Merge pull request #137 from NeurodataWithoutBorders/missing_unit

[Add Check]: missing 'unit' in TimeSeries

Author: CodyCBakerPhD

docs/best_practices/time_series.rst

@@ -35,6 +35,8 @@ Every :nwb-schema:ref:`sec-TimeSeries` instance has ``unit`` as an attribute, wh
 measurement for that data, using the appropriate type from the
 :wikipedia:`International System of Units (SI) <International_System_of_Units>`.
 
+Check function: :py:meth:`~nwbinspector.checks.time_series.check_missing_unit`
+
 
 
 .. _best_practice_time_series_global_time_reference:

nwbinspector/checks/time_series.py

@@ -68,34 +68,23 @@ def check_timestamps_ascending(time_series: TimeSeries, nelems=200):
         return InspectorMessage(f"{time_series.name} timestamps are not ascending.")
 
 
+@register_check(importance=Importance.BEST_PRACTICE_VIOLATION, neurodata_type=TimeSeries)
+def check_missing_unit(time_series: TimeSeries):
+    """
+    Check if the TimeSeries.unit field is empty.
+
+    Best Practice: :ref:`best_practice_unit_of_measurement`
+    """
+    if not time_series.unit:
+        return InspectorMessage(
+            message="Missing text for attribute 'unit'. Please specify the scientific unit of the 'data'."
+        )
+
+
 @register_check(importance=Importance.BEST_PRACTICE_VIOLATION, neurodata_type=TimeSeries)
 def check_resolution(time_series: TimeSeries):
     """Check the resolution value of a TimeSeries for proper format (-1.0 or NaN for unknown)."""
     if time_series.resolution != -1.0 and time_series.resolution <= 0:
         return InspectorMessage(
             message=f"'resolution' should use -1.0 or NaN for unknown instead of {time_series.resolution}."
         )
-
-
-# TODO: break up logic of extra stuff into separate checks
-# def check_timeseries(nwbfile):
-#     """Check dataset values in TimeSeries objects"""
-#     for ts in all_of_type(nwbfile, pynwb.TimeSeries):
-#         if ts.data is None:
-#             # exception to the rule: ImageSeries objects are allowed to have no data
-#             if not isinstance(ts, pynwb.image.ImageSeries):
-#                 error_code = "A101"
-#                 print("- %s: '%s' %s data is None" % (error_code, ts.name, type(ts).__name__))
-#             else:
-#                 if ts.external_file is None:
-#                     error_code = "A101"
-#                     print(
-#                         "- %s: '%s' %s data is None and external_file is None"
-#                         % (error_code, ts.name, type(ts).__name__)
-#                     )
-#             continue
-
-#         if not ts.unit:
-#             error_code = "A101"
-#             print("- %s: '%s' %s data is missing text for attribute 'unit'"
-# % (error_code, ts.name, type(ts).__name__))

tests/unit_tests/test_time_series.py

@@ -7,6 +7,7 @@
     check_data_orientation,
     check_timestamps_match_first_dimension,
     check_timestamps_ascending,
+    check_missing_unit,
     check_resolution,
     Importance,
 )
@@ -117,6 +118,23 @@ def test_pass_check_timestamps_ascending():
     assert check_timestamps_ascending(time_series) is None
 
 
+def test_check_missing_unit_pass():
+    time_series = pynwb.TimeSeries(name="test_time_series", unit="test_units", data=[1, 2, 3], timestamps=[1, 2, 3])
+    assert check_missing_unit(time_series) is None
+
+
+def test_check_missing_unit_fail():
+    time_series = pynwb.TimeSeries(name="test_time_series", unit="", data=[1, 2, 3], timestamps=[1, 2, 3])
+    assert check_missing_unit(time_series) == InspectorMessage(
+        message="Missing text for attribute 'unit'. Please specify the scientific unit of the 'data'.",
+        importance=Importance.BEST_PRACTICE_VIOLATION,
+        check_function_name="check_missing_unit",
+        object_type="TimeSeries",
+        object_name="test_time_series",
+        location="/",
+    )
+
+
 def test_check_positive_resolution_pass():
     time_series = pynwb.TimeSeries(name="test", unit="test_units", data=[1, 2, 3], timestamps=[1, 2, 3], resolution=3.4)
     assert check_timestamps_ascending(time_series) is None