[New Check]: Non-required Electrode columns (nwb-schema >= 2.5.0)

nwbinspector/checks/ecephys.py

@@ -1,12 +1,14 @@
 """Check functions specific to extracellular electrophysiology neurodata types."""
-import numpy as np
+from packaging import version
 
+import numpy as np
+from pynwb.file import ElectrodeTable
 from pynwb.misc import Units
 from pynwb.ecephys import ElectricalSeries
-
 from hdmf.utils import get_data_shape
 
 from ..register_checks import register_check, Importance, InspectorMessage
+from ..utils import get_package_version
 
 
 @register_check(importance=Importance.BEST_PRACTICE_VIOLATION, neurodata_type=Units)
@@ -79,3 +81,17 @@ def check_spike_times_not_in_unobserved_interval(units_table: Units, nunits: int
                     "observed intervals."
                 )
             )
+
+
+@register_check(importance=Importance.BEST_PRACTICE_SUGGESTION, neurodata_type=ElectrodeTable)
+def check_optional_columns_electrode_table(electrode_table: ElectrodeTable):
+    """Check that the ElectrodeTable columns which are optional for nwb-schema>=2.5.0 are not specified as NaN."""
+    if get_package_version(name="pynwb") < version.Version("2.1.0"):
+        return
+    if any(x.isnan() in electrode_table for x in ["x", "y", "z", "imp", "filtering"]):
+        return InspectorMessage(
+            message=(
+                "The ElectrodeTable contains NaN values on optional columns - "
+                "as of nwb-schema 2.5.0, there is no need to write these columns."
+            )
+        )

tests/unit_tests/test_ecephys.py

@@ -1,9 +1,12 @@
 from datetime import datetime
 from unittest import TestCase
 from uuid import uuid4
+from packaging import version
 
+import pytest
 import numpy as np
 from pynwb import NWBFile
+from pynwb.file import ElectrodeTable, ElectrodeGroup, Device
 from pynwb.ecephys import ElectricalSeries
 from pynwb.misc import Units
 from hdmf.common.table import DynamicTableRegion, DynamicTable
@@ -15,7 +18,9 @@
     check_electrical_series_dims,
     check_electrical_series_reference_electrodes_table,
     check_spike_times_not_in_unobserved_interval,
+    check_optional_columns_electrode_table,
 )
+from nwbinspector.utils import get_package_version
 
 
 def test_check_negative_spike_times_all_positive():
@@ -220,3 +225,43 @@ def test_check_spike_times_not_in_unobserved_interval_multiple_units():
         object_name="TestUnits",
         location="/",
     )
+
+
+@pytest.mark.skipif(get_package_version(name="pynwb") < version.Version("2.1.0"))
+def test_check_optional_columns_electrode_table_pass():
+    electrode_table = ElectrodeTable(name="electrodes")
+    electrode_table.add_row(
+        location="unknown",
+        group=ElectrodeGroup(name="test_group", description="", device=Device(name="test_device"), location="unknown"),
+        group_name="test_group",
+    )
+    assert check_optional_columns_electrode_table(electrode_table=electrode_table) is None
+
+
+@pytest.mark.skip  # TODO: when fixed on PyNWB side, unskip
+def test_check_optional_columns_electrode_table_fail():
+    electrode_table = ElectrodeTable(name="electrodes")
+    electrode_table.add_row(
+        x=np.nan,
+        y=np.nan,
+        z=np.nan,
+        imp=np.nan,
+        location="unknown",
+        filtering="unknown",
+        group=ElectrodeGroup(name="test_group", description="", device=Device(name="test_device"), location="unknown"),
+        group_name="test_group",
+    )
+    if get_package_version(name="pynwb") >= version.Version("2.1.0"):
+        assert check_optional_columns_electrode_table(electrode_table=electrode_table) == InspectorMessage(
+            message=(
+                "The ElectrodeTable contains NaN values on optional columns - "
+                "as of nwb-schema 2.5.0, there is no need to write these columns."
+            ),
+            importance=Importance.BEST_PRACTICE_SUGGESTION,
+            check_function_name="check_optional_columns_electrode_table",
+            object_type="ElectrodeTable",
+            object_name="electrodes",
+            location="/",
+        )
+    else:
+        assert check_optional_columns_electrode_table(electrode_table=electrode_table) is None

tests/unit_tests/test_tables.py

@@ -1,6 +1,7 @@
 import platform
 import json
 from unittest import TestCase
+from packaging import version
 
 import numpy as np
 from hdmf.common import DynamicTable, DynamicTableRegion
@@ -17,6 +18,7 @@
     check_single_row,
     check_table_values_for_dict,
 )
+from nwbinspector.utils import get_package_version
 
 
 class TestCheckDynamicTableRegion(TestCase):
@@ -237,16 +239,27 @@ def test_check_single_row_ignore_electrodes():
     table = ElectrodeTable(
         name="electrodes",  # default name when building through nwbfile
     )
-    table.add_row(
-        x=np.nan,
-        y=np.nan,
-        z=np.nan,
-        imp=np.nan,
-        location="unknown",
-        filtering="unknown",
-        group=ElectrodeGroup(name="test_group", description="", device=Device(name="test_device"), location="unknown"),
-        group_name="test_group",
-    )
+    if get_package_version(name="pynwb") >= version.Version("2.1.0"):
+        table.add_row(
+            location="unknown",
+            group=ElectrodeGroup(
+                name="test_group", description="", device=Device(name="test_device"), location="unknown"
+            ),
+            group_name="test_group",
+        )
+    else:
+        table.add_row(
+            x=np.nan,
+            y=np.nan,
+            z=np.nan,
+            imp=np.nan,
+            location="unknown",
+            filtering="unknown",
+            group=ElectrodeGroup(
+                name="test_group", description="", device=Device(name="test_device"), location="unknown"
+            ),
+            group_name="test_group",
+        )
     assert check_single_row(table=table) is None