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change 'electrode_group' col of Units to be ElectrodeGroup type #820

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merged 8 commits into from
Feb 25, 2019
Merged

change 'electrode_group' col of Units to be ElectrodeGroup type #820

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345f76e
change 'electrode_group' col of Units to be ElectrodeGroup type
bendichter Feb 18, 2019
0acf004
add test for electrode_group column in Units table
bendichter Feb 18, 2019
d6a5019
add test for electrode_group on Units table
bendichter Feb 18, 2019
1f6dd24
Merge branch 'dev' into fix/electrode_group_col
bendichter Feb 19, 2019
4f26dce
Merge branch 'dev' into fix/electrode_group_col
bendichter Feb 19, 2019
ecf8323
Merge branch 'dev' into fix/electrode_group_col
bendichter Feb 20, 2019
9326dc7
add ui test for electrode columns
bendichter Feb 22, 2019
d403b33
Merge remote-tracking branch 'origin/fix/electrode_group_col' into fi…
bendichter Feb 22, 2019
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2 changes: 1 addition & 1 deletion src/pynwb/misc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -212,7 +212,7 @@ def __init__(self, **kwargs):
'default': None, 'shape': (None, 2)},
{'name': 'electrodes', 'type': 'array_data', 'doc': 'the electrodes that each unit came from',
'default': None},
{'name': 'electrode_group', 'type': 'array_data', 'default': None,
{'name': 'electrode_group', 'type': 'ElectrodeGroup', 'default': None,
'doc': 'the electrode group that each unit came from'},
{'name': 'waveform_mean', 'type': 'array_data', 'doc': 'the spike waveform mean for each unit',
'default': None},
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4 changes: 2 additions & 2 deletions tests/integration/ui_write/test_misc.py
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Expand Up @@ -97,8 +97,8 @@ def addContainer(self, nwbfile):
location='CA1', filtering='none',
group=electrode_group)

nwbfile.add_unit(id=1, electrodes=[1])
nwbfile.add_unit(id=2, electrodes=[1])
nwbfile.add_unit(id=1, electrodes=[1], electrode_group=electrode_group)
nwbfile.add_unit(id=2, electrodes=[1], electrode_group=electrode_group)
nwbfile.units.to_dataframe()
self.container = nwbfile.units

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9 changes: 9 additions & 0 deletions tests/unit/pynwb_tests/test_misc.py
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Expand Up @@ -6,6 +6,8 @@
DecompositionSeries
from pynwb.file import TimeSeries, DynamicTable
from pynwb.core import VectorData
from pynwb.device import Device
from pynwb.ecephys import ElectrodeGroup


class AnnotationSeriesConstructor(unittest.TestCase):
Expand Down Expand Up @@ -149,6 +151,13 @@ def test_times_and_intervals(self):
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)


if __name__ == '__main__':
unittest.main()