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test_ecephys.py
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test_ecephys.py
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import unittest2 as unittest
import re
import numpy as np
from pynwb.ecephys import ElectricalSeries, SpikeEventSeries, EventDetection, Clustering, EventWaveform,\
ClusterWaveforms, LFP, FilteredEphys, FeatureExtraction, ElectrodeGroup
from pynwb.device import Device
from pynwb.file import ElectrodeTable
from pynwb.core import DynamicTableRegion
def make_electrode_table():
table = ElectrodeTable()
dev1 = Device('dev1') # noqa: F405
group = ElectrodeGroup('tetrode1', 'tetrode description', 'tetrode location', dev1) # noqa: F405
table.add_row(id=1, x=1.0, y=2.0, z=3.0, imp=-1.0, location='CA1', filtering='none',
group=group, group_name='tetrode1')
table.add_row(id=2, x=1.0, y=2.0, z=3.0, imp=-2.0, location='CA1', filtering='none',
group=group, group_name='tetrode1')
table.add_row(id=3, x=1.0, y=2.0, z=3.0, imp=-3.0, location='CA1', filtering='none',
group=group, group_name='tetrode1')
table.add_row(id=4, x=1.0, y=2.0, z=3.0, imp=-4.0, location='CA1', filtering='none',
group=group, group_name='tetrode1')
return table
class ElectricalSeriesConstructor(unittest.TestCase):
def test_init(self):
data = list(range(10))
ts = [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0]
table = make_electrode_table()
region = DynamicTableRegion('electrodes', [0, 2], 'the first and third electrodes', table)
eS = ElectricalSeries('test_eS', data, region, timestamps=ts) # noqa: F405
self.assertEqual(eS.name, 'test_eS')
self.assertEqual(eS.data, data)
self.assertEqual(eS.timestamps, ts)
def test_link(self):
table = make_electrode_table()
region = DynamicTableRegion('electrodes', [0, 2], 'the first and third electrodes', table)
ts1 = ElectricalSeries('test_ts1', [0, 1, 2, 3, 4, 5], region, timestamps=[0.0, 0.1, 0.2, 0.3, 0.4, 0.5])
ts2 = ElectricalSeries('test_ts2', ts1, region, timestamps=ts1)
ts3 = ElectricalSeries('test_ts3', ts2, region, timestamps=ts2)
self.assertEqual(ts2.data, [0, 1, 2, 3, 4, 5])
self.assertEqual(ts2.timestamps, [0.0, 0.1, 0.2, 0.3, 0.4, 0.5])
self.assertEqual(ts3.data, [0, 1, 2, 3, 4, 5])
self.assertEqual(ts3.timestamps, [0.0, 0.1, 0.2, 0.3, 0.4, 0.5])
def test_invalid_data_shape(self):
table = make_electrode_table()
region = DynamicTableRegion('electrodes', [0, 2], 'the first and third electrodes', table)
with self.assertRaisesRegex(ValueError, re.escape("incorrect shape for 'data' (got '(2, 2, 2, 2)', expected "
"'((None,), (None, None), (None, None, None))')")):
ElectricalSeries('test_ts1', np.ones((2, 2, 2, 2)), region, timestamps=[0.0, 0.1, 0.2, 0.3, 0.4, 0.5])
class SpikeEventSeriesConstructor(unittest.TestCase):
def test_init(self):
table = make_electrode_table()
region = DynamicTableRegion('electrodes', [1, 3], 'the second and fourth electrodes', table)
data = ((1, 1, 1), (2, 2, 2))
timestamps = np.arange(2)
sES = SpikeEventSeries('test_sES', data, timestamps, region) # noqa: F405
self.assertEqual(sES.name, 'test_sES')
# self.assertListEqual(sES.data, data)
np.testing.assert_array_equal(sES.data, data)
np.testing.assert_array_equal(sES.timestamps, timestamps)
def test_no_rate(self):
table = make_electrode_table()
region = DynamicTableRegion('electrodes', [1, 3], 'the second and fourth electrodes', table)
data = ((1, 1, 1), (2, 2, 2))
with self.assertRaises(TypeError):
SpikeEventSeries('test_sES', data, region, rate=1.) # noqa: F405
class ElectrodeGroupConstructor(unittest.TestCase):
def test_init(self):
dev1 = Device('dev1') # noqa: F405
group = ElectrodeGroup( # noqa: F405
'elec1', 'electrode description', 'electrode location', dev1)
self.assertEqual(group.name, 'elec1')
self.assertEqual(group.description, 'electrode description')
self.assertEqual(group.location, 'electrode location')
self.assertEqual(group.device, dev1)
class EventDetectionConstructor(unittest.TestCase):
def test_init(self):
data = list(range(10))
ts = [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0]
table = make_electrode_table()
region = DynamicTableRegion('electrodes', [0, 2], 'the first and third electrodes', table)
eS = ElectricalSeries('test_eS', data, region, timestamps=ts) # noqa: F405
eD = EventDetection('detection_method', eS, (1, 2, 3), (0.1, 0.2, 0.3)) # noqa: F405
self.assertEqual(eD.detection_method, 'detection_method')
self.assertEqual(eD.source_electricalseries, eS)
self.assertEqual(eD.source_idx, (1, 2, 3))
self.assertEqual(eD.times, (0.1, 0.2, 0.3))
self.assertEqual(eD.unit, 'seconds')
class EventWaveformConstructor(unittest.TestCase):
def test_init(self):
dev1 = Device('dev1') # noqa: F405
group = ElectrodeGroup( # noqa: F405, F841
'tetrode1', 'tetrode description', 'tetrode location', dev1)
table = make_electrode_table()
region = DynamicTableRegion('electrodes', [0, 2], 'the first and third electrodes', table)
sES = SpikeEventSeries( # noqa: F405
'test_sES', list(range(10)), list(range(10)), region)
ew = EventWaveform(sES) # noqa: F405
self.assertEqual(ew.spike_event_series['test_sES'], sES)
self.assertEqual(ew['test_sES'], ew.spike_event_series['test_sES'])
class ClusteringConstructor(unittest.TestCase):
def test_init(self):
times = [1.3, 2.3]
num = [3, 4]
peak_over_rms = [5.3, 6.3]
with self.assertWarnsRegex(DeprecationWarning, r'use pynwb\.misc\.Units or NWBFile\.units instead'):
cc = Clustering('description', num, peak_over_rms, times) # noqa: F405
self.assertEqual(cc.description, 'description')
self.assertEqual(cc.num, num)
self.assertEqual(cc.peak_over_rms, peak_over_rms)
self.assertEqual(cc.times, times)
class ClusterWaveformsConstructor(unittest.TestCase):
def test_init(self):
times = [1.3, 2.3]
num = [3, 4]
peak_over_rms = [5.3, 6.3]
with self.assertWarnsRegex(DeprecationWarning, r'use pynwb\.misc\.Units or NWBFile\.units instead'):
cc = Clustering('description', num, peak_over_rms, times) # noqa: F405
means = [[7.3, 7.3]]
stdevs = [[8.3, 8.3]]
with self.assertWarnsRegex(DeprecationWarning, r'use pynwb\.misc\.Units or NWBFile\.units instead'):
cw = ClusterWaveforms(cc, 'filtering', means, stdevs) # noqa: F405
self.assertEqual(cw.clustering_interface, cc)
self.assertEqual(cw.waveform_filtering, 'filtering')
self.assertEqual(cw.waveform_mean, means)
self.assertEqual(cw.waveform_sd, stdevs)
class LFPTest(unittest.TestCase):
def test_add_electrical_series(self):
lfp = LFP() # noqa: F405
dev1 = Device('dev1') # noqa: F405
group = ElectrodeGroup( # noqa: F405, F841
'tetrode1', 'tetrode description', 'tetrode location', dev1)
table = make_electrode_table()
region = DynamicTableRegion('electrodes', [0, 2], 'the first and third electrodes', table)
eS = ElectricalSeries( # noqa: F405
'test_eS', [0, 1, 2, 3], region, timestamps=[0.1, 0.2, 0.3, 0.4])
lfp.add_electrical_series(eS)
self.assertEqual(lfp.electrical_series.get('test_eS'), eS)
class FilteredEphysTest(unittest.TestCase):
def test_init(self):
dev1 = Device('dev1') # noqa: F405
group = ElectrodeGroup( # noqa: F405, F841
'tetrode1', 'tetrode description', 'tetrode location', dev1)
table = make_electrode_table()
region = DynamicTableRegion('electrodes', [0, 2], 'the first and third electrodes', table)
eS = ElectricalSeries( # noqa: F405
'test_eS', [0, 1, 2, 3], region, timestamps=[0.1, 0.2, 0.3, 0.4])
fe = FilteredEphys(eS) # noqa: F405
self.assertEqual(fe.electrical_series.get('test_eS'), eS)
self.assertEqual(fe['test_eS'], fe.electrical_series.get('test_eS'))
def test_add_electrical_series(self):
fe = FilteredEphys() # noqa: F405
dev1 = Device('dev1') # noqa: F405
group = ElectrodeGroup( # noqa: F405, F841
'tetrode1', 'tetrode description', 'tetrode location', dev1)
table = make_electrode_table()
region = DynamicTableRegion('electrodes', [0, 2], 'the first and third electrodes', table)
eS = ElectricalSeries( # noqa: F405
'test_eS', [0, 1, 2, 3], region, timestamps=[0.1, 0.2, 0.3, 0.4])
fe.add_electrical_series(eS)
self.assertEqual(fe.electrical_series.get('test_eS'), eS)
self.assertEqual(fe['test_eS'], fe.electrical_series.get('test_eS'))
class FeatureExtractionConstructor(unittest.TestCase):
def test_init(self):
event_times = [1.9, 3.5]
table = make_electrode_table()
region = DynamicTableRegion('electrodes', [0, 2], 'the first and third electrodes', table)
description = ['desc1', 'desc2', 'desc3']
features = [[[0, 1, 2], [3, 4, 5]], [[6, 7, 8], [9, 10, 11]]]
fe = FeatureExtraction(region, description, event_times, features) # noqa: F405
self.assertEqual(fe.description, description)
self.assertEqual(fe.times, event_times)
self.assertEqual(fe.features, features)
def test_invalid_init_mismatched_event_times(self):
event_times = [] # Need 1 event time but give 0
table = make_electrode_table()
electrodes = DynamicTableRegion('electrodes', [0, 2], 'the first and third electrodes', table)
description = ['desc1', 'desc2', 'desc3']
features = [[[0, 1, 2], [3, 4, 5]]]
self.assertRaises(
ValueError, FeatureExtraction, electrodes,
description, event_times, features)
def test_invalid_init_mismatched_electrodes(self):
event_times = [1]
table = make_electrode_table()
electrodes = DynamicTableRegion('electrodes', [0], 'the first electrodes', table)
description = ['desc1', 'desc2', 'desc3']
features = [[[0, 1, 2], [3, 4, 5]]]
self.assertRaises(ValueError, FeatureExtraction, electrodes,
description, event_times, features)
def test_invalid_init_mismatched_description(self):
event_times = [1]
table = make_electrode_table()
electrodes = DynamicTableRegion('electrodes', [0, 2], 'the first and third electrodes', table)
description = ['desc1', 'desc2', 'desc3', 'desc4'] # Need 3 descriptions but give 4
features = [[[0, 1, 2], [3, 4, 5]]]
self.assertRaises(
ValueError, FeatureExtraction, electrodes, description, event_times, features)
def test_invalid_init_mismatched_description2(self): # noqa: F811
event_times = [1]
table = make_electrode_table()
electrodes = DynamicTableRegion('electrodes', [0, 2], 'the first and third electrodes', table)
description = ['desc1', 'desc2', 'desc3']
features = [[0, 1, 2], [3, 4, 5]] # Need 3D feature array but give only 2D array
self.assertRaises(ValueError, FeatureExtraction, # noqa: F405
electrodes, description, event_times, features)
if __name__ == '__main__':
unittest.main()