diff --git a/doc/user-guide/io.rst b/doc/user-guide/io.rst index 986d43ce4b7..1cee4597836 100644 --- a/doc/user-guide/io.rst +++ b/doc/user-guide/io.rst @@ -1021,6 +1021,22 @@ reads. Because this fall-back option is so much slower, xarray issues a instead of falling back to try reading non-consolidated metadata. +Fill Values +~~~~~~~~~~~ + +Zarr arrays have a ``fill_value`` that is used for chunks that were never written to disk. +For the Zarr version 2 format, Xarray will set ``fill_value`` to be equal to the CF/NetCDF ``"_FillValue"``. +This is ``np.nan`` by default for floats, and unset otherwise. Note that the Zarr library will set a +default ``fill_value`` if not specified (usually ``0``). + +For the Zarr version 3 format, ``_FillValue`` and ```fill_value`` are decoupled. +So you can set ``fill_value`` in ``encoding`` as usual. + +Note that at read-time, you can control whether ``_FillValue`` is masked using the +``mask_and_scale`` kwarg; and whether Zarr's ``fill_value`` is treated as synonymous +with ``_FillValue`` using the ``use_zarr_fill_value_as_mask`` kwarg to :py:func:`xarray.open_zarr`. + + .. _io.kerchunk: Kerchunk diff --git a/doc/whats-new.rst b/doc/whats-new.rst index 088ffcc76dc..bdab3c4c8b4 100644 --- a/doc/whats-new.rst +++ b/doc/whats-new.rst @@ -22,6 +22,8 @@ v2025.03.1 (unreleased) New Features ~~~~~~~~~~~~ +- Allow setting a ``fill_value`` for Zarr format 3 arrays. Specify ``fill_value`` in ``encoding`` as usual. + (:issue:`10064`). By `Deepak Cherian `_. Breaking changes ~~~~~~~~~~~~~~~~ diff --git a/xarray/backends/zarr.py b/xarray/backends/zarr.py index 6c2719544d2..5b7e9d7af47 100644 --- a/xarray/backends/zarr.py +++ b/xarray/backends/zarr.py @@ -426,6 +426,7 @@ def extract_zarr_variable_encoding( raise_on_invalid=False, name=None, *, + zarr_format: ZarrFormat, safe_chunks=True, region=None, mode=None, @@ -443,6 +444,7 @@ def extract_zarr_variable_encoding( region: tuple[slice, ...], optional mode: str, optional shape: tuple[int, ...], optional + zarr_format: Literal[2,3] Returns ------- encoding : dict @@ -463,6 +465,8 @@ def extract_zarr_variable_encoding( "cache_metadata", "write_empty_chunks", } + if zarr_format == 3: + valid_encodings.add("fill_value") for k in safe_to_drop: if k in encoding: @@ -470,9 +474,14 @@ def extract_zarr_variable_encoding( if raise_on_invalid: invalid = [k for k in encoding if k not in valid_encodings] + if "fill_value" in invalid and zarr_format == 2: + msg = " Use `_FillValue` to set the Zarr array `fill_value`" + else: + msg = "" + if invalid: raise ValueError( - f"unexpected encoding parameters for zarr backend: {invalid!r}" + f"unexpected encoding parameters for zarr backend: {invalid!r}." + msg ) else: for k in list(encoding): @@ -1147,7 +1156,7 @@ def set_variables(self, variables, check_encoding_set, writer, unlimited_dims=No if self._use_zarr_fill_value_as_mask: fill_value = attrs.pop("_FillValue", None) else: - fill_value = None + fill_value = v.encoding.pop("fill_value", None) if "_FillValue" in attrs: # replace with encoded fill value fv = attrs.pop("_FillValue") @@ -1198,6 +1207,7 @@ def set_variables(self, variables, check_encoding_set, writer, unlimited_dims=No region=region, mode=self._mode, shape=zarr_shape, + zarr_format=3 if is_zarr_v3_format else 2, ) if self._mode == "w" or name not in existing_keys: diff --git a/xarray/tests/test_backends.py b/xarray/tests/test_backends.py index b2841e0da48..ab7b8298618 100644 --- a/xarray/tests/test_backends.py +++ b/xarray/tests/test_backends.py @@ -13,6 +13,7 @@ import tempfile import uuid import warnings +from collections import ChainMap from collections.abc import Generator, Iterator, Mapping from contextlib import ExitStack from io import BytesIO @@ -3343,6 +3344,67 @@ def test_cache_members(self) -> None: observed_keys_2 = sorted(zstore_mut.array_keys()) assert observed_keys_2 == sorted(array_keys + [new_key]) + @requires_dask + @pytest.mark.parametrize("dtype", [int, float]) + def test_zarr_fill_value_setting(self, dtype): + # When zarr_format=2, _FillValue sets fill_value + # When zarr_format=3, fill_value is set independently + # We test this by writing a dask array with compute=False, + # on read we should receive chunks filled with `fill_value` + fv = -1 + ds = xr.Dataset( + {"foo": ("x", dask.array.from_array(np.array([0, 0, 0], dtype=dtype)))} + ) + expected = xr.Dataset({"foo": ("x", [fv] * 3)}) + + zarr_format_2 = ( + has_zarr_v3 and zarr.config.get("default_zarr_format") == 2 + ) or not has_zarr_v3 + if zarr_format_2: + attr = "_FillValue" + expected.foo.attrs[attr] = fv + else: + attr = "fill_value" + if dtype is float: + # for floats, Xarray inserts a default `np.nan` + expected.foo.attrs["_FillValue"] = np.nan + + # turn off all decoding so we see what Zarr returns to us. + # Since chunks, are not written, we should receive on `fill_value` + open_kwargs = { + "mask_and_scale": False, + "consolidated": False, + "use_zarr_fill_value_as_mask": False, + } + save_kwargs = dict(compute=False, consolidated=False) + with self.roundtrip( + ds, + save_kwargs=ChainMap(save_kwargs, dict(encoding={"foo": {attr: fv}})), + open_kwargs=open_kwargs, + ) as actual: + assert_identical(actual, expected) + + ds.foo.encoding[attr] = fv + with self.roundtrip( + ds, save_kwargs=save_kwargs, open_kwargs=open_kwargs + ) as actual: + assert_identical(actual, expected) + + if zarr_format_2: + ds = ds.drop_encoding() + with pytest.raises(ValueError, match="_FillValue"): + with self.roundtrip( + ds, + save_kwargs=ChainMap( + save_kwargs, dict(encoding={"foo": {"fill_value": fv}}) + ), + open_kwargs=open_kwargs, + ): + pass + # TODO: this doesn't fail because of the + # ``raise_on_invalid=vn in check_encoding_set`` line in zarr.py + # ds.foo.encoding["fill_value"] = fv + @requires_zarr @pytest.mark.skipif( @@ -5827,23 +5889,23 @@ def test_encode_zarr_attr_value() -> None: @requires_zarr def test_extract_zarr_variable_encoding() -> None: var = xr.Variable("x", [1, 2]) - actual = backends.zarr.extract_zarr_variable_encoding(var) + actual = backends.zarr.extract_zarr_variable_encoding(var, zarr_format=3) assert "chunks" in actual assert actual["chunks"] == ("auto" if has_zarr_v3 else None) var = xr.Variable("x", [1, 2], encoding={"chunks": (1,)}) - actual = backends.zarr.extract_zarr_variable_encoding(var) + actual = backends.zarr.extract_zarr_variable_encoding(var, zarr_format=3) assert actual["chunks"] == (1,) # does not raise on invalid var = xr.Variable("x", [1, 2], encoding={"foo": (1,)}) - actual = backends.zarr.extract_zarr_variable_encoding(var) + actual = backends.zarr.extract_zarr_variable_encoding(var, zarr_format=3) # raises on invalid var = xr.Variable("x", [1, 2], encoding={"foo": (1,)}) with pytest.raises(ValueError, match=r"unexpected encoding parameters"): actual = backends.zarr.extract_zarr_variable_encoding( - var, raise_on_invalid=True + var, raise_on_invalid=True, zarr_format=3 ) pFad - Phonifier reborn

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