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)
<ipython-input-3-1d8f822243a8> in <module>
----> 1 import zarr
ModuleNotFoundError: No module named 'zarr'
In [4]: ds = xr.tutorial.load_dataset("rasm")
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
/build/python-xarray-CcvSgw/python-xarray-2022.06.0/xarray/tutorial.py in open_dataset(name, cache, cache_dir, engine, **kws)
123 try:
--> 124 import pooch
125 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)
<ipython-input-4-1d37fb2cd247> in <module>
----> 1 ds = xr.tutorial.load_dataset("rasm")
/build/python-xarray-CcvSgw/python-xarray-2022.06.0/xarray/tutorial.py in load_dataset(*args, **kwargs)
261 load_dataset
262 """
--> 263 with open_dataset(*args, **kwargs) as ds:
264 return ds.load()
265
/build/python-xarray-CcvSgw/python-xarray-2022.06.0/xarray/tutorial.py in open_dataset(name, cache, cache_dir, engine, **kws)
124 import pooch
125 except ImportError as e:
--> 126 raise ImportError(
127 "tutorial.open_dataset depends on pooch to download and manage datasets."
128 " To proceed please install pooch."
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)
<ipython-input-5-a17f574debc7> in <module>
----> 1 ds.to_zarr("rasm.zarr", mode="w")
/build/python-xarray-CcvSgw/python-xarray-2022.06.0/xarray/core/dataset.py in to_zarr(self, store, chunk_store, mode, synchronizer, group, encoding, compute, consolidated, append_dim, region, safe_chunks, storage_options)
2058 from ..backends.api import to_zarr
2059
-> 2060 return to_zarr( # type: ignore
2061 self,
2062 store=store,
/build/python-xarray-CcvSgw/python-xarray-2022.06.0/xarray/backends/api.py in to_zarr(dataset, store, chunk_store, mode, synchronizer, group, encoding, compute, consolidated, append_dim, region, safe_chunks, storage_options)
1595 already_consolidated = False
1596 consolidate_on_close = consolidated or consolidated is None
-> 1597 zstore = backends.ZarrStore.open_group(
1598 store=mapper,
1599 mode=mode,
/build/python-xarray-CcvSgw/python-xarray-2022.06.0/xarray/backends/zarr.py in open_group(cls, store, mode, synchronizer, group, consolidated, consolidate_on_close, chunk_store, storage_options, append_dim, write_region, safe_chunks, stacklevel)
404 zarr_group = zarr.open_consolidated(store, **open_kwargs)
405 else:
--> 406 zarr_group = zarr.open_group(store, **open_kwargs)
407 return cls(
408 zarr_group,
NameError: name 'zarr' is not defined
In [6]: zgroup = zarr.open("rasm.zarr")
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-6-8a67f9d1bdc2> in <module>
----> 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)
<ipython-input-7-f130858be832> in <module>
----> 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)
<ipython-input-8-292a016afe52> in <module>
----> 1 print(zgroup.tree())
NameError: name 'zgroup' is not defined
In [9]: dict(zgroup["Tair"].attrs)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-9-2ab81eb1d230> in <module>
----> 1 dict(zgroup["Tair"].attrs)
NameError: name 'zgroup' is not defined