Zarr Encoding Specification

In implementing support for the Zarr storage format, Xarray developers made some ad hoc choices about how to store NetCDF data in Zarr. Future versions of the Zarr spec will likely include a more formal convention for the storage of the NetCDF data model in Zarr; see Zarr spec repo for ongoing discussion.

First, Xarray can only read and write Zarr groups. There is currently no support for reading / writing individual Zarr arrays. Zarr groups are mapped to Xarray Dataset objects.

Second, from Xarray’s point of view, the key difference between NetCDF and Zarr is that all NetCDF arrays have dimension names while Zarr arrays do not. Therefore, in order to store NetCDF data in Zarr, Xarray must somehow encode and decode the name of each array’s dimensions.

To accomplish this, Xarray developers decided to define a special Zarr array attribute: _ARRAY_DIMENSIONS. The value of this attribute is a list of dimension names (strings), for example ["time", "lon", "lat"]. When writing data to Zarr, Xarray sets this attribute on all variables based on the variable dimensions. When reading a Zarr group, Xarray looks for this attribute on all arrays, raising an error if it can’t be found. The attribute is used to define the variable dimension names and then removed from the attributes dictionary returned to the user.

Because of these choices, Xarray cannot read arbitrary array data, but only Zarr data with valid _ARRAY_DIMENSIONS or NCZarr attributes on each array (NCZarr dimension names are defined in the .zarray file).

After decoding the _ARRAY_DIMENSIONS or NCZarr attribute and assigning the variable dimensions, Xarray proceeds to [optionally] decode each variable using its standard CF decoding machinery used for NetCDF data (see decode_cf()).

Finally, it’s worth noting that Xarray writes (and attempts to read) “consolidated metadata” by default (the .zmetadata file), which is another non-standard Zarr extension, albeit one implemented upstream in Zarr-Python. You do not need to write consolidated metadata to make Zarr stores readable in Xarray, but because Xarray can open these stores much faster, users will see a warning about poor performance when reading non-consolidated stores unless they explicitly set consolidated=False. See Consolidated Metadata for more details.

As a concrete example, here we write a tutorial dataset to Zarr and then re-open it directly with Zarr:

In [1]: import os

In [2]: import xarray as xr

In [3]: import zarr
---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
Cell In [3], line 1
----> 1 import zarr

ModuleNotFoundError: No module named 'zarr'

In [4]: ds = xr.tutorial.load_dataset("rasm")
---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
File /build/python-xarray-x7F8vs/python-xarray-2022.10.0/xarray/tutorial.py:131, in open_dataset(name, cache, cache_dir, engine, **kws)
    130 try:
--> 131     import pooch
    132 except ImportError as e:

ModuleNotFoundError: No module named 'pooch'

The above exception was the direct cause of the following exception:

ImportError                               Traceback (most recent call last)
Cell In [4], line 1
----> 1 ds = xr.tutorial.load_dataset("rasm")

File /build/python-xarray-x7F8vs/python-xarray-2022.10.0/xarray/tutorial.py:270, in load_dataset(*args, **kwargs)
    233 def load_dataset(*args, **kwargs) -> Dataset:
    234     """
    235     Open, load into memory, and close a dataset from the online repository
    236     (requires internet).
   (...)
    268     load_dataset
    269     """
--> 270     with open_dataset(*args, **kwargs) as ds:
    271         return ds.load()

File /build/python-xarray-x7F8vs/python-xarray-2022.10.0/xarray/tutorial.py:133, in open_dataset(name, cache, cache_dir, engine, **kws)
    131     import pooch
    132 except ImportError as e:
--> 133     raise ImportError(
    134         "tutorial.open_dataset depends on pooch to download and manage datasets."
    135         " To proceed please install pooch."
    136     ) from e
    138 logger = pooch.get_logger()
    139 logger.setLevel("WARNING")

ImportError: tutorial.open_dataset depends on pooch to download and manage datasets. To proceed please install pooch.

In [5]: ds.to_zarr("rasm.zarr", mode="w")
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In [5], line 1
----> 1 ds.to_zarr("rasm.zarr", mode="w")

File /build/python-xarray-x7F8vs/python-xarray-2022.10.0/xarray/core/dataset.py:2077, in Dataset.to_zarr(self, store, chunk_store, mode, synchronizer, group, encoding, compute, consolidated, append_dim, region, safe_chunks, storage_options)
   1967 """Write dataset contents to a zarr group.
   1968 
   1969 Zarr chunks are determined in the following way:
   (...)
   2073     The I/O user guide, with more details and examples.
   2074 """
   2075 from ..backends.api import to_zarr
-> 2077 return to_zarr(  # type: ignore
   2078     self,
   2079     store=store,
   2080     chunk_store=chunk_store,
   2081     storage_options=storage_options,
   2082     mode=mode,
   2083     synchronizer=synchronizer,
   2084     group=group,
   2085     encoding=encoding,
   2086     compute=compute,
   2087     consolidated=consolidated,
   2088     append_dim=append_dim,
   2089     region=region,
   2090     safe_chunks=safe_chunks,
   2091 )

File /build/python-xarray-x7F8vs/python-xarray-2022.10.0/xarray/backends/api.py:1617, in to_zarr(dataset, store, chunk_store, mode, synchronizer, group, encoding, compute, consolidated, append_dim, region, safe_chunks, storage_options)
   1615     already_consolidated = False
   1616     consolidate_on_close = consolidated or consolidated is None
-> 1617 zstore = backends.ZarrStore.open_group(
   1618     store=mapper,
   1619     mode=mode,
   1620     synchronizer=synchronizer,
   1621     group=group,
   1622     consolidated=already_consolidated,
   1623     consolidate_on_close=consolidate_on_close,
   1624     chunk_store=chunk_mapper,
   1625     append_dim=append_dim,
   1626     write_region=region,
   1627     safe_chunks=safe_chunks,
   1628     stacklevel=4,  # for Dataset.to_zarr()
   1629 )
   1631 if mode in ["a", "r+"]:
   1632     _validate_datatypes_for_zarr_append(zstore, dataset)

File /build/python-xarray-x7F8vs/python-xarray-2022.10.0/xarray/backends/zarr.py:409, in ZarrStore.open_group(cls, store, mode, synchronizer, group, consolidated, consolidate_on_close, chunk_store, storage_options, append_dim, write_region, safe_chunks, stacklevel)
    407     zarr_group = zarr.open_consolidated(store, **open_kwargs)
    408 else:
--> 409     zarr_group = zarr.open_group(store, **open_kwargs)
    410 return cls(
    411     zarr_group,
    412     mode,
   (...)
    416     safe_chunks,
    417 )

NameError: name 'zarr' is not defined

In [6]: zgroup = zarr.open("rasm.zarr")
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In [6], line 1
----> 1 zgroup = zarr.open("rasm.zarr")

NameError: name 'zarr' is not defined

In [7]: print(os.listdir("rasm.zarr"))
---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
Cell In [7], line 1
----> 1 print(os.listdir("rasm.zarr"))

FileNotFoundError: [Errno 2] No such file or directory: 'rasm.zarr'

In [8]: print(zgroup.tree())
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In [8], line 1
----> 1 print(zgroup.tree())

NameError: name 'zgroup' is not defined

In [9]: dict(zgroup["Tair"].attrs)
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In [9], line 1
----> 1 dict(zgroup["Tair"].attrs)

NameError: name 'zgroup' is not defined