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-a90CVg/python-xarray-2023.01.0/xarray/tutorial.py:132, in open_dataset(name, cache, cache_dir, engine, **kws)
131 try:
--> 132 import pooch
133 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-a90CVg/python-xarray-2023.01.0/xarray/tutorial.py:284, in load_dataset(*args, **kwargs)
247 def load_dataset(*args, **kwargs) -> Dataset:
248 """
249 Open, load into memory, and close a dataset from the online repository
250 (requires internet).
(...)
282 load_dataset
283 """
--> 284 with open_dataset(*args, **kwargs) as ds:
285 return ds.load()
File /build/python-xarray-a90CVg/python-xarray-2023.01.0/xarray/tutorial.py:134, in open_dataset(name, cache, cache_dir, engine, **kws)
132 import pooch
133 except ImportError as e:
--> 134 raise ImportError(
135 "tutorial.open_dataset depends on pooch to download and manage datasets."
136 " To proceed please install pooch."
137 ) from e
139 logger = pooch.get_logger()
140 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")
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
Cell In [5], line 1
----> 1 ds.to_zarr("rasm.zarr", mode="w")
File /build/python-xarray-a90CVg/python-xarray-2023.01.0/xarray/core/dataset.py:2099, in Dataset.to_zarr(self, store, chunk_store, mode, synchronizer, group, encoding, compute, consolidated, append_dim, region, safe_chunks, storage_options, zarr_version)
1982 """Write dataset contents to a zarr group.
1983
1984 Zarr chunks are determined in the following way:
(...)
2095 The I/O user guide, with more details and examples.
2096 """
2097 from xarray.backends.api import to_zarr
-> 2099 return to_zarr( # type: ignore
2100 self,
2101 store=store,
2102 chunk_store=chunk_store,
2103 storage_options=storage_options,
2104 mode=mode,
2105 synchronizer=synchronizer,
2106 group=group,
2107 encoding=encoding,
2108 compute=compute,
2109 consolidated=consolidated,
2110 append_dim=append_dim,
2111 region=region,
2112 safe_chunks=safe_chunks,
2113 zarr_version=zarr_version,
2114 )
File /build/python-xarray-a90CVg/python-xarray-2023.01.0/xarray/backends/api.py:1629, in to_zarr(dataset, store, chunk_store, mode, synchronizer, group, encoding, compute, consolidated, append_dim, region, safe_chunks, storage_options, zarr_version)
1627 already_consolidated = False
1628 consolidate_on_close = consolidated or consolidated is None
-> 1629 zstore = backends.ZarrStore.open_group(
1630 store=mapper,
1631 mode=mode,
1632 synchronizer=synchronizer,
1633 group=group,
1634 consolidated=already_consolidated,
1635 consolidate_on_close=consolidate_on_close,
1636 chunk_store=chunk_mapper,
1637 append_dim=append_dim,
1638 write_region=region,
1639 safe_chunks=safe_chunks,
1640 stacklevel=4, # for Dataset.to_zarr()
1641 zarr_version=zarr_version,
1642 )
1644 if mode in ["a", "r+"]:
1645 _validate_datatypes_for_zarr_append(zstore, dataset)
File /build/python-xarray-a90CVg/python-xarray-2023.01.0/xarray/backends/zarr.py:363, in ZarrStore.open_group(cls, store, mode, synchronizer, group, consolidated, consolidate_on_close, chunk_store, storage_options, append_dim, write_region, safe_chunks, stacklevel, zarr_version)
346 @classmethod
347 def open_group(
348 cls,
(...)
361 zarr_version=None,
362 ):
--> 363 import zarr
365 # zarr doesn't support pathlib.Path objects yet. zarr-python#601
366 if isinstance(store, os.PathLike):
ModuleNotFoundError: No module named 'zarr'
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