=epoch.times[epoch_idx] + epoch.durations[epoch_idx])
has_epoch = len(sliced_epoch) > 0
if has_epoch:
self.assertTrue(
isinstance(block2.segments[epoch_idx].epochs[0], Epoch))
assert_same_attributes(block2.segments[epoch_idx].epochs[0],
sliced_epoch)
def test__time_slice(self):
time_slice = [.5, 5.6] * pq.s
epoch2 = Epoch([0.6, 9.5, 16.8, 34.1] * pq.s,
durations=[4.5, 4.8, 5.0, 5.0] * pq.s,
t_start=.1 * pq.s)
epoch2.annotate(epoch_type='b')
epoch2.array_annotate(trial_id=[1, 2, 3, 4])
event = Event(times=[0.5, 10.0, 25.2] * pq.s, t_start=.1 * pq.s)
event.annotate(event_type='trial start')
event.array_annotate(trial_id=[1, 2, 3])
anasig = AnalogSignal(np.arange(50.0) * pq.mV,
t_start=.1 * pq.s,
sampling_rate=1.0 * pq.Hz)
irrsig = IrregularlySampledSignal(signal=np.arange(50.0) * pq.mV,
times=anasig.times,
t_start=.1 * pq.s)
st = SpikeTrain(
np.arange(0.5, 50, 7) * pq.s,
t_start=.1 * pq.s,
t_stop=50.0 * pq.s,
waveforms=np.array(
[[[0., 1.], [0.1, 1.1]], [[2., 3.], [2.1, 3.1]],
[[4., 5.], [4.1, 5.1]], [[6., 7.], [6.1, 7.1]],
[[8., 9.], [8.1, 9.1]], [[12., 13.], [12.1, 13.1]],
[[14., 15.], [14.1, 15.1]], [[16., 17.], [16.1, 17.1]]]) *
pq.mV,
array_annotations={'spikenum': np.arange(1, 9)})
seg = Segment()
seg.epochs = [epoch2]
seg.events = [event]
seg.analogsignals = [anasig]
seg.irregularlysampledsignals = [irrsig]
seg.spiketrains = [st]
block = Block()
block.segments = [seg]
block.create_many_to_one_relationship()
# test without resetting the time
sliced = seg.time_slice(time_slice[0], time_slice[1])
assert_neo_object_is_compliant(sliced)
self.assertEqual(len(sliced.events), 1)
self.assertEqual(len(sliced.spiketrains), 1)
self.assertEqual(len(sliced.analogsignals), 1)
self.assertEqual(len(sliced.irregularlysampledsignals), 1)
self.assertEqual(len(sliced.epochs), 1)
assert_same_attributes(
sliced.spiketrains[0],
st.time_slice(t_start=time_slice[0], t_stop=time_slice[1]))
assert_same_attributes(
sliced.analogsignals[0],
anasig.time_slice(t_start=time_slice[0], t_stop=time_slice[1]))
assert_same_attributes(
sliced.irregularlysampledsignals[0],
irrsig.time_slice(t_start=time_slice[0], t_stop=time_slice[1]))
assert_same_attributes(
sliced.events[0],
event.time_slice(t_start=time_slice[0], t_stop=time_slice[1]))
assert_same_attributes(
sliced.epochs[0],
epoch2.time_slice(t_start=time_slice[0], t_stop=time_slice[1]))
seg = Segment()
seg.epochs = [epoch2]
seg.events = [event]
seg.analogsignals = [anasig]
seg.irregularlysampledsignals = [irrsig]
seg.spiketrains = [st]
block = Block()
block.segments = [seg]
block.create_many_to_one_relationship()
# test with resetting the time
sliced = seg.time_slice(time_slice[0], time_slice[1], reset_time=True)
assert_neo_object_is_compliant(sliced)
self.assertEqual(len(sliced.events), 1)
self.assertEqual(len(sliced.spiketrains), 1)
self.assertEqual(len(sliced.analogsignals), 1)
self.assertEqual(len(sliced.irregularlysampledsignals), 1)
self.assertEqual(len(sliced.epochs), 1)
assert_same_attributes(
sliced.spiketrains[0],
st.time_shift(-time_slice[0]).time_slice(t_start=0 * pq.s,
t_stop=time_slice[1] -
time_slice[0]))
anasig_target = anasig.copy()
anasig_target = anasig_target.time_shift(-time_slice[0]).time_slice(
t_start=0 * pq.s, t_stop=time_slice[1] - time_slice[0])
assert_same_attributes(sliced.analogsignals[0], anasig_target)
irrsig_target = irrsig.copy()
irrsig_target = irrsig_target.time_shift(-time_slice[0]).time_slice(
t_start=0 * pq.s, t_stop=time_slice[1] - time_slice[0])
assert_same_attributes(sliced.irregularlysampledsignals[0],
irrsig_target)
assert_same_attributes(
sliced.events[0],
event.time_shift(-time_slice[0]).time_slice(t_start=0 * pq.s,
t_stop=time_slice[1] -
time_slice[0]))
assert_same_attributes(
sliced.epochs[0],
epoch2.time_shift(-time_slice[0]).time_slice(t_start=0 * pq.s,
t_stop=time_slice[1] -
time_slice[0]))
seg = Segment()
reader = ExampleRawIO(filename='my_filename.fake')
reader.parse_header()
proxy_anasig = AnalogSignalProxy(rawio=reader,
stream_index=0,
inner_stream_channels=None,
block_index=0,
seg_index=0)
seg.analogsignals.append(proxy_anasig)
proxy_st = SpikeTrainProxy(rawio=reader,
spike_channel_index=0,
block_index=0,
seg_index=0)
seg.spiketrains.append(proxy_st)
proxy_event = EventProxy(rawio=reader,
event_channel_index=0,
block_index=0,
seg_index=0)
seg.events.append(proxy_event)
proxy_epoch = EpochProxy(rawio=reader,
event_channel_index=1,
block_index=0,
seg_index=0)
proxy_epoch.annotate(pick='me')
seg.epochs.append(proxy_epoch)
loaded_epoch = proxy_epoch.load()
loaded_event = proxy_event.load()
loaded_st = proxy_st.load()
loaded_anasig = proxy_anasig.load()
block = Block()
block.segments = [seg]
block.create_many_to_one_relationship()
# test with proxy objects
sliced = seg.time_slice(time_slice[0], time_slice[1])
assert_neo_object_is_compliant(sliced)
sliced_event = loaded_event.time_slice(t_start=time_slice[0],
t_stop=time_slice[1])
has_event = len(sliced_event) > 0
sliced_anasig = loaded_anasig.time_slice(t_start=time_slice[0],
t_stop=time_slice[1])
sliced_st = loaded_st.time_slice(t_start=time_slice[0],
t_stop=time_slice[1])
self.assertEqual(len(sliced.events), int(has_event))
self.assertEqual(len(sliced.spiketrains), 1)
self.assertEqual(len(sliced.analogsignals), 1)
self.assertTrue(isinstance(sliced.spiketrains[0], SpikeTrain))
assert_same_attributes(sliced.spiketrains[0], sliced_st)
self.assertTrue(isinstance(sliced.analogsignals[0], AnalogSignal))
assert_same_attributes(sliced.analogsignals[0], sliced_anasig)
if has_event:
self.assertTrue(isinstance(sliced.events[0], Event))
assert_same_attributes(sliced.events[0], sliced_event)