Merge pull request #404 from catalystneuro/add-check-rate-of-timeseri…

…es-is-not-zero

[New Check]: TimeSeries rate is zero

CHANGELOG.md

@@ -1,5 +1,9 @@
 # Upcoming
 
+### New Checks
+
+* Added `check_rate_is_not_zero` for ensuring non-zero rate value of `TimeSeries` that has more than one frame. [#389](https://github.com/NeurodataWithoutBorders/nwbinspector/issues/389)
+
 # v0.4.30
 
 ### Fixes

docs/best_practices/time_series.rst

@@ -157,3 +157,14 @@ Unknown Resolution
 If the ``resolution`` of a :ref:`nwb-schema:sec-TimeSeries` is unknown, use ``-1.0`` or ``NaN`` to indicate this.
 
 Check function: :py::meth:`~nwbinspector.checks.time_series.check_resolution`
+
+
+
+.. _best_practice_non_zero_rate:
+
+Zero Rate
+~~~~~~~~~
+
+If the ``data`` field of :ref:`nwb-schema:sec-TimeSeries` has more than one frame, and according to :ref:`best_practice_data_orientation` this axis ought to be time, then the ``rate`` field should not be ``0.0``.
+
+Check function: :py::meth:`~nwbinspector.checks.time_series.check_rate_is_not_zero`

src/nwbinspector/checks/time_series.py

@@ -129,3 +129,14 @@ def check_resolution(time_series: TimeSeries):
         return InspectorMessage(
             message=f"'resolution' should use -1.0 or NaN for unknown instead of {time_series.resolution}."
         )
+
+
+@register_check(importance=Importance.CRITICAL, neurodata_type=TimeSeries)
+def check_rate_is_not_zero(time_series: TimeSeries):
+    if time_series.data is None:
+        return
+    data_shape = get_data_shape(time_series.data)
+    if time_series.rate == 0.0 and data_shape[0] > 1:
+        return InspectorMessage(
+            f"{time_series.name} has a sampling rate value of 0.0Hz but the series has more than one frame."
+        )

tests/unit_tests/test_time_series.py

@@ -15,6 +15,7 @@
     check_missing_unit,
     check_resolution,
     check_timestamp_of_the_first_sample_is_not_negative,
+    check_rate_is_not_zero,
 )
 from nwbinspector.tools import make_minimal_nwbfile
 from nwbinspector.testing import check_streaming_tests_enabled
@@ -199,6 +200,28 @@ def test_check_timestamps_empty_timestamps():
     )
 
 
+def test_check_rate_is_not_zero_pass():
+    time_series = pynwb.TimeSeries(name="test", unit="test_units", data=[1, 2, 3], rate=4.0)
+    assert check_rate_is_not_zero(time_series) is None
+
+
+def test_check_rate_is_not_zero_single_frame_pass():
+    time_series = pynwb.TimeSeries(name="test", unit="test_units", data=[1], rate=0.0)
+    assert check_rate_is_not_zero(time_series) is None
+
+
+def test_check_rate_is_not_zero_fail():
+    time_series = pynwb.TimeSeries(name="TimeSeriesTest", unit="n.a.", data=[1, 2, 3], rate=0.0)
+    assert check_rate_is_not_zero(time_series) == InspectorMessage(
+        message="TimeSeriesTest has a sampling rate value of 0.0Hz but the series has more than one frame.",
+        importance=Importance.CRITICAL,
+        check_function_name="check_rate_is_not_zero",
+        object_type="TimeSeries",
+        object_name="TimeSeriesTest",
+        location="/",
+    )
+
+
 def test_pass_check_timestamps_ascending_pass():
     time_series = pynwb.TimeSeries(name="test_time_series", unit="test_units", data=[1, 2, 3], timestamps=[1, 2, 3])
     assert check_timestamps_ascending(time_series) is None