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import numpy as np
from hdmf.common import DynamicTable, VectorData, DynamicTableRegion
from pynwb.misc import AnnotationSeries, AbstractFeatureSeries, IntervalSeries, Units, DecompositionSeries
from pynwb.file import TimeSeries, ElectrodeTable as get_electrode_table
from pynwb.device import Device
from pynwb.ecephys import ElectrodeGroup
from pynwb.testing import TestCase
class AnnotationSeriesConstructor(TestCase):
def test_init(self):
aS = AnnotationSeries('test_aS', data=[1, 2, 3], timestamps=[1., 2., 3.])
self.assertEqual(aS.name, 'test_aS')
aS.add_annotation(2.0, 'comment')
class AbstractFeatureSeriesConstructor(TestCase):
def test_init(self):
aFS = AbstractFeatureSeries('test_aFS', ['feature units'], ['features'], timestamps=list())
self.assertEqual(aFS.name, 'test_aFS')
self.assertEqual(aFS.feature_units, ['feature units'])
self.assertEqual(aFS.features, ['features'])
aFS.add_features(2.0, [1.])
class DecompositionSeriesConstructor(TestCase):
def test_init(self):
timeseries = TimeSeries(name='dummy timeseries', description='desc',
data=np.ones((3, 3)), unit='Volts',
timestamps=[1., 2., 3.])
bands = DynamicTable(name='bands', description='band info for LFPSpectralAnalysis', columns=[
VectorData(name='band_name', description='name of bands', data=['alpha', 'beta', 'gamma']),
VectorData(name='band_limits', description='low and high cutoffs in Hz', data=np.ones((3, 2))),
VectorData(name='band_mean', description='mean gaussian filters in Hz', data=np.ones((3,))),
VectorData(
name='band_stdev',
description='standard deviation of gaussian filters in Hz',
data=np.ones((3,))
),
])
spec_anal = DecompositionSeries(name='LFPSpectralAnalysis',
description='my description',
data=np.ones((3, 3, 3)),
timestamps=[1., 2., 3.],
source_timeseries=timeseries,
metric='amplitude',
bands=bands)
self.assertEqual(spec_anal.name, 'LFPSpectralAnalysis')
self.assertEqual(spec_anal.description, 'my description')
np.testing.assert_equal(spec_anal.data, np.ones((3, 3, 3)))
np.testing.assert_equal(spec_anal.timestamps, [1., 2., 3.])
self.assertEqual(spec_anal.bands['band_name'].data, ['alpha', 'beta', 'gamma'])
np.testing.assert_equal(spec_anal.bands['band_limits'].data, np.ones((3, 2)))
np.testing.assert_equal(spec_anal.bands['band_mean'].data, np.ones((3,)))
np.testing.assert_equal(spec_anal.bands['band_stdev'].data, np.ones((3,)))
self.assertEqual(spec_anal.source_timeseries, timeseries)
self.assertEqual(spec_anal.metric, 'amplitude')
def test_init_delayed_bands(self):
timeseries = TimeSeries(name='dummy timeseries', description='desc',
data=np.ones((3, 3)), unit='Volts',
timestamps=np.ones((3,)))
spec_anal = DecompositionSeries(name='LFPSpectralAnalysis',
description='my description',
data=np.ones((3, 3, 3)),
timestamps=[1., 2., 3.],
source_timeseries=timeseries,
metric='amplitude')
for band_name in ['alpha', 'beta', 'gamma']:
spec_anal.add_band(band_name=band_name, band_limits=(1., 1.), band_mean=1., band_stdev=1.)
self.assertEqual(spec_anal.name, 'LFPSpectralAnalysis')
self.assertEqual(spec_anal.description, 'my description')
np.testing.assert_equal(spec_anal.data, np.ones((3, 3, 3)))
np.testing.assert_equal(spec_anal.timestamps, [1., 2., 3.])
self.assertEqual(spec_anal.bands['band_name'].data, ['alpha', 'beta', 'gamma'])
np.testing.assert_equal(spec_anal.bands['band_limits'].data, np.ones((3, 2)))
self.assertEqual(spec_anal.source_timeseries, timeseries)
self.assertEqual(spec_anal.metric, 'amplitude')
@staticmethod
def make_electrode_table(self):
""" Make an electrode table, electrode group, and device """
self.table = get_electrode_table()
self.dev1 = Device(name='dev1')
self.group = ElectrodeGroup(name='tetrode1',
description='tetrode description',
location='tetrode location',
device=self.dev1)
for i in range(4):
self.table.add_row(location='CA1', group=self.group, group_name='tetrode1')
def test_init_with_source_channels(self):
self.make_electrode_table(self)
region = DynamicTableRegion(name='source_channels',
data=[0, 2],
description='the first and third electrodes',
table=self.table)
data = np.random.randn(100, 2, 30)
timestamps = np.arange(100)/100
ds = DecompositionSeries(name='test_DS',
data=data,
source_channels=region,
timestamps=timestamps,
metric='amplitude')
self.assertIs(ds.source_channels, region)
class IntervalSeriesConstructor(TestCase):
def test_init(self):
data = [1.0, -1.0, 1.0, -1.0]
timestamps = [0.0, 1.0, 2.0, 3.0]
iS = IntervalSeries('test_iS', data=data, timestamps=timestamps)
self.assertEqual(iS.name, 'test_iS')
self.assertEqual(iS.data, data)
self.assertEqual(iS.timestamps, timestamps)
def test_add_interval(self):
data = [1.0, -1.0, 1.0, -1.0]
timestamps = [0.0, 1.0, 2.0, 3.0]
iS = IntervalSeries('test_iS', data=data, timestamps=timestamps)
iS.add_interval(4.0, 5.0)
data.append(1.0)
data.append(-1.0)
timestamps.append(4.0)
timestamps.append(5.0)
self.assertEqual(iS.data, data)
self.assertEqual(iS.timestamps, timestamps)
class UnitsTests(TestCase):
def test_init(self):
ut = Units()
self.assertEqual(ut.name, 'Units')
self.assertFalse(ut.columns)
def test_add_spike_times(self):
ut = Units()
ut.add_unit(spike_times=[0, 1, 2])
ut.add_unit(spike_times=[3, 4, 5])
self.assertEqual(ut.id.data, [0, 1])
self.assertEqual(ut['spike_times'].target.data, [0, 1, 2, 3, 4, 5])
self.assertEqual(ut['spike_times'].data, [3, 6])
self.assertEqual(ut['spike_times'][0], [0, 1, 2])
self.assertEqual(ut['spike_times'][1], [3, 4, 5])
def test_add_waveforms(self):
ut = Units()
wf1 = [
[ # elec 1
[1, 2, 3],
[1, 2, 3],
[1, 2, 3]
], [ # elec 2
[1, 2, 3],
[1, 2, 3],
[1, 2, 3]
]
]
wf2 = [
[ # elec 1
[1, 2, 3], # spike 1, [sample 1, sample 2, sample 3]
[1, 2, 3], # spike 2
[1, 2, 3], # spike 3
[1, 2, 3] # spike 4
], [ # elec 2
[1, 2, 3], # spike 1
[1, 2, 3], # spike 2
[1, 2, 3], # spike 3
[1, 2, 3] # spike 4
], [ # elec 3
[1, 2, 3], # spike 1
[1, 2, 3], # spike 2
[1, 2, 3], # spike 3
[1, 2, 3] # spike 4
]
]
ut.add_unit(waveforms=wf1)
ut.add_unit(waveforms=wf2)
self.assertEqual(ut.id.data, [0, 1])
self.assertEqual(ut['waveforms'].target.data, [3, 6, 10, 14, 18])
self.assertEqual(ut['waveforms'].data, [2, 5])
self.assertListEqual(ut['waveforms'][0], wf1)
self.assertListEqual(ut['waveforms'][1], wf2)
def test_get_spike_times(self):
ut = Units()
ut.add_unit(spike_times=[0, 1, 2])
ut.add_unit(spike_times=[3, 4, 5])
self.assertTrue(all(ut.get_unit_spike_times(0) == np.array([0, 1, 2])))
self.assertTrue(all(ut.get_unit_spike_times(1) == np.array([3, 4, 5])))
@staticmethod
def test_get_spike_times_interval():
ut = Units()
ut.add_unit(spike_times=[0, 1, 2])
ut.add_unit(spike_times=[3, 4, 5])
np.testing.assert_array_equal(ut.get_unit_spike_times(0, (.5, 3)), [1, 2])
np.testing.assert_array_equal(ut.get_unit_spike_times(0, (-.5, 1.1)), [0, 1])
def test_get_spike_times_multi(self):
ut = Units()
ut.add_unit(spike_times=[0, 1, 2])
ut.add_unit(spike_times=[3, 4, 5])
np.testing.assert_array_equal(ut.get_unit_spike_times((0, 1)), [[0, 1, 2], [3, 4, 5]])
def test_get_spike_times_multi_interval(self):
ut = Units()
ut.add_unit(spike_times=[0, 1, 2])
ut.add_unit(spike_times=[3, 4, 5])
np.testing.assert_array_equal(ut.get_unit_spike_times((0, 1), (1.5, 3.5)), [[2], [3]])
def test_times(self):
ut = Units()
ut.add_unit(spike_times=[0, 1, 2])
ut.add_unit(spike_times=[3, 4, 5])
self.assertTrue(all(ut['spike_times'][0] == np.array([0, 1, 2])))
self.assertTrue(all(ut['spike_times'][1] == np.array([3, 4, 5])))
def test_get_obs_intervals(self):
ut = Units()
ut.add_unit(obs_intervals=[[0, 1]])
ut.add_unit(obs_intervals=[[2, 3], [4, 5]])
self.assertTrue(np.all(ut.get_unit_obs_intervals(0) == np.array([[0, 1]])))
self.assertTrue(np.all(ut.get_unit_obs_intervals(1) == np.array([[2, 3], [4, 5]])))
def test_obs_intervals(self):
ut = Units()
ut.add_unit(obs_intervals=[[0, 1]])
ut.add_unit(obs_intervals=[[2, 3], [4, 5]])
self.assertTrue(np.all(ut['obs_intervals'][0] == np.array([[0, 1]])))
self.assertTrue(np.all(ut['obs_intervals'][1] == np.array([[2, 3], [4, 5]])))
def test_times_and_intervals(self):
ut = Units()
ut.add_unit(spike_times=[0, 1, 2], obs_intervals=[[0, 2]])
ut.add_unit(spike_times=[3, 4, 5], obs_intervals=[[2, 3], [4, 5]])
self.assertTrue(all(ut['spike_times'][0] == np.array([0, 1, 2])))
self.assertTrue(all(ut['spike_times'][1] == np.array([3, 4, 5])))
self.assertTrue(np.all(ut['obs_intervals'][0] == np.array([[0, 2]])))
self.assertTrue(np.all(ut['obs_intervals'][1] == np.array([[2, 3], [4, 5]])))
def test_electrode_group(self):
ut = Units()
device = Device('test_device')
electrode_group = ElectrodeGroup('test_electrode_group', 'description', 'location', device)
ut.add_unit(electrode_group=electrode_group)
self.assertEqual(ut['electrode_group'][0], electrode_group)
def test_waveform_attrs(self):
ut = Units(waveform_rate=40000.)
self.assertEqual(ut.waveform_rate, 40000.)
self.assertEqual(ut.waveform_unit, 'volts')
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