Fix NWBData shadowing the data attribute it inherits from Data

CHANGELOG.md

@@ -12,6 +12,7 @@
 - Fixed `mock_DeviceModel` defaulting `manufacturer` to `None`. The mock now defaults it to `"manufacturer"`. @HugoFara [#2232](https://github.com/NeurodataWithoutBorders/pynwb/pull/2232)
 - Fixed reading a file whose dates carry a sub-minute UTC offset (e.g. `1900-10-01T00:00:00-05:50:36`). @h-mayorquin [#2230](https://github.com/NeurodataWithoutBorders/pynwb/pull/2230)
 - Fixed wide pandas DataFrames in the tutorials spilling out of the content column and into the right margin. @bendichter [#2236](https://github.com/NeurodataWithoutBorders/pynwb/pull/2236)
+- Fixed `set_data_io` being silently ignored on `NWBData` subclasses (`GrayscaleImage`, `RGBImage`, `RGBAImage`, `ExternalImage`, `ImageReferences`, and `ScratchData`), so requested chunking and compression were dropped without warning and the datasets were written uncompressed. @h-mayorquin [#2233](https://github.com/NeurodataWithoutBorders/pynwb/pull/2233)
 
 
 ## PyNWB 4.1.0 (July 23, 2026)

src/pynwb/core.py

@@ -1,7 +1,5 @@
 from warnings import warn
 
-import numpy as np
-
 from hdmf import Container, Data
 from hdmf.container import AbstractContainer, MultiContainerInterface as hdmf_MultiContainerInterface, Table
 from hdmf.common import DynamicTable, DynamicTableRegion  # noqa: F401
@@ -102,50 +100,6 @@ class NWBData(NWBMixin, Data):
             allow_positional=AllowPositional.WARNING,)
     def __init__(self, **kwargs):
         super().__init__(**kwargs)
-        self.__data = kwargs['data']
-
-    @property
-    def data(self):
-        """The data managed by this object"""
-        return self.__data
-
-    def __len__(self):
-        """Size of the data. Same as len(self.data)"""
-        return len(self.__data)
-
-    def __getitem__(self, args):
-        if isinstance(self.data, (tuple, list)) and isinstance(args, (tuple, list)):
-            return [self.data[i] for i in args]
-        return self.data[args]
-
-    def append(self, arg):
-        """
-        Append a single element to the data
-
-        Note: The arg to append should be 1 dimension less than the data.
-        For example, if the data is a 2D array, arg should be a 1D array.
-        Appending to scalar data is not supported. To append multiple
-        elements, use extend.
-        """
-        if isinstance(self.data, list):
-            self.data.append(arg)
-        elif isinstance(self.data, np.ndarray):
-            self.__data = np.concatenate((self.__data, [arg]))
-        else:
-            msg = "NWBData cannot append to object of type '%s'" % type(self.__data)
-            raise ValueError(msg)
-
-    def extend(self, arg):
-        """
-        Extend the data with multiple elements.
-        """
-        if isinstance(self.data, list):
-            self.data.extend(arg)
-        elif isinstance(self.data, np.ndarray):
-            self.__data = np.concatenate((self.__data, arg))
-        else:
-            msg = "NWBData cannot extend object of type '%s'" % type(self.__data)
-            raise ValueError(msg)
 
 
 @register_class('ScratchData', CORE_NAMESPACE)

tests/unit/test_core.py

@@ -2,10 +2,11 @@
 from dateutil.tz import tzlocal
 
 import numpy as np
+from hdmf.backends.hdf5 import H5DataIO
 from hdmf.utils import docval
 
 from pynwb import NWBFile, TimeSeries, available_namespaces
-from pynwb.core import NWBContainer, NWBData
+from pynwb.core import NWBContainer, NWBData, ScratchData
 from pynwb.testing import TestCase
 
 
@@ -99,7 +100,24 @@ def test_extend_scalar(self):
         obj = NWBData(name="obj1", data=1)
         with self.assertRaises(ValueError):
             obj.extend(2)
-
+
+    def test_set_data_io_visible_through_data(self):
+        """set_data_io is inherited from Data, so its wrapping must be visible on NWBData.data.
+
+        NWBData used to declare its own data storage, which shadowed the parent's, so the DataIO
+        was applied to the parent attribute and then never read back. See #2233.
+        """
+        obj = MyNWBData("obj1", data=np.array([1, 2, 3]))
+        obj.set_data_io(H5DataIO, dict(compression="gzip"))
+        self.assertIsInstance(obj.data, H5DataIO)
+        self.assertEqual(obj.data.io_settings["compression"], "gzip")
+
+    def test_set_data_io_visible_through_data_on_scratch_data(self):
+        """The shadow was on NWBData, so every subclass was affected, not only the image types."""
+        obj = ScratchData(name="obj1", data=np.array([1, 2, 3]), description="test")
+        obj.set_data_io(H5DataIO, dict(compression="gzip"))
+        self.assertIsInstance(obj.data, H5DataIO)
+
     def test_slicing_list_with_list(self):
         obj = MyNWBData("obj1", data=[[1, 2, 3], [4, 5, 6]])
         self.assertEqual(obj[[1,]], [[4, 5, 6]])