Add check_spike_times_without_nans

CHANGELOG.md

@@ -6,6 +6,7 @@
 * Added `check_time_intervals_start_time_not_constant` to flag TimeIntervals tables where all start_time values are identical, indicating times were likely not set relative to session start. [#677](https://github.com/NeurodataWithoutBorders/nwbinspector/issues/677)
 * Added `check_units_resolution_is_set` to flag when the Units table has spike_times but resolution is not set to a meaningful positive float. [#686](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/686)
 * Added `check_spike_times_not_in_samples` to flag when spike times appear to be stored as sample indices rather than seconds, detected by all values being integer-valued with implausibly large magnitudes.
+* Added `check_spike_times_without_nans` to detect NaN values in Units spike times, which indicate conversion bugs or unclean array padding. [#689](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/689)
 * Added `check_units_table_has_spikes` to flag Units tables that do not contain a spike_times column. [#691](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/691)
 
 

docs/best_practices/ecephys.rst

@@ -151,6 +151,19 @@ Check function: :py:meth:`~nwbinspector.checks._ecephys.check_spike_times_not_in
 
 
 
+.. _best_practice_spike_times_without_nans:
+
+No NaN Spike Times
+~~~~~~~~~~~~~~~~~~
+
+Spike times are physical event timestamps and must always be valid floating-point numbers. A NaN value in the
+``spike_times`` column typically indicates a conversion bug or array padding that was not cleaned up before writing
+to NWB. Unlike missing data in continuous signals, a spike either occurred at a specific time or it did not, so
+NaN is never meaningful. Clean your spike time arrays to remove any NaN values before adding them to the Units table.
+
+Check function: :py:meth:`~nwbinspector.checks._ecephys.check_spike_times_without_nans`
+
+
 .. _best_practice_ascending_spike_times:
 
 Ascending Spike Times

docs/checks_by_importance.rst

@@ -0,0 +1,95 @@
+Checks by Importance
+======================
+
+This section lists the available checks organized by their importance level.
+
+CRITICAL
+---------
+
+*  :py:func:`~nwbinspector.checks._behavior.check_spatial_series_dims`
+*  :py:func:`~nwbinspector.checks._ecephys.check_electrical_series_dims`
+*  :py:func:`~nwbinspector.checks._ecephys.check_ascending_spike_times`
+*  :py:func:`~nwbinspector.checks._ecephys.check_units_table_duration`
+*  :py:func:`~nwbinspector.checks._general.check_name_slashes`
+*  :py:func:`~nwbinspector.checks._image_series.check_image_series_external_file_valid`
+*  :py:func:`~nwbinspector.checks._nwbfile_metadata.check_session_start_time_future_date`
+*  :py:func:`~nwbinspector.checks._nwbfile_metadata.check_subject_exists`
+*  :py:func:`~nwbinspector.checks._nwbfile_metadata.check_subject_age`
+*  :py:func:`~nwbinspector.checks._nwbfile_metadata.check_subject_id_exists`
+*  :py:func:`~nwbinspector.checks._nwbfile_metadata.check_subject_weight`
+*  :py:func:`~nwbinspector.checks._nwbfile_metadata.check_subject_sex`
+*  :py:func:`~nwbinspector.checks._ophys.check_roi_response_series_dims`
+*  :py:func:`~nwbinspector.checks._tables.check_dynamic_table_region_data_validity`
+*  :py:func:`~nwbinspector.checks._tables.check_ids_unique`
+*  :py:func:`~nwbinspector.checks._tables.check_time_intervals_duration`
+*  :py:func:`~nwbinspector.checks._time_series.check_data_orientation`
+*  :py:func:`~nwbinspector.checks._time_series.check_timestamps_match_first_dimension`
+*  :py:func:`~nwbinspector.checks._time_series.check_rate_is_not_zero`
+*  :py:func:`~nwbinspector.checks._time_series.check_rate_is_positive`
+
+BEST PRACTICE VIOLATION
+------------------------
+
+*  :py:func:`~nwbinspector.checks._behavior.check_compass_direction_unit`
+*  :py:func:`~nwbinspector.checks._behavior.check_spatial_series_radians_magnitude`
+*  :py:func:`~nwbinspector.checks._behavior.check_spatial_series_degrees_magnitude`
+*  :py:func:`~nwbinspector.checks._ecephys.check_negative_spike_times`
+*  :py:func:`~nwbinspector.checks._ecephys.check_electrical_series_reference_electrodes_table`
+*  :py:func:`~nwbinspector.checks._ecephys.check_spike_times_not_in_unobserved_interval`
+*  :py:func:`~nwbinspector.checks._ecephys.check_electrical_series_unscaled_data`
+*  :py:func:`~nwbinspector.checks._ecephys.check_electrodes_location_allen_ccf`
+*  :py:func:`~nwbinspector.checks._icephys.check_intracellular_electrode_cell_id_exists`
+*  :py:func:`~nwbinspector.checks._icephys.check_sweeptable_deprecated`
+*  :py:func:`~nwbinspector.checks._icephys.check_intracellular_electrode_location_allen_ccf`
+*  :py:func:`~nwbinspector.checks._image_series.check_image_series_external_file_relative`
+*  :py:func:`~nwbinspector.checks._image_series.check_image_series_data_size`
+*  :py:func:`~nwbinspector.checks._image_series.check_image_series_starting_frame_without_external_file`
+*  :py:func:`~nwbinspector.checks._images.check_order_of_images_unique`
+*  :py:func:`~nwbinspector.checks._images.check_order_of_images_len`
+*  :py:func:`~nwbinspector.checks._images.check_index_series_points_to_image`
+*  :py:func:`~nwbinspector.checks._nwb_containers.check_large_dataset_compression`
+*  :py:func:`~nwbinspector.checks._nwbfile_metadata.check_subject_species_exists`
+*  :py:func:`~nwbinspector.checks._nwbfile_metadata.check_subject_species_form`
+*  :py:func:`~nwbinspector.checks._nwbfile_metadata.check_session_id_no_slashes`
+*  :py:func:`~nwbinspector.checks._nwbfile_metadata.check_subject_id_no_slashes`
+*  :py:func:`~nwbinspector.checks._ogen.check_optogenetic_stimulus_site_has_optogenetic_series`
+*  :py:func:`~nwbinspector.checks._ophys.check_roi_response_series_link_to_plane_segmentation`
+*  :py:func:`~nwbinspector.checks._ophys.check_emission_lambda_in_nm`
+*  :py:func:`~nwbinspector.checks._ophys.check_excitation_lambda_in_nm`
+*  :py:func:`~nwbinspector.checks._ophys.check_plane_segmentation_image_mask_shape_against_ref_images`
+*  :py:func:`~nwbinspector.checks._ophys.check_imaging_plane_location_allen_ccf`
+*  :py:func:`~nwbinspector.checks._tables.check_empty_table`
+*  :py:func:`~nwbinspector.checks._tables.check_time_interval_time_columns`
+*  :py:func:`~nwbinspector.checks._tables.check_time_intervals_stop_after_start`
+*  :py:func:`~nwbinspector.checks._tables.check_table_values_for_dict`
+*  :py:func:`~nwbinspector.checks._time_series.check_regular_timestamps`
+*  :py:func:`~nwbinspector.checks._time_series.check_timestamps_ascending`
+*  :py:func:`~nwbinspector.checks._time_series.check_timestamps_without_nans`
+*  :py:func:`~nwbinspector.checks._time_series.check_missing_unit`
+*  :py:func:`~nwbinspector.checks._time_series.check_resolution`
+*  :py:func:`~nwbinspector.checks._time_series.check_time_series_duration`
+*  :py:func:`~nwbinspector.checks._time_series.check_time_series_data_is_not_empty`
+*  :py:func:`~nwbinspector.checks._time_series.check_rate_not_below_threshold`
+
+BEST PRACTICE SUGGESTION
+-------------------------
+
+*  :py:func:`~nwbinspector.checks._general.check_name_colons`
+*  :py:func:`~nwbinspector.checks._general.check_description`
+*  :py:func:`~nwbinspector.checks._nwb_containers.check_small_dataset_compression`
+*  :py:func:`~nwbinspector.checks._nwb_containers.check_empty_string_for_optional_attribute`
+*  :py:func:`~nwbinspector.checks._nwbfile_metadata.check_session_start_time_old_date`
+*  :py:func:`~nwbinspector.checks._nwbfile_metadata.check_experimenter_exists`
+*  :py:func:`~nwbinspector.checks._nwbfile_metadata.check_experimenter_form`
+*  :py:func:`~nwbinspector.checks._nwbfile_metadata.check_experiment_description`
+*  :py:func:`~nwbinspector.checks._nwbfile_metadata.check_institution`
+*  :py:func:`~nwbinspector.checks._nwbfile_metadata.check_keywords`
+*  :py:func:`~nwbinspector.checks._nwbfile_metadata.check_doi_publications`
+*  :py:func:`~nwbinspector.checks._nwbfile_metadata.check_subject_proper_age_range`
+*  :py:func:`~nwbinspector.checks._nwbfile_metadata.check_processing_module_name`
+*  :py:func:`~nwbinspector.checks._nwbfile_metadata.check_file_extension`
+*  :py:func:`~nwbinspector.checks._tables.check_column_binary_capability`
+*  :py:func:`~nwbinspector.checks._tables.check_single_row`
+*  :py:func:`~nwbinspector.checks._tables.check_col_not_nan`
+*  :py:func:`~nwbinspector.checks._tables.check_table_time_columns_are_not_negative`
+*  :py:func:`~nwbinspector.checks._time_series.check_timestamp_of_the_first_sample_is_not_negative`

src/nwbinspector/checks/__init__.py

@@ -13,6 +13,7 @@
     check_negative_spike_times,
     check_spike_times_not_in_samples,
     check_spike_times_not_in_unobserved_interval,
+    check_spike_times_without_nans,
     check_units_resolution_is_set,
     check_units_resolution_is_valid,
     check_units_table_duration,
@@ -184,6 +185,7 @@
     "check_spatial_series_dims",
     "check_spatial_series_degrees_magnitude",
     "check_ascending_spike_times",
+    "check_spike_times_without_nans",
     "check_electrical_series_unscaled_data",
     "check_units_resolution_is_valid",
     "check_units_resolution_is_set",

src/nwbinspector/checks/_ecephys.py

@@ -244,6 +244,23 @@ def check_spike_times_not_in_unobserved_interval(units_table: Units, nunits: int
     return None
 
 
+@register_check(importance=Importance.CRITICAL, neurodata_type=Units)
+def check_spike_times_without_nans(units_table: Units) -> Optional[InspectorMessage]:
+    """
+    Check if the Units table contains NaN values in spike times.
+
+    Best Practice: :ref:`best_practice_spike_times_without_nans`
+    """
+    if "spike_times" not in units_table:
+        return None
+
+    if np.any(np.isnan(np.asarray(units_table["spike_times"].target.data[:]))):
+        return InspectorMessage(
+            message="Units table contains NaN spike times. Spike times should be valid timestamps in seconds."
+        )
+    return None
+
+
 @register_check(importance=Importance.CRITICAL, neurodata_type=Units)
 def check_ascending_spike_times(units_table: Units, nelems: Optional[int] = NELEMS) -> Optional[InspectorMessage]:
     """

tests/unit_tests/test_ecephys.py

@@ -20,6 +20,7 @@
     check_negative_spike_times,
     check_spike_times_not_in_samples,
     check_spike_times_not_in_unobserved_interval,
+    check_spike_times_without_nans,
     check_units_resolution_is_set,
     check_units_resolution_is_valid,
     check_units_table_duration,
@@ -437,6 +438,30 @@ def test_check_spike_times_not_in_unobserved_interval_multiple_units():
     )
 
 
+class TestCheckSpikeTimesWithoutNans(TestCase):
+    def setUp(self):
+        self.units_table = Units()
+
+    def test_spike_times_without_nans_valid(self):
+        self.units_table.add_unit(spike_times=[0.0, 0.1, 0.2])
+        self.units_table.add_unit(spike_times=[1.0, 1.1, 1.2])
+        assert check_spike_times_without_nans(units_table=self.units_table) is None
+
+    def test_spike_times_with_nans(self):
+        self.units_table.add_unit(spike_times=[0.0, np.nan, 0.2])
+        assert check_spike_times_without_nans(units_table=self.units_table) == InspectorMessage(
+            message="Units table contains NaN spike times. Spike times should be valid timestamps in seconds.",
+            importance=Importance.CRITICAL,
+            check_function_name="check_spike_times_without_nans",
+            object_type="Units",
+            object_name="Units",
+            location="/",
+        )
+
+    def test_spike_times_without_nans_empty(self):
+        assert check_spike_times_without_nans(units_table=self.units_table) is None
+
+
 class TestCheckAscendingSpikeTimes(TestCase):
     def setUp(self):
         self.units_table = Units()