def test_time_slice_None(self):
time_slices = [(None, 5.0 * pq.s), (5.0 * pq.s, None), (None, None)]
anasig = AnalogSignal(np.arange(50.0) * pq.mV,
sampling_rate=1.0 * pq.Hz)
seg = Segment()
seg.analogsignals = [anasig]
block = Block()
block.segments = [seg]
block.create_many_to_one_relationship()
# test without resetting the time
for t_start, t_stop in time_slices:
sliced = seg.time_slice(t_start, t_stop)
assert_neo_object_is_compliant(sliced)
self.assertEqual(len(sliced.analogsignals), 1)
exp_t_start, exp_t_stop = t_start, t_stop
if exp_t_start is None:
exp_t_start = seg.t_start
if exp_t_stop is None:
exp_t_stop = seg.t_stop
self.assertEqual(exp_t_start, sliced.t_start)
self.assertEqual(exp_t_stop, sliced.t_stop)
def test__children(self):
blk = Block(name='block1')
blk.segments = [self.seg1]
blk.create_many_to_one_relationship(force=True)
assert_neo_object_is_compliant(self.seg1)
assert_neo_object_is_compliant(blk)
childobjs = ('AnalogSignal', 'Epoch', 'Event',
'IrregularlySampledSignal', 'SpikeTrain', 'ImageSequence')
childconts = ('analogsignals', 'epochs', 'events',
'irregularlysampledsignals', 'spiketrains',
'imagesequences')
self.assertEqual(self.seg1._container_child_objects, ())
self.assertEqual(self.seg1._data_child_objects, childobjs)
self.assertEqual(self.seg1._single_parent_objects, ('Block', ))
self.assertEqual(self.seg1._multi_child_objects, ())
self.assertEqual(self.seg1._multi_parent_objects, ())
self.assertEqual(self.seg1._child_properties, ())
self.assertEqual(self.seg1._single_child_objects, childobjs)
self.assertEqual(self.seg1._container_child_containers, ())
self.assertEqual(self.seg1._data_child_containers, childconts)
self.assertEqual(self.seg1._single_child_containers, childconts)
self.assertEqual(self.seg1._single_parent_containers, ('block', ))
self.assertEqual(self.seg1._multi_child_containers, ())
self.assertEqual(self.seg1._multi_parent_containers, ())
self.assertEqual(self.seg1._child_objects, childobjs)
self.assertEqual(self.seg1._child_containers, childconts)
self.assertEqual(self.seg1._parent_objects, ('Block', ))
self.assertEqual(self.seg1._parent_containers, ('block', ))
totchildren = (
self.nchildren * 2 + # epoch/event
self.nchildren + # analogsignal
self.nchildren**2 + # spiketrain
self.nchildren + # irregsignal
self.nchildren) # imagesequence
self.assertEqual(len(self.seg1._single_children), totchildren)
self.assertEqual(len(self.seg1.data_children), totchildren)
self.assertEqual(len(self.seg1.children), totchildren)
self.assertEqual(len(self.seg1.data_children_recur), totchildren)
self.assertEqual(len(self.seg1.children_recur), totchildren)
self.assertEqual(len(self.seg1._multi_children), 0)
self.assertEqual(len(self.seg1.container_children), 0)
self.assertEqual(len(self.seg1.container_children_recur), 0)
children = (self.sigarrs1a + self.epcs1a + self.evts1a +
self.irsigs1a + self.trains1a + self.img_seqs1a)
assert_same_sub_schema(list(self.seg1._single_children), children)
assert_same_sub_schema(list(self.seg1.data_children), children)
assert_same_sub_schema(list(self.seg1.data_children_recur), children)
assert_same_sub_schema(list(self.seg1.children), children)
assert_same_sub_schema(list(self.seg1.children_recur), children)
self.assertEqual(len(self.seg1.parents), 1)
self.assertEqual(self.seg1.parents[0].name, 'block1')
def simple_block():
block = Block(
name="test block",
species="rat",
brain_region="cortex"
)
block.segments = [
Segment(name="test segment #1",
cell_type="spiny stellate"),
Segment(name="test segment #2",
cell_type="pyramidal",
thing="amajig")
]
for segment in block.segments:
segment.block = block
block.segments[0].analogsignals.extend((
random_signal(name="signal #1 in segment #1", thing="wotsit"),
random_signal(name="signal #2 in segment #1", thing="frooble"),
))
block.segments[1].analogsignals.extend((
random_signal(name="signal #1 in segment #2", thing="amajig"),
))
block.segments[1].irregularlysampledsignals.extend((
random_irreg_signal(name="signal #1 in segment #2", thing="amajig"),
))
block.segments[0].events.extend((
random_event(name="event array #1 in segment #1", thing="frooble"),
))
block.segments[1].events.extend((
random_event(name="event array #1 in segment #2", thing="wotsit"),
))
block.segments[0].spiketrains.extend((
random_spiketrain(name="spiketrain #1 in segment #1", thing="frooble"),
random_spiketrain(name="spiketrain #2 in segment #1", thing="wotsit")
))
return block
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__cut_block_by_epochs(self):
epoch = Epoch([0.5, 10.0, 25.2] * pq.s,
durations=[5.1, 4.8, 5.0] * pq.s,
t_start=.1 * pq.s)
epoch.annotate(epoch_type='a', pick='me')
epoch.array_annotate(trial_id=[1, 2, 3])
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()
seg2 = Segment(name='NoCut')
seg.epochs = [epoch, epoch2]
seg.events = [event]
seg.analogsignals = [anasig]
seg.irregularlysampledsignals = [irrsig]
seg.spiketrains = [st]
block = Block()
block.segments = [seg, seg2]
block.create_many_to_one_relationship()
# test without resetting the time
cut_block_by_epochs(block, properties={'pick': 'me'})
assert_neo_object_is_compliant(block)
self.assertEqual(len(block.segments), 3)
for epoch_idx in range(len(epoch)):
self.assertEqual(len(block.segments[epoch_idx].events), 1)
self.assertEqual(len(block.segments[epoch_idx].spiketrains), 1)
self.assertEqual(len(block.segments[epoch_idx].analogsignals), 1)
self.assertEqual(
len(block.segments[epoch_idx].irregularlysampledsignals), 1)
if epoch_idx != 0:
self.assertEqual(len(block.segments[epoch_idx].epochs), 1)
else:
self.assertEqual(len(block.segments[epoch_idx].epochs), 2)
assert_same_attributes(
block.segments[epoch_idx].spiketrains[0],
st.time_slice(t_start=epoch.times[epoch_idx],
t_stop=epoch.times[epoch_idx] +
epoch.durations[epoch_idx]))
assert_same_attributes(
block.segments[epoch_idx].analogsignals[0],
anasig.time_slice(t_start=epoch.times[epoch_idx],
t_stop=epoch.times[epoch_idx] +
epoch.durations[epoch_idx]))
assert_same_attributes(
block.segments[epoch_idx].irregularlysampledsignals[0],
irrsig.time_slice(t_start=epoch.times[epoch_idx],
t_stop=epoch.times[epoch_idx] +
epoch.durations[epoch_idx]))
assert_same_attributes(
block.segments[epoch_idx].events[0],
event.time_slice(t_start=epoch.times[epoch_idx],
t_stop=epoch.times[epoch_idx] +
epoch.durations[epoch_idx]))
assert_same_attributes(
block.segments[0].epochs[0],
epoch.time_slice(t_start=epoch.times[0],
t_stop=epoch.times[0] + epoch.durations[0]))
assert_same_attributes(
block.segments[0].epochs[1],
epoch2.time_slice(t_start=epoch.times[0],
t_stop=epoch.times[0] + epoch.durations[0]))
seg = Segment()
seg2 = Segment(name='NoCut')
seg.epochs = [epoch, epoch2]
seg.events = [event]
seg.analogsignals = [anasig]
seg.irregularlysampledsignals = [irrsig]
seg.spiketrains = [st]
block = Block()
block.segments = [seg, seg2]
block.create_many_to_one_relationship()
# test with resetting the time
cut_block_by_epochs(block, properties={'pick': 'me'}, reset_time=True)
assert_neo_object_is_compliant(block)
self.assertEqual(len(block.segments), 3)
for epoch_idx in range(len(epoch)):
self.assertEqual(len(block.segments[epoch_idx].events), 1)
self.assertEqual(len(block.segments[epoch_idx].spiketrains), 1)
self.assertEqual(len(block.segments[epoch_idx].analogsignals), 1)
self.assertEqual(
len(block.segments[epoch_idx].irregularlysampledsignals), 1)
if epoch_idx != 0:
self.assertEqual(len(block.segments[epoch_idx].epochs), 1)
else:
self.assertEqual(len(block.segments[epoch_idx].epochs), 2)
assert_same_attributes(
block.segments[epoch_idx].spiketrains[0],
st.time_shift(-epoch.times[epoch_idx]).time_slice(
t_start=0 * pq.s, t_stop=epoch.durations[epoch_idx]))
anasig_target = anasig.time_shift(-epoch.times[epoch_idx])
anasig_target = anasig_target.time_slice(
t_start=0 * pq.s, t_stop=epoch.durations[epoch_idx])
assert_same_attributes(block.segments[epoch_idx].analogsignals[0],
anasig_target)
irrsig_target = irrsig.time_shift(-epoch.times[epoch_idx])
irrsig_target = irrsig_target.time_slice(
t_start=0 * pq.s, t_stop=epoch.durations[epoch_idx])
assert_same_attributes(
block.segments[epoch_idx].irregularlysampledsignals[0],
irrsig_target)
assert_same_attributes(
block.segments[epoch_idx].events[0],
event.time_shift(-epoch.times[epoch_idx]).time_slice(
t_start=0 * pq.s, t_stop=epoch.durations[epoch_idx]))
assert_same_attributes(
block.segments[0].epochs[0],
epoch.time_shift(-epoch.times[0]).time_slice(
t_start=0 * pq.s, t_stop=epoch.durations[0]))
assert_same_attributes(
block.segments[0].epochs[1],
epoch2.time_shift(-epoch.times[0]).time_slice(
t_start=0 * pq.s, t_stop=epoch.durations[0]))
def test__get_events(self):
starts_1 = Event(times=[0.5, 10.0, 25.2] * pq.s)
starts_1.annotate(event_type='trial start', pick='me')
starts_1.array_annotate(trial_id=[1, 2, 3])
stops_1 = Event(times=[5.5, 14.9, 30.1] * pq.s)
stops_1.annotate(event_type='trial stop')
stops_1.array_annotate(trial_id=[1, 2, 3])
starts_2 = Event(times=[33.2, 41.7, 52.4] * pq.s)
starts_2.annotate(event_type='trial start')
starts_2.array_annotate(trial_id=[4, 5, 6])
stops_2 = Event(times=[37.6, 46.1, 57.0] * pq.s)
stops_2.annotate(event_type='trial stop')
stops_2.array_annotate(trial_id=[4, 5, 6])
seg = Segment()
seg2 = Segment()
seg.events = [starts_1, stops_1]
seg2.events = [starts_2, stops_2]
block = Block()
block.segments = [seg, seg2]
# test getting one whole event via annotation
extracted_starts1 = get_events(seg, event_type='trial start')
extracted_starts1b = get_events(block, pick='me')
self.assertEqual(len(extracted_starts1), 1)
self.assertEqual(len(extracted_starts1b), 1)
extracted_starts1 = extracted_starts1[0]
extracted_starts1b = extracted_starts1b[0]
assert_same_attributes(extracted_starts1, starts_1)
assert_same_attributes(extracted_starts1b, starts_1)
# test getting an empty list by searching for a non-existent property
empty1 = get_events(seg, foo='bar')
self.assertEqual(len(empty1), 0)
# test getting an empty list by searching for a non-existent property value
empty2 = get_events(seg, event_type='undefined')
self.assertEqual(len(empty2), 0)
# test getting only one event time of one event
trial_2 = get_events(block, trial_id=2, event_type='trial start')
self.assertEqual(len(trial_2), 1)
trial_2 = trial_2[0]
self.assertEqual(starts_1.name, trial_2.name)
self.assertEqual(starts_1.description, trial_2.description)
self.assertEqual(starts_1.file_origin, trial_2.file_origin)
self.assertEqual(starts_1.annotations['event_type'],
trial_2.annotations['event_type'])
assert_arrays_equal(trial_2.array_annotations['trial_id'],
np.array([2]))
self.assertIsInstance(trial_2.array_annotations, ArrayDict)
# test getting only one event time of more than one event
trial_2b = get_events(block, trial_id=2)
self.assertEqual(len(trial_2b), 2)
start_idx = np.where(
np.array([ev.annotations['event_type']
for ev in trial_2b]) == 'trial start')[0][0]
trial_2b_start = trial_2b[start_idx]
trial_2b_stop = trial_2b[start_idx - 1]
assert_same_attributes(trial_2b_start, trial_2)
self.assertEqual(stops_1.name, trial_2b_stop.name)
self.assertEqual(stops_1.description, trial_2b_stop.description)
self.assertEqual(stops_1.file_origin, trial_2b_stop.file_origin)
self.assertEqual(stops_1.annotations['event_type'],
trial_2b_stop.annotations['event_type'])
assert_arrays_equal(trial_2b_stop.array_annotations['trial_id'],
np.array([2]))
self.assertIsInstance(trial_2b_stop.array_annotations, ArrayDict)
# test getting more than one event time of one event
trials_1_2 = get_events(block,
trial_id=[1, 2],
event_type='trial start')
self.assertEqual(len(trials_1_2), 1)
trials_1_2 = trials_1_2[0]
self.assertEqual(starts_1.name, trials_1_2.name)
self.assertEqual(starts_1.description, trials_1_2.description)
self.assertEqual(starts_1.file_origin, trials_1_2.file_origin)
self.assertEqual(starts_1.annotations['event_type'],
trials_1_2.annotations['event_type'])
assert_arrays_equal(trials_1_2.array_annotations['trial_id'],
np.array([1, 2]))
self.assertIsInstance(trials_1_2.array_annotations, ArrayDict)
# test getting more than one event time of more than one event
trials_1_2b = get_events(block, trial_id=[1, 2])
self.assertEqual(len(trials_1_2b), 2)
start_idx = np.where(
np.array([ev.annotations['event_type']
for ev in trials_1_2b]) == 'trial start')[0][0]
trials_1_2b_start = trials_1_2b[start_idx]
trials_1_2b_stop = trials_1_2b[start_idx - 1]
assert_same_attributes(trials_1_2b_start, trials_1_2)
self.assertEqual(stops_1.name, trials_1_2b_stop.name)
self.assertEqual(stops_1.description, trials_1_2b_stop.description)
self.assertEqual(stops_1.file_origin, trials_1_2b_stop.file_origin)
self.assertEqual(stops_1.annotations['event_type'],
trials_1_2b_stop.annotations['event_type'])
assert_arrays_equal(trials_1_2b_stop.array_annotations['trial_id'],
np.array([1, 2]))
self.assertIsInstance(trials_1_2b_stop.array_annotations, ArrayDict)
def test__get_epochs(self):
a_1 = Epoch([0.5, 10.0, 25.2] * pq.s, durations=[5.1, 4.8, 5.0] * pq.s)
a_1.annotate(epoch_type='a', pick='me')
a_1.array_annotate(trial_id=[1, 2, 3])
b_1 = Epoch([5.5, 14.9, 30.1] * pq.s, durations=[4.7, 4.9, 5.2] * pq.s)
b_1.annotate(epoch_type='b')
b_1.array_annotate(trial_id=[1, 2, 3])
a_2 = Epoch([33.2, 41.7, 52.4] * pq.s,
durations=[5.3, 5.0, 5.1] * pq.s)
a_2.annotate(epoch_type='a')
a_2.array_annotate(trial_id=[4, 5, 6])
b_2 = Epoch([37.6, 46.1, 57.0] * pq.s,
durations=[4.9, 5.2, 5.1] * pq.s)
b_2.annotate(epoch_type='b')
b_2.array_annotate(trial_id=[4, 5, 6])
seg = Segment()
seg2 = Segment()
seg.epochs = [a_1, b_1]
seg2.epochs = [a_2, b_2]
block = Block()
block.segments = [seg, seg2]
# test getting one whole event via annotation
extracted_a_1 = get_epochs(seg, epoch_type='a')
extracted_a_1b = get_epochs(block, pick='me')
self.assertEqual(len(extracted_a_1), 1)
self.assertEqual(len(extracted_a_1b), 1)
extracted_a_1 = extracted_a_1[0]
extracted_a_1b = extracted_a_1b[0]
assert_same_attributes(extracted_a_1, a_1)
assert_same_attributes(extracted_a_1b, a_1)
# test getting an empty list by searching for a non-existent property
empty1 = get_epochs(seg, foo='bar')
self.assertEqual(len(empty1), 0)
# test getting an empty list by searching for a non-existent property value
empty2 = get_epochs(seg, epoch_type='undefined')
self.assertEqual(len(empty2), 0)
# test getting only one event time of one event
trial_2 = get_epochs(block, trial_id=2, epoch_type='a')
self.assertEqual(len(trial_2), 1)
trial_2 = trial_2[0]
self.assertEqual(a_1.name, trial_2.name)
self.assertEqual(a_1.description, trial_2.description)
self.assertEqual(a_1.file_origin, trial_2.file_origin)
self.assertEqual(a_1.annotations['epoch_type'],
trial_2.annotations['epoch_type'])
assert_arrays_equal(trial_2.array_annotations['trial_id'],
np.array([2]))
self.assertIsInstance(trial_2.array_annotations, ArrayDict)
# test getting only one event time of more than one event
trial_2b = get_epochs(block, trial_id=2)
self.assertEqual(len(trial_2b), 2)
a_idx = np.where(
np.array([ev.annotations['epoch_type']
for ev in trial_2b]) == 'a')[0][0]
trial_2b_a = trial_2b[a_idx]
trial_2b_b = trial_2b[a_idx - 1]
assert_same_attributes(trial_2b_a, trial_2)
self.assertEqual(b_1.name, trial_2b_b.name)
self.assertEqual(b_1.description, trial_2b_b.description)
self.assertEqual(b_1.file_origin, trial_2b_b.file_origin)
self.assertEqual(b_1.annotations['epoch_type'],
trial_2b_b.annotations['epoch_type'])
assert_arrays_equal(trial_2b_b.array_annotations['trial_id'],
np.array([2]))
self.assertIsInstance(trial_2b_b.array_annotations, ArrayDict)
# test getting more than one event time of one event
trials_1_2 = get_epochs(block, trial_id=[1, 2], epoch_type='a')
self.assertEqual(len(trials_1_2), 1)
trials_1_2 = trials_1_2[0]
self.assertEqual(a_1.name, trials_1_2.name)
self.assertEqual(a_1.description, trials_1_2.description)
self.assertEqual(a_1.file_origin, trials_1_2.file_origin)
self.assertEqual(a_1.annotations['epoch_type'],
trials_1_2.annotations['epoch_type'])
assert_arrays_equal(trials_1_2.array_annotations['trial_id'],
np.array([1, 2]))
self.assertIsInstance(trials_1_2.array_annotations, ArrayDict)
# test getting more than one event time of more than one event
trials_1_2b = get_epochs(block, trial_id=[1, 2])
self.assertEqual(len(trials_1_2b), 2)
a_idx = np.where(
np.array([ev.annotations['epoch_type']
for ev in trials_1_2b]) == 'a')[0][0]
trials_1_2b_a = trials_1_2b[a_idx]
trials_1_2b_b = trials_1_2b[a_idx - 1]
assert_same_attributes(trials_1_2b_a, trials_1_2)
self.assertEqual(b_1.name, trials_1_2b_b.name)
self.assertEqual(b_1.description, trials_1_2b_b.description)
self.assertEqual(b_1.file_origin, trials_1_2b_b.file_origin)
self.assertEqual(b_1.annotations['epoch_type'],
trials_1_2b_b.annotations['epoch_type'])
assert_arrays_equal(trials_1_2b_b.array_annotations['trial_id'],
np.array([1, 2]))
self.assertIsInstance(trials_1_2b_b.array_annotations, ArrayDict)
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)
def test__children(self):
blk = Block(name='block1')
blk.segments = [self.seg1]
blk.create_many_to_one_relationship(force=True)
assert_neo_object_is_compliant(self.seg1)
assert_neo_object_is_compliant(blk)
childobjs = ('AnalogSignal',
'Epoch', 'Event',
'IrregularlySampledSignal',
'SpikeTrain')
childconts = ('analogsignals',
'epochs', 'events',
'irregularlysampledsignals',
'spiketrains')
self.assertEqual(self.seg1._container_child_objects, ())
self.assertEqual(self.seg1._data_child_objects, childobjs)
self.assertEqual(self.seg1._single_parent_objects, ('Block',))
self.assertEqual(self.seg1._multi_child_objects, ())
self.assertEqual(self.seg1._multi_parent_objects, ())
self.assertEqual(self.seg1._child_properties, ())
self.assertEqual(self.seg1._single_child_objects, childobjs)
self.assertEqual(self.seg1._container_child_containers, ())
self.assertEqual(self.seg1._data_child_containers, childconts)
self.assertEqual(self.seg1._single_child_containers, childconts)
self.assertEqual(self.seg1._single_parent_containers, ('block',))
self.assertEqual(self.seg1._multi_child_containers, ())
self.assertEqual(self.seg1._multi_parent_containers, ())
self.assertEqual(self.seg1._child_objects, childobjs)
self.assertEqual(self.seg1._child_containers, childconts)
self.assertEqual(self.seg1._parent_objects, ('Block',))
self.assertEqual(self.seg1._parent_containers, ('block',))
totchildren = (self.nchildren*2 + # epoch/event
self.nchildren + # analogsignal
self.nchildren**2 + # spiketrain
self.nchildren) # irregsignal
self.assertEqual(len(self.seg1._single_children), totchildren)
self.assertEqual(len(self.seg1.data_children), totchildren)
self.assertEqual(len(self.seg1.children), totchildren)
self.assertEqual(len(self.seg1.data_children_recur), totchildren)
self.assertEqual(len(self.seg1.children_recur), totchildren)
self.assertEqual(len(self.seg1._multi_children), 0)
self.assertEqual(len(self.seg1.container_children), 0)
self.assertEqual(len(self.seg1.container_children_recur), 0)
children = (self.sigarrs1a +
self.epcs1a + self.evts1a +
self.irsigs1a +
self.trains1a)
assert_same_sub_schema(list(self.seg1._single_children), children)
assert_same_sub_schema(list(self.seg1.data_children), children)
assert_same_sub_schema(list(self.seg1.data_children_recur), children)
assert_same_sub_schema(list(self.seg1.children), children)
assert_same_sub_schema(list(self.seg1.children_recur), children)
self.assertEqual(len(self.seg1.parents), 1)
self.assertEqual(self.seg1.parents[0].name, 'block1')
def test__children(self):
blk = Block(name='block1')
blk.segments = [self.segment1]
blk.create_many_to_one_relationship()
self.assertEqual(self.segment1._container_child_objects, ())
self.assertEqual(self.segment1._data_child_objects,
('AnalogSignal', 'AnalogSignalArray',
'Epoch', 'EpochArray',
'Event', 'EventArray',
'IrregularlySampledSignal',
'Spike', 'SpikeTrain'))
self.assertEqual(self.segment1._single_parent_objects, ('Block',))
self.assertEqual(self.segment1._multi_child_objects, ())
self.assertEqual(self.segment1._multi_parent_objects, ())
self.assertEqual(self.segment1._child_properties, ())
self.assertEqual(self.segment1._single_child_objects,
('AnalogSignal', 'AnalogSignalArray',
'Epoch', 'EpochArray',
'Event', 'EventArray',
'IrregularlySampledSignal',
'Spike', 'SpikeTrain'))
self.assertEqual(self.segment1._container_child_containers, ())
self.assertEqual(self.segment1._data_child_containers,
('analogsignals', 'analogsignalarrays',
'epochs', 'epocharrays',
'events', 'eventarrays',
'irregularlysampledsignals',
'spikes', 'spiketrains'))
self.assertEqual(self.segment1._single_child_containers,
('analogsignals', 'analogsignalarrays',
'epochs', 'epocharrays',
'events', 'eventarrays',
'irregularlysampledsignals',
'spikes', 'spiketrains'))
self.assertEqual(self.segment1._single_parent_containers, ('block',))
self.assertEqual(self.segment1._multi_child_containers, ())
self.assertEqual(self.segment1._multi_parent_containers, ())
self.assertEqual(self.segment1._child_objects,
('AnalogSignal', 'AnalogSignalArray',
'Epoch', 'EpochArray',
'Event', 'EventArray',
'IrregularlySampledSignal',
'Spike', 'SpikeTrain'))
self.assertEqual(self.segment1._child_containers,
('analogsignals', 'analogsignalarrays',
'epochs', 'epocharrays',
'events', 'eventarrays',
'irregularlysampledsignals',
'spikes', 'spiketrains'))
self.assertEqual(self.segment1._parent_objects, ('Block',))
self.assertEqual(self.segment1._parent_containers, ('block',))
self.assertEqual(len(self.segment1.children),
(len(self.sig1) +
len(self.sigarr1) +
len(self.epoch1) +
len(self.epocharr1) +
len(self.event1) +
len(self.eventarr1) +
len(self.irsig1) +
len(self.spike1) +
len(self.train1)))
self.assertEqual(self.segment1.children[0].name, self.signames1[0])
self.assertEqual(self.segment1.children[1].name, self.signames1[1])
self.assertEqual(self.segment1.children[2].name, self.sigarrnames1[0])
self.assertEqual(self.segment1.children[3].name, self.sigarrnames1[1])
self.assertEqual(self.segment1.children[4].name, self.epochnames1[0])
self.assertEqual(self.segment1.children[5].name, self.epochnames1[1])
self.assertEqual(self.segment1.children[6].name,
self.epocharrnames1[0])
self.assertEqual(self.segment1.children[7].name,
self.epocharrnames1[1])
self.assertEqual(self.segment1.children[8].name, self.eventnames1[0])
self.assertEqual(self.segment1.children[9].name, self.eventnames1[1])
self.assertEqual(self.segment1.children[10].name,
self.eventarrnames1[0])
self.assertEqual(self.segment1.children[11].name,
self.eventarrnames1[1])
self.assertEqual(self.segment1.children[12].name, self.irsignames1[0])
self.assertEqual(self.segment1.children[13].name, self.irsignames1[1])
self.assertEqual(self.segment1.children[14].name, self.spikenames1[0])
self.assertEqual(self.segment1.children[15].name, self.spikenames1[1])
self.assertEqual(self.segment1.children[16].name, self.trainnames1[0])
self.assertEqual(self.segment1.children[17].name, self.trainnames1[1])
self.assertEqual(len(self.segment1.parents), 1)
self.assertEqual(self.segment1.parents[0].name, 'block1')
self.segment1.create_many_to_one_relationship()
self.segment1.create_many_to_many_relationship()
self.segment1.create_relationship()
assert_neo_object_is_compliant(self.segment1)