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-iFXG89/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-iFXG89/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-iFXG89/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-iFXG89/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-iFXG89/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-iFXG89/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