Merge pull request #178 from NeurodataWithoutBorders/spatial_series_dims

add check and tests for spatial_series with improper dimensions

Author: CodyCBakerPhD

nwbinspector/__init__.py

@@ -8,3 +8,4 @@
 from .checks.ecephys import *
 from .checks.ogen import *
 from .checks.image_series import *
+from .checks.behavior import *

nwbinspector/checks/behavior.py

@@ -0,0 +1,13 @@
+"""Checks for types belonging to the pynwb.behavior module."""
+from pynwb.behavior import SpatialSeries
+
+from ..register_checks import register_check, Importance, InspectorMessage
+
+
+@register_check(importance=Importance.CRITICAL, neurodata_type=SpatialSeries)
+def check_spatial_series_dims(spatial_series: SpatialSeries):
+    """Check if a SpatialSeries has the correct dimensions."""
+    if len(spatial_series.data.shape) > 1 and spatial_series.data.shape[1] > 3:
+        return InspectorMessage(
+            message="SpatialSeries should have 1 column (x), 2 columns (x, y), or 3 columns (x, y, z)."
+        )

tests/unit_tests/test_behavior.py

@@ -0,0 +1,49 @@
+from pynwb.behavior import SpatialSeries
+import numpy as np
+
+from nwbinspector import InspectorMessage, Importance, check_spatial_series_dims
+
+
+def test_check_spatial_series_dims():
+
+    spatial_series = SpatialSeries(
+        name="SpatialSeries",
+        description="description",
+        data=np.ones((10, 4)),
+        rate=3.0,
+        reference_frame="reference_frame",
+    )
+    assert check_spatial_series_dims(spatial_series) == InspectorMessage(
+        message="SpatialSeries should have 1 column (x), 2 columns (x, y), or 3 columns (x, y, z).",
+        importance=Importance.CRITICAL,
+        check_function_name="check_spatial_series_dims",
+        object_type="SpatialSeries",
+        object_name="SpatialSeries",
+        location="/",
+    )
+
+
+def test_pass_check_spatial_series_dims():
+
+    spatial_series = SpatialSeries(
+        name="SpatialSeries",
+        description="description",
+        data=np.ones((10, 3)),
+        rate=3.0,
+        reference_frame="reference_frame",
+    )
+
+    assert check_spatial_series_dims(spatial_series) is None
+
+
+def test_pass_check_spatial_series_dims_1d():
+
+    spatial_series = SpatialSeries(
+        name="SpatialSeries",
+        description="description",
+        data=np.ones((10,)),
+        rate=3.0,
+        reference_frame="reference_frame",
+    )
+
+    assert check_spatial_series_dims(spatial_series) is None