Add data orientation check exception for SpikeEventSeries (#592)

* add special orientation case for spike event series

* add test for spikeeventseries orientation

* update test

* update CHANGELOG

---------

Co-authored-by: Ryan Ly <rly@lbl.gov>

Author: stephprince

CHANGELOG.md

@@ -1,9 +1,9 @@
 # v0.6.4 (Upcoming)
 
 ### Fixes
+* Fixed incorrect data orientation check for SpikeEventSeries [#592](https://github.com/NeurodataWithoutBorders/nwbinspector/issues/592)
 * Fix dimensionality check for SpikeEventSeries validation [#581](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/581)
 
-
 # v0.6.3 (March 13, 2025)
 
 ### Improvements

src/nwbinspector/checks/_time_series.py

@@ -4,6 +4,7 @@
 
 import numpy as np
 from pynwb import TimeSeries
+from pynwb.ecephys import SpikeEventSeries
 from pynwb.image import ImageSeries, IndexSeries
 
 from .._registration import Importance, InspectorMessage, Severity, register_check
@@ -41,6 +42,12 @@ def check_regular_timestamps(
 @register_check(importance=Importance.CRITICAL, neurodata_type=TimeSeries)
 def check_data_orientation(time_series: TimeSeries) -> Optional[InspectorMessage]:
     """If the TimeSeries has data, check if the longest axis (almost always time) is also the zero-axis."""
+
+    # Skip this check for SpikeEventSeries since its data structure is (events, channels, waveform samples)
+    # and it's valid for the number of waveform samples to be larger than the number of events
+    if isinstance(time_series, SpikeEventSeries):
+        return None
+
     if time_series.data is None:
         return None
 

tests/unit_tests/test_ecephys.py

@@ -11,6 +11,7 @@
 from nwbinspector import Importance, InspectorMessage
 from nwbinspector.checks import (
     check_ascending_spike_times,
+    check_data_orientation,
     check_electrical_series_dims,
     check_electrical_series_reference_electrodes_table,
     check_negative_spike_times,
@@ -156,44 +157,72 @@ def test_trigger_check_electrical_series_reference_electrodes_table(self):
         )
 
 
-def test_spikeeventseries_dims_check():
-    """
-    Test that 2D SpikeEventSeries does not trigger a warning,
-    but 3D SpikeEventSeries with mismatched electrodes does.
-    """
-
-    nwbfile = NWBFile(session_description="", identifier=str(uuid4()), session_start_time=datetime.now().astimezone())
-    device = nwbfile.create_device(name="dev")
-    group = nwbfile.create_electrode_group(name="electrode_group", description="desc", location="loc", device=device)
-    for _ in range(3):
-        nwbfile.add_electrode(x=3.0, y=3.0, z=3.0, imp=-1.0, location="unknown", filtering="unknown", group=group)
-    electrodes = nwbfile.create_electrode_table_region(region=[0, 1, 2], description="three elecs")
-
-    # 2D data: [num_events, num_samples] (should NOT trigger warning)
-    ses_2d = SpikeEventSeries(
-        name="spike_events_2d",
-        data=np.zeros((10, 5)),
-        electrodes=electrodes,
-        timestamps=[0.1 * i for i in range(10)],
-    )
-    assert check_electrical_series_dims(ses_2d) is None
-
-    # 3D data: [num_events, num_channels, num_samples] with mismatched num_channels (should trigger warning)
-    ses_3d = SpikeEventSeries(
-        name="spike_events_3d",
-        data=np.zeros((10, 4, 5)),  # 4 != 3 electrodes
-        electrodes=electrodes,
-        timestamps=[0.1 * i for i in range(10)],
-    )
-    result = check_electrical_series_dims(ses_3d)
-    assert result == InspectorMessage(
-        message=("The second dimension of data does not match the length of electrodes. Your data may be transposed."),
-        importance=Importance.CRITICAL,
-        check_function_name="check_electrical_series_dims",
-        object_type="SpikeEventSeries",
-        object_name="spike_events_3d",
-        location="/",
-    )
+class TestCheckSpikeEventSeries(TestCase):
+    def setUp(self):
+        nwbfile = NWBFile(
+            session_description="", identifier=str(uuid4()), session_start_time=datetime.now().astimezone()
+        )
+        device = nwbfile.create_device(name="dev")
+        group = nwbfile.create_electrode_group(
+            name="electrode_group", description="desc", location="loc", device=device
+        )
+        for _ in range(3):
+            nwbfile.add_electrode(location="unknown", group=group)
+        self.nwbfile = nwbfile
+
+    def test_check_data_orientation_spike_event_series(self):
+        """Test that SpikeEventSeries with more waveform samples than events doesn't trigger the data orientation check."""
+
+        # create data with shape (events, channels, waveform_samples) where waveform_samples > events
+        data = np.zeros((5, 3, 10))
+        timestamps = np.arange(5)
+        electrodes = self.nwbfile.create_electrode_table_region(region=[0, 1, 2], description="three elecs")
+
+        spike_event_series = SpikeEventSeries(
+            name="spike_events",
+            description="test spike events",
+            data=data,
+            timestamps=timestamps,
+            electrodes=electrodes,
+        )
+
+        assert check_data_orientation(spike_event_series) is None
+
+    def test_spikeeventseries_dims_check(self):
+        """
+        Test that 2D SpikeEventSeries does not trigger a warning,
+        but 3D SpikeEventSeries with mismatched electrodes does.
+        """
+
+        electrodes = self.nwbfile.create_electrode_table_region(region=[0, 1, 2], description="three elecs")
+
+        # 2D data: [num_events, num_samples] (should NOT trigger warning)
+        ses_2d = SpikeEventSeries(
+            name="spike_events_2d",
+            data=np.zeros((10, 5)),
+            electrodes=electrodes,
+            timestamps=[0.1 * i for i in range(10)],
+        )
+        assert check_electrical_series_dims(ses_2d) is None
+
+        # 3D data: [num_events, num_channels, num_samples] with mismatched num_channels (should trigger warning)
+        ses_3d = SpikeEventSeries(
+            name="spike_events_3d",
+            data=np.zeros((10, 4, 5)),  # 4 != 3 electrodes
+            electrodes=electrodes,
+            timestamps=[0.1 * i for i in range(10)],
+        )
+        result = check_electrical_series_dims(ses_3d)
+        assert result == InspectorMessage(
+            message=(
+                "The second dimension of data does not match the length of electrodes. Your data may be transposed."
+            ),
+            importance=Importance.CRITICAL,
+            check_function_name="check_electrical_series_dims",
+            object_type="SpikeEventSeries",
+            object_name="spike_events_3d",
+            location="/",
+        )
 
 
 def test_check_spike_times_not_in_unobserved_interval_pass():