Warn instead of raise error if SpatialSeries has more than 3 columns (#1480)

Author: rly

CHANGELOG.md

@@ -3,7 +3,7 @@
 ## PyNWB 2.1.0 (Upcoming)
 
 ### Breaking changes:
-- Restrict `SpatialSeries.data` to have no more than 3 columns (#1455)
+- Raise a warning if `SpatialSeries.data` has more than 3 columns (#1455, #1480)
 - Updated ``TimeIntervals`` to use the new  ``TimeSeriesReferenceVectorData`` type. This does not alter the overall
   structure of ``TimeIntervals`` in a major way aside from changing the value of the ``neurodata_type`` attribute of the
   ``TimeIntervals.timeseries`` column from ``VectorData`` to ``TimeSeriesReferenceVectorData``. This change facilitates

src/pynwb/behavior.py

@@ -1,4 +1,6 @@
-from hdmf.utils import docval, popargs, get_docval
+import warnings
+
+from hdmf.utils import docval, popargs, get_docval, get_data_shape
 
 from . import register_class, CORE_NAMESPACE
 from .core import MultiContainerInterface
@@ -21,9 +23,7 @@ class SpatialSeries(TimeSeries):
     __nwbfields__ = ('reference_frame',)
 
     @docval(*get_docval(TimeSeries.__init__, 'name'),  # required
-            {'name': 'data', 'type': ('array_data', 'data', TimeSeries), 'shape': (
-                    (None, ), (None, 1), (None, 2), (None, 3)
-            ),  # required
+            {'name': 'data', 'type': ('array_data', 'data', TimeSeries), 'shape': ((None, ), (None, None)),  # required
              'doc': ('The data values. Can be 1D or 2D. The first dimension must be time. If 2D, there can be 1, 2, '
                      'or 3 columns, which represent x, y, and z.')},
             {'name': 'reference_frame', 'type': str,   # required
@@ -38,8 +38,26 @@ def __init__(self, **kwargs):
         """
         name, data, reference_frame, unit = popargs('name', 'data', 'reference_frame', 'unit', kwargs)
         super(SpatialSeries, self).__init__(name, data, unit, **kwargs)
+
+        # NWB 2.5 restricts length of second dimension to be <= 3
+        allowed_data_shapes = ((None, ), (None, 1), (None, 2), (None, 3))
+        data_shape = get_data_shape(data)
+        if not any(self._validate_data_shape(data_shape, a) for a in allowed_data_shapes):
+            warnings.warn("SpatialSeries '%s' has data shape %s which is not compliant with NWB 2.5 and greater. "
+                          "The second dimension should have length <= 3 to represent at most x, y, z." %
+                          (name, str(data_shape)))
+
         self.reference_frame = reference_frame
 
+    @staticmethod
+    def _validate_data_shape(valshape, argshape):
+        if not len(valshape) == len(argshape):
+            return False
+        for a, b in zip(valshape, argshape):
+            if b not in (a, None):
+                return False
+        return True
+
 
 @register_class('BehavioralEpochs', CORE_NAMESPACE)
 class BehavioralEpochs(MultiContainerInterface):

tests/unit/test_behavior.py

@@ -20,15 +20,11 @@ def test_set_unit(self):
         self.assertEqual(sS.unit, 'degrees')
 
     def test_gt_3_cols(self):
-        with self.assertRaises(ValueError) as error:
+        msg = ("SpatialSeries 'test_sS' has data shape (5, 4) which is not compliant with NWB 2.5 and greater. "
+               "The second dimension should have length <= 3 to represent at most x, y, z.")
+        with self.assertWarnsWith(UserWarning, msg):
             SpatialSeries("test_sS", np.ones((5, 4)), "reference_frame", "meters", rate=30.)
 
-        self.assertEqual(
-            "SpatialSeries.__init__: incorrect shape for 'data' (got '(5, 4)', expected "
-            "'((None,), (None, 1), (None, 2), (None, 3))')",
-            str(error.exception)
-        )
-
 
 class BehavioralEpochsConstructor(TestCase):
     def test_init(self):