fix: preserve Numcodecs filter shape and decode order

changes/4553.bugfix.md

@@ -0,0 +1 @@
+Preserve the declared chunk shape after Numcodecs filters and decode transposed chunks in logical C order.

src/zarr/codecs/numcodecs/_codecs.py

@@ -155,7 +155,7 @@ def __init__(self, **codec_config: JSON) -> None:
         super().__init__(**codec_config)
 
     def _decode_sync(self, chunk_data: NDBuffer, chunk_spec: ArraySpec) -> NDBuffer:
-        chunk_ndarray = chunk_data.as_ndarray_like()
+        chunk_ndarray = np.ascontiguousarray(chunk_data.as_ndarray_like())
         out = self._codec.decode(chunk_ndarray)
         return chunk_spec.prototype.nd_buffer.from_ndarray_like(out.reshape(chunk_spec.shape))
 
@@ -164,6 +164,7 @@ def _encode_sync(self, chunk_data: NDBuffer, chunk_spec: ArraySpec) -> NDBuffer:
         # would be encoded in transposed element order (gh-3558)
         chunk_ndarray = np.ascontiguousarray(chunk_data.as_ndarray_like())
         out = self._codec.encode(chunk_ndarray)
+        out = out.reshape(self.resolve_metadata(chunk_spec).shape)
         return chunk_spec.prototype.nd_buffer.from_ndarray_like(out)
 
     async def _encode_single(self, chunk_data: NDBuffer, chunk_spec: ArraySpec) -> NDBuffer:

tests/test_codecs/test_numcodecs.py

@@ -10,6 +10,7 @@
 
 from zarr import config, create_array, open_array
 from zarr.abc.numcodec import _is_numcodec, _is_numcodec_cls
+from zarr.codecs import TransposeCodec
 from zarr.codecs import numcodecs as _numcodecs
 from zarr.errors import UnknownCodecError
 from zarr.registry import get_codec_class, get_numcodec
@@ -135,9 +136,11 @@ def test_generic_compressor(codec_class: type[_numcodecs._NumcodecsBytesBytesCod
         "astype",
     ],
 )
+@pytest.mark.parametrize("transpose", [False, True])
 def test_generic_filter(
     codec_class: type[_numcodecs._NumcodecsArrayArrayCodec],
     codec_config: dict[str, JSON],
+    transpose: bool,
 ) -> None:
     data = np.linspace(0, 10, 256, dtype="float32").reshape((16, 16))
 
@@ -149,6 +152,7 @@ def test_generic_filter(
         fill_value=0,
         filters=[
             codec_class(**codec_config),
+            *([TransposeCodec(order=(1, 0))] if transpose else []),
         ],
     )