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Fix the Units waveforms test fixtures and assert the doubly indexed structure #2240

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Fix the Units waveforms test fixtures and assert the doubly indexed structure #2240

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93972b6
Fix the Units waveforms test fixtures and assert the doubly indexed s…
adityasingh2400 Aug 5, 2026
5f4e6ff
Add CHANGELOG entry for #2240
adityasingh2400 Aug 5, 2026
abc1503
Merge branch 'dev' into fix-2220-units-waveforms-fixture
adityasingh2400 Aug 12, 2026
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
- Fixed reading a file whose dates carry a sub-minute UTC offset (e.g. `1900-10-01T00:00:00-05:50:36`). @h-mayorquin [#2230](https://github.com/NeurodataWithoutBorders/pynwb/pull/2230)
- Fixed wide pandas DataFrames in the tutorials spilling out of the content column and into the right margin. @bendichter [#2236](https://github.com/NeurodataWithoutBorders/pynwb/pull/2236)
- Fixed `set_data_io` being silently ignored on `NWBData` subclasses (`GrayscaleImage`, `RGBImage`, `RGBAImage`, `ExternalImage`, `ImageReferences`, and `ScratchData`), so requested chunking and compression were dropped without warning and the datasets were written uncompressed. @h-mayorquin [#2233](https://github.com/NeurodataWithoutBorders/pynwb/pull/2233)
- Fixed the `Units` waveforms test fixtures, which labelled the dimensions of the 3-D `add_unit` waveforms input as `(num_electrodes, num_spikes, num_samples)` when `add_unit` reads them as `(num_spikes, num_electrodes, num_samples)`, and so encoded a number of spike events that disagreed with the unit's `spike_times`. Added `TestUnitsIO.test_waveforms_structure` asserting `waveforms_index_index`, `waveforms_index`, and the 2-D `waveforms` dataset after a roundtrip. @adityasingh2400 [#2240](https://github.com/NeurodataWithoutBorders/pynwb/pull/2240)


## PyNWB 4.1.0 (July 23, 2026)
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78 changes: 44 additions & 34 deletions tests/integration/hdf5/test_misc.py
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Expand Up @@ -15,40 +15,30 @@ class TestUnitsIO(AcquisitionH5IOMixin, TestCase):

def setUpContainer(self):
""" Return the test Units to read/write """
# A 3-D waveforms input to add_unit is ordered (num_spikes, num_electrodes, num_samples).
# Dim 0 indexes spike events and becomes waveforms_index_index, dim 1 indexes the electrodes
# that observed each spike event and becomes waveforms_index, and dim 2 holds the samples of
# each waveform. Every unit below has one waveform per electrode per spike time, so the
# number of spike events matches the number of spike_times.
ut = Units(name='UnitsTest', description='a simple table for testing Units')
ut.add_unit(spike_times=[0., 1., 2.], obs_intervals=[[0., 1.], [2., 3.]],
waveform_mean=[1., 2., 3.], waveform_sd=[4., 5., 6.],
waveforms=[
[ # elec 1
[1, 2, 3],
[1, 2, 3],
[1, 2, 3]
], [ # elec 2
[1, 2, 3],
[1, 2, 3],
[1, 2, 3]
waveforms=[ # 3 spike times, 2 electrodes, 3 samples
[ # spike 1
[1, 2, 3], # elec 1, [sample 1, sample 2, sample 3]
[4, 5, 6] # elec 2
], [ # spike 2
[7, 8, 9],
[10, 11, 12]
], [ # spike 3
[13, 14, 15],
[16, 17, 18]
]
])
ut.add_unit(spike_times=[3., 4., 5.], obs_intervals=[[2., 5.], [6., 7.]],
waveform_mean=[1., 2., 3.], waveform_sd=[4., 5., 6.],
waveforms=np.array([
[ # 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
]
]))
# 3 spike times, 4 electrodes, 3 samples, continuing the sample values above
waveforms=np.arange(19, 55).reshape(3, 4, 3))
ut.waveform_rate = 40000.
ut.resolution = 1/40000
return ut
Expand All @@ -71,6 +61,24 @@ def test_get_obs_intervals(self):
np.testing.assert_array_equal(received, [[2., 5.], [6., 7.]])
np.testing.assert_array_equal(ut['obs_intervals'][:], [[[0., 1.], [2., 3.]], [[2., 5.], [6., 7.]]])

def test_waveforms_structure(self):
""" Test the structure of the doubly indexed waveforms column read from file """
ut = self.roundtripContainer()
waveforms_index_index = ut['waveforms']
waveforms_index = waveforms_index_index.target
waveforms = waveforms_index.target

# waveforms_index_index holds the number of spike events of each unit
np.testing.assert_array_equal(waveforms_index_index.data[:], [3, 6])
# waveforms_index holds the number of waveforms, one per electrode, of each spike event
np.testing.assert_array_equal(waveforms_index.data[:], [2, 4, 6, 10, 14, 18])
# the waveforms dataset itself is 2-D, (num_waveforms, num_samples)
np.testing.assert_array_equal(waveforms.data[:], np.arange(1, 55).reshape(18, 3))

# unit 0 has 2 electrodes per spike event, unit 1 has 4
self.assertEqual([len(spike_event) for spike_event in waveforms_index_index[0]], [2, 2, 2])
self.assertEqual([len(spike_event) for spike_event in waveforms_index_index[1]], [4, 4, 4])


class TestUnitsWaveformsOnlyIO(AcquisitionH5IOMixin, TestCase):
"""Test roundtripping waveform metadata when only waveforms are present."""
Expand All @@ -79,27 +87,29 @@ def setUpContainer(self):
ut = Units(name='UnitsWaveformsOnlyTest', description='a simple table for testing Units waveforms')
ut.add_unit(
spike_times=[0., 1., 2.],
waveforms=[
[
[1, 2, 3],
waveforms=[ # 3 spike times, 2 electrodes, 3 samples
[ # spike 1
[1, 2, 3], # elec 1, [sample 1, sample 2, sample 3]
[1, 2, 3] # elec 2
], [ # spike 2
[1, 2, 3],
[1, 2, 3]
], [
[1, 2, 3],
], [ # spike 3
[1, 2, 3],
[1, 2, 3]
]
]
)
ut.add_unit(
spike_times=[3., 4., 5.],
waveforms=np.array([
waveforms=np.array([ # 3 spike times, 2 electrodes, 3 samples
[
[1, 2, 3],
[1, 2, 3],
[1, 2, 3]
], [
[1, 2, 3],
[1, 2, 3]
], [
[1, 2, 3],
[1, 2, 3]
]
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