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import warnings
import numpy as np
from pynwb.base import ProcessingModule
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.testing import TestCase
from pynwb.testing.mock.ecephys import mock_ElectricalSeries
from hdmf.common import DynamicTableRegion
def make_electrode_table():
table = ElectrodeTable()
dev1 = Device('dev1')
group = ElectrodeGroup('tetrode1', 'tetrode description', 'tetrode location', dev1)
table.add_row(location='CA1', group=group, group_name='tetrode1')
table.add_row(location='CA1', group=group, group_name='tetrode1')
table.add_row(location='CA1', group=group, group_name='tetrode1')
table.add_row(location='CA1', group=group, group_name='tetrode1')
return table
class ElectricalSeriesConstructor(TestCase):
def _create_table_and_region(self):
table = make_electrode_table()
region = DynamicTableRegion(
name='electrodes',
data=[0, 2],
description='the first and third electrodes',
table=table
)
return table, region
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]
channel_conversion = [2., 6.3]
filtering = 'Low-pass filter at 300 Hz'
table, region = self._create_table_and_region()
eS = ElectricalSeries(
name='test_eS',
data=data,
electrodes=region,
channel_conversion=channel_conversion,
filtering=filtering,
timestamps=ts
)
self.assertEqual(eS.name, 'test_eS')
self.assertEqual(eS.data, data)
self.assertEqual(eS.electrodes, region)
self.assertEqual(eS.timestamps, ts)
self.assertEqual(eS.channel_conversion, [2., 6.3])
self.assertEqual(eS.filtering, filtering)
def test_link(self):
table, region = self._create_table_and_region()
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, region = self._create_table_and_region()
with self.assertRaisesWith(ValueError, ("ElectricalSeries.__init__: 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])
def test_dimensions_warning(self):
table, region = self._create_table_and_region()
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
ElectricalSeries(
name="test_ts1",
data=np.ones((6, 3)),
electrodes=region,
timestamps=[0.0, 0.1, 0.2, 0.3, 0.4, 0.5]
)
self.assertEqual(len(w), 1)
assert (
"ElectricalSeries 'test_ts1': The second dimension of data does not match the length of electrodes. "
"Your data may be transposed."
) in str(w[-1].message)
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
ElectricalSeries(
name="test_ts1",
data=np.ones((2, 6)),
electrodes=region,
rate=30000.,
)
self.assertEqual(len(w), 1)
assert (
"ElectricalSeries 'test_ts1': The second dimension of data does not match the length of electrodes, "
"but instead the first does. Data is oriented incorrectly and should be transposed."
) in str(w[-1].message)
def test_get_data_in_units(self):
samples = 100
channels = 5
conversion = 10.0
offset = 3.0
channel_conversion = np.random.rand(channels)
electrical_series = mock_ElectricalSeries(
data=np.ones((samples, channels)),
conversion=conversion,
offset=offset,
channel_conversion=channel_conversion,
)
data_in_units = electrical_series.get_data_in_units()
for channel_index in range(channels):
np.testing.assert_almost_equal(
data_in_units[:, channel_index],
np.ones(samples) * conversion * channel_conversion[channel_index] + offset
)
class SpikeEventSeriesConstructor(TestCase):
def _create_table_and_region(self):
table = make_electrode_table()
region = DynamicTableRegion(
name='electrodes',
data=[1, 3],
description='the second and fourth electrodes',
table=table
)
return table, region
def test_init(self):
table, region = self._create_table_and_region()
data = ((1, 1), (2, 2), (3, 3))
timestamps = np.arange(3)
sES = SpikeEventSeries(name='test_sES', data=data, timestamps=timestamps, electrodes=region)
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, region = self._create_table_and_region()
data = ((1, 1, 1), (2, 2, 2))
with self.assertRaises(TypeError):
SpikeEventSeries(name='test_sES', data=data, electrodes=region, rate=1.)
def test_incorrect_timestamps(self):
table, region = self._create_table_and_region()
data = ((1, 1, 1), (2, 2, 2))
with self.assertRaisesWith(ValueError, "Must provide the same number of timestamps and spike events"):
SpikeEventSeries(name='test_sES', data=data, electrodes=region, timestamps=[1.0, 2.0, 3.0])
class ElectrodeGroupConstructor(TestCase):
def test_init(self):
dev1 = Device('dev1')
group = ElectrodeGroup('elec1', 'electrode description', 'electrode location', dev1, (1, 2, 3))
self.assertEqual(group.name, 'elec1')
self.assertEqual(group.description, 'electrode description')
self.assertEqual(group.location, 'electrode location')
self.assertEqual(group.device, dev1)
self.assertEqual(group.position, (1, 2, 3))
def test_init_position_none(self):
dev1 = Device('dev1')
group = ElectrodeGroup('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)
self.assertIsNone(group.position)
def test_init_position_bad(self):
dev1 = Device('dev1')
with self.assertRaises(ValueError):
ElectrodeGroup('elec1', 'electrode description', 'electrode location', dev1, (1, 2))
class EventDetectionConstructor(TestCase):
def _create_table_and_region(self):
table = make_electrode_table()
region = DynamicTableRegion(
name='electrodes',
data=[0, 2],
description='the first and third electrodes',
table=table
)
return table, region
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, region = self._create_table_and_region()
eS = ElectricalSeries('test_eS', data, region, timestamps=ts)
eD = EventDetection('detection_method', eS, (1, 2, 3), (0.1, 0.2, 0.3))
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(TestCase):
def _create_table_and_region(self):
table = make_electrode_table()
region = DynamicTableRegion(
name='electrodes',
data=[0, 2],
description='the first and third electrodes',
table=table
)
return table, region
def test_init(self):
table, region = self._create_table_and_region()
sES = SpikeEventSeries('test_sES', list(range(10)), list(range(10)), region)
pm = ProcessingModule(name='test_module', description='a test module')
ew = EventWaveform()
pm.add(table)
pm.add(ew)
ew.add_spike_event_series(sES)
self.assertEqual(ew.spike_event_series['test_sES'], sES)
self.assertEqual(ew['test_sES'], ew.spike_event_series['test_sES'])
class ClusteringConstructor(TestCase):
def test_init(self):
times = [1.3, 2.3]
num = [3, 4]
peak_over_rms = [5.3, 6.3]
with self.assertWarnsWith(DeprecationWarning, 'use pynwb.misc.Units or NWBFile.units instead'):
cc = Clustering(description='description', num=num, peak_over_rms=peak_over_rms, times=times)
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(TestCase):
def test_init(self):
times = [1.3, 2.3]
num = [3, 4]
peak_over_rms = [5.3, 6.3]
with self.assertWarnsWith(DeprecationWarning, 'use pynwb.misc.Units or NWBFile.units instead'):
cc = Clustering(description='description', num=num, peak_over_rms=peak_over_rms, times=times)
means = [[7.3, 7.3]]
stdevs = [[8.3, 8.3]]
with self.assertWarnsWith(DeprecationWarning, 'use pynwb.misc.Units or NWBFile.units instead'):
cw = ClusterWaveforms(
clustering_interface=cc,
waveform_filtering='filtering',
waveform_mean=means,
waveform_sd=stdevs
)
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(TestCase):
def _create_table_and_region(self):
table = make_electrode_table()
region = DynamicTableRegion(
name='electrodes',
data=[0, 2],
description='the first and third electrodes',
table=table
)
return table, region
def test_init(self):
_, region = self._create_table_and_region()
eS = ElectricalSeries('test_eS', [0, 1, 2, 3], region, timestamps=[0.1, 0.2, 0.3, 0.4])
msg = (
"The linked table for DynamicTableRegion 'electrodes' does not share "
"an ancestor with the DynamicTableRegion."
)
with self.assertWarnsRegex(UserWarning, msg):
lfp = LFP(eS)
self.assertEqual(lfp.electrical_series.get('test_eS'), eS)
self.assertEqual(lfp['test_eS'], lfp.electrical_series.get('test_eS'))
def test_add_electrical_series(self):
lfp = LFP()
table, region = self._create_table_and_region()
eS = ElectricalSeries('test_eS', [0, 1, 2, 3], region, timestamps=[0.1, 0.2, 0.3, 0.4])
pm = ProcessingModule(name='test_module', description='a test module')
pm.add(table)
pm.add(lfp)
lfp.add_electrical_series(eS)
self.assertEqual(lfp.electrical_series.get('test_eS'), eS)
class FilteredEphysTest(TestCase):
def _create_table_and_region(self):
table = make_electrode_table()
region = DynamicTableRegion(
name='electrodes',
data=[0, 2],
description='the first and third electrodes',
table=table
)
return table, region
def test_init(self):
_, region = self._create_table_and_region()
eS = ElectricalSeries('test_eS', [0, 1, 2, 3], region, timestamps=[0.1, 0.2, 0.3, 0.4])
msg = (
"The linked table for DynamicTableRegion 'electrodes' does not share "
"an ancestor with the DynamicTableRegion."
)
with self.assertWarnsRegex(UserWarning, msg):
fe = FilteredEphys(eS)
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):
table, region = self._create_table_and_region()
eS = ElectricalSeries('test_eS', [0, 1, 2, 3], region, timestamps=[0.1, 0.2, 0.3, 0.4])
pm = ProcessingModule(name='test_module', description='a test module')
fe = FilteredEphys()
pm.add(table)
pm.add(fe)
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(TestCase):
def _create_table_and_region(self):
table = make_electrode_table()
region = DynamicTableRegion(
name='electrodes',
data=[0, 2],
description='the first and third electrodes',
table=table
)
return table, region
def test_init(self):
event_times = [1.9, 3.5]
table, region = self._create_table_and_region()
description = ['desc1', 'desc2', 'desc3']
features = [[[0, 1, 2], [3, 4, 5]], [[6, 7, 8], [9, 10, 11]]]
fe = FeatureExtraction(region, description, event_times, features)
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, region = self._create_table_and_region()
description = ['desc1', 'desc2', 'desc3']
features = [[[0, 1, 2], [3, 4, 5]]]
self.assertRaises(ValueError, FeatureExtraction, region, description, event_times, features)
def test_invalid_init_mismatched_electrodes(self):
event_times = [1]
table = make_electrode_table()
region = DynamicTableRegion(name='electrodes', data=[0], description='the first electrode', table=table)
description = ['desc1', 'desc2', 'desc3']
features = [[[0, 1, 2], [3, 4, 5]]]
self.assertRaises(ValueError, FeatureExtraction, region, description, event_times, features)
def test_invalid_init_mismatched_description(self):
event_times = [1]
table, region = self._create_table_and_region()
description = ['desc1', 'desc2', 'desc3', 'desc4'] # Need 3 descriptions but give 4
features = [[[0, 1, 2], [3, 4, 5]]]
self.assertRaises(ValueError, FeatureExtraction, region, description, event_times, features)
def test_invalid_init_mismatched_description2(self):
event_times = [1]
table, region = self._create_table_and_region()
description = ['desc1', 'desc2', 'desc3']
features = [[0, 1, 2], [3, 4, 5]] # Need 3D feature array but give only 2D array
self.assertRaises(ValueError, FeatureExtraction, region, description, event_times, features)
|
