def test_segment_with_proxy(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_sptr = SpikeTrainProxy(rawio=self.reader,
unit_index=0,
block_index=0,
seg_index=0)
seg.spiketrains.append(proxy_sptr)
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)
seg.epochs.append(proxy_epoch)
def setUp(self):
spike_time_array = np.array([0.5, 0.6, 0.7, 1.1, 11.2, 23.6, 88.5, 99.2])
channel_id_array = np.array([0, 0, 1, 2, 1, 0, 2, 0])
all_channel_ids = (0, 1, 2, 3)
self.stl_from_array = SpikeTrainList.from_spike_time_array(
spike_time_array,
channel_id_array,
all_channel_ids=all_channel_ids,
units='ms',
t_start=0 * pq.ms,
t_stop=100.0 * pq.ms,
identifier=["A", "B", "C", "D"] # annotation
)
self.stl_from_obj_list = SpikeTrainList(items=(
SpikeTrain([0.5, 0.6, 23.6, 99.2], units="ms",
t_start=0 * pq.ms, t_stop=100.0 * pq.ms, channel_id=101),
SpikeTrain([0.0007, 0.0112], units="s", t_start=0 * pq.ms, t_stop=100.0 * pq.ms,
channel_id=102),
SpikeTrain([1100, 88500], units="us", t_start=0 * pq.ms, t_stop=100.0 * pq.ms,
channel_id=103),
SpikeTrain([], units="ms", t_start=0 * pq.ms, t_stop=100.0 * pq.ms,
channel_id=104),
))
self.stl_from_obj_list_incl_proxy = SpikeTrainList(items=(
SpikeTrain([0.5, 0.6, 23.6, 99.2], units="ms",
t_start=0 * pq.ms, t_stop=100.0 * pq.ms),
SpikeTrain([0.0007, 0.0112], units="s", t_start=0 * pq.ms, t_stop=100.0 * pq.ms),
SpikeTrainProxy(rawio=MockRawIO(), spike_channel_index=0),
SpikeTrain([], units="ms", t_start=0 * pq.ms, t_stop=100.0 * pq.ms),
))
def test_SpikeTrainProxy(self):
proxy_sptr = SpikeTrainProxy(rawio=self.reader, spike_channel_index=0,
block_index=0, seg_index=0)
assert proxy_sptr.name == 'unit0'
assert proxy_sptr.t_start == 0 * pq.s
assert proxy_sptr.t_stop == 10 * pq.s
assert proxy_sptr.shape == (20,)
assert proxy_sptr.left_sweep == 0.002 * pq.s
assert proxy_sptr.sampling_rate == 10 * pq.kHz
# full load
full_sptr = proxy_sptr.load(time_slice=None)
assert isinstance(full_sptr, SpikeTrain)
assert_same_attributes(proxy_sptr, full_sptr)
assert full_sptr.shape == proxy_sptr.shape
# slice time
sptr = proxy_sptr.load(time_slice=(250 * pq.ms, 500 * pq.ms))
assert sptr.t_start == .25 * pq.s
assert sptr.t_stop == .5 * pq.s
assert sptr.shape == (6,)
assert_same_attributes(proxy_sptr.time_slice(250 * pq.ms, 500 * pq.ms), sptr)
# buggy time slice
with self.assertRaises(AssertionError):
sptr = proxy_sptr.load(time_slice=(2. * pq.s, 15 * pq.s))
sptr = proxy_sptr.load(time_slice=(2. * pq.s, 15 * pq.s), strict_slicing=False)
assert sptr.t_stop == 10 * pq.s
# magnitude mode rescaled
sptr_float = proxy_sptr.load(magnitude_mode='rescaled')
assert sptr_float.dtype == 'float64'
assert sptr_float.units == pq.s
# magnitude mode raw
# TODO when raw mode implemented
# sptr_int = proxy_sptr.load(magnitude_mode='raw')
# assert sptr_int.dtype=='int64'
# assert sptr_int.units==pq.CompoundUnit('1/10000*s')
# assert_arrays_almost_equal(sptr_float, sptr_int.rescale('s'), 1e-9)
# Without waveforms
sptr = proxy_sptr.load(load_waveforms=False)
assert sptr.waveforms is None
# With waveforms
sptr = proxy_sptr.load(load_waveforms=True, magnitude_mode='rescaled')
assert sptr.waveforms is not None
assert sptr.waveforms.shape == (20, 1, 50)
assert sptr.waveforms.units == 1 * pq.uV
# slice waveforms
sptr = proxy_sptr.load(load_waveforms=True, time_slice=(250 * pq.ms, 500 * pq.ms))
assert sptr.waveforms.shape == (6, 1, 50)
# test array_annotations
assert '__array_annotations__' not in proxy_sptr.annotations
assert 'amplitudes' in proxy_sptr.array_annotations
def read_segment(self,
block_index=0,
seg_index=0,
lazy=False,
signal_group_mode=None,
load_waveforms=False,
time_slice=None,
strict_slicing=True):
"""
:param block_index: int default 0. In case of several block block_index can be specified.
:param seg_index: int default 0. Index of segment.
:param lazy: False by default.
:param signal_group_mode: 'split-all' or 'group-by-same-units' (default depend IO):
This control behavior for grouping channels in AnalogSignal.
* 'split-all': each channel will give an AnalogSignal
* 'group-by-same-units' all channel sharing the same quantity units ar grouped in
a 2D AnalogSignal
:param load_waveforms: False by default. Control SpikeTrains.waveforms is None or not.
:param time_slice: None by default means no limit.
A time slice is (t_start, t_stop) both are quantities.
All object AnalogSignal, SpikeTrain, Event, Epoch will load only in the slice.
:param strict_slicing: True by default.
Control if an error is raise or not when one of time_slice member (t_start or t_stop)
is outside the real time range of the segment.
"""
if lazy:
assert time_slice is None, 'For lazy=true you must specify time_slice when loading'
if signal_group_mode is None:
signal_group_mode = self._prefered_signal_group_mode
# annotations
seg_annotations = dict(
self.raw_annotations['blocks'][block_index]['segments'][seg_index])
for k in ('signals', 'units', 'events'):
seg_annotations.pop(k)
seg_annotations = check_annotations(seg_annotations)
seg = Segment(index=seg_index, **seg_annotations)
# AnalogSignal
signal_channels = self.header['signal_channels']
if signal_channels.size > 0:
channel_indexes_list = self.get_group_channel_indexes()
for channel_indexes in channel_indexes_list:
for i, (ind_within,
ind_abs) in self._make_signal_channel_subgroups(
channel_indexes,
signal_group_mode=signal_group_mode).items():
# make a proxy...
anasig = AnalogSignalProxy(rawio=self,
global_channel_indexes=ind_abs,
block_index=block_index,
seg_index=seg_index)
if not lazy:
# ... and get the real AnalogSIgnal if not lazy
anasig = anasig.load(time_slice=time_slice,
strict_slicing=strict_slicing)
# TODO magnitude_mode='rescaled'/'raw'
anasig.segment = seg
seg.analogsignals.append(anasig)
# SpikeTrain and waveforms (optional)
unit_channels = self.header['unit_channels']
for unit_index in range(len(unit_channels)):
# make a proxy...
sptr = SpikeTrainProxy(rawio=self,
unit_index=unit_index,
block_index=block_index,
seg_index=seg_index)
if not lazy:
# ... and get the real SpikeTrain if not lazy
sptr = sptr.load(time_slice=time_slice,
strict_slicing=strict_slicing,
load_waveforms=load_waveforms)
# TODO magnitude_mode='rescaled'/'raw'
sptr.segment = seg
seg.spiketrains.append(sptr)
# Events/Epoch
event_channels = self.header['event_channels']
for chan_ind in range(len(event_channels)):
if event_channels['type'][chan_ind] == b'event':
e = EventProxy(rawio=self,
event_channel_index=chan_ind,
block_index=block_index,
seg_index=seg_index)
if not lazy:
e = e.load(time_slice=time_slice,
strict_slicing=strict_slicing)
e.segment = seg
seg.events.append(e)
elif event_channels['type'][chan_ind] == b'epoch':
e = EpochProxy(rawio=self,
event_channel_index=chan_ind,
block_index=block_index,
seg_index=seg_index)
if not lazy:
e = e.load(time_slice=time_slice,
strict_slicing=strict_slicing)
e.segment = seg
seg.epochs.append(e)
seg.create_many_to_one_relationship()
return seg
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)
def test_times(self):
for seg in [self.seg1, self.seg2]:
# calculate target values for t_start and t_stop
t_starts, t_stops = [], []
for children in [
seg.analogsignals, seg.epochs, seg.events,
seg.irregularlysampledsignals, seg.spiketrains
]:
for child in children:
if hasattr(child, 't_start'):
t_starts.append(child.t_start)
if hasattr(child, 't_stop'):
t_stops.append(child.t_stop)
if hasattr(child, 'time'):
t_starts.append(child.time)
t_stops.append(child.time)
if hasattr(child, 'times'):
t_starts.append(child.times[0])
t_stops.append(child.times[-1])
targ_t_start = min(t_starts)
targ_t_stop = max(t_stops)
self.assertEqual(seg.t_start, targ_t_start)
self.assertEqual(seg.t_stop, targ_t_stop)
# Testing times with ProxyObjects
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)
seg.epochs.append(proxy_epoch)
t_starts, t_stops = [], []
for children in [
seg.analogsignals, seg.epochs, seg.events,
seg.irregularlysampledsignals, seg.spiketrains
]:
for child in children:
if hasattr(child, 't_start'):
t_starts.append(child.t_start)
if hasattr(child, 't_stop'):
t_stops.append(child.t_stop)
if hasattr(child, 'time'):
t_starts.append(child.time)
t_stops.append(child.time)
if hasattr(child, 'times'):
t_starts.append(child.times[0])
t_stops.append(child.times[-1])
targ_t_start = min(t_starts)
targ_t_stop = max(t_stops)
self.assertEqual(seg.t_start, targ_t_start)
self.assertEqual(seg.t_stop, targ_t_stop)