def _extract_dataset_zattrs(dataset: xr.Dataset):
""" helper function to create zattrs dictionary from Dataset global attrs """
zattrs = {}
for k, v in dataset.attrs.items():
zattrs[k] = encode_zarr_attr_value(v)
# remove xpublish internal attribute
zattrs.pop(DATASET_ID_ATTR_KEY, None)
return zattrs
def _extract_dataarray_zattrs(da):
""" helper function to extract zattrs dictionary from DataArray """
zattrs = {}
for k, v in da.attrs.items():
zattrs[k] = encode_zarr_attr_value(v)
zattrs[DIMENSION_KEY] = list(da.dims)
# We don't want `_FillValue` in `.zattrs`
# It should go in `fill_value` section of `.zarray`
_ = zattrs.pop('_FillValue', None)
return zattrs
def _encode_zarr_attributes(attrs):
return {k: encode_zarr_attr_value(v) for k, v in attrs.items()}
def rechunk_dataset(
source: xarray.Dataset,
encoding: Mapping,
max_mem,
target_store,
temp_store=None,
executor: Union[str, Executor] = "dask",
):
def _encode_zarr_attributes(attrs):
return {k: encode_zarr_attr_value(v) for k, v in attrs.items()}
if isinstance(executor, str):
executor = _get_executor(executor)
if temp_store:
temp_group = zarr.group(temp_store)
else:
temp_group = zarr.group(
tempfile.mkdtemp(".zarr", "temp_store_")
) # pragma: no cover
target_group = zarr.group(target_store)
target_group.attrs.update(_encode_zarr_attributes(source.attrs))
copy_specs = []
for variable in source:
array = source[variable].copy()
# Update the array encoding with provided parameters and apply it
has_chunk_encoding = "chunks" in array.encoding
array.encoding.update(encoding.get(variable, {}))
array = encode_zarr_variable(array)
# Determine target chunking for array and remove it prior to
# validation/extraction ONLY if the array isn't also coming
# from a Zarr store (otherwise blocks need to be checked for overlap)
target_chunks = array.encoding.get("chunks")
if not has_chunk_encoding:
array.encoding.pop("chunks", None)
array_encoding = extract_zarr_variable_encoding(
array, raise_on_invalid=True, name=variable
)
# Default to chunking based on array shape if not explicitly provided
default_chunks = array_encoding.pop("chunks")
target_chunks = target_chunks or default_chunks
# Extract array attributes along with reserved property for
# xarray dimension names
array_attrs = _encode_zarr_attributes(array.attrs)
array_attrs[DIMENSION_KEY] = encode_zarr_attr_value(array.dims)
copy_spec = _setup_array_rechunk(
dask.array.asarray(array),
target_chunks,
max_mem,
target_group,
target_options=array_encoding,
temp_store_or_group=temp_group,
temp_options=array_encoding,
name=variable,
)
copy_spec.write.array.attrs.update(array_attrs) # type: ignore
copy_specs.append(copy_spec)
plan = executor.prepare_plan(copy_specs)
return Rechunked(executor, plan, source, temp_group, target_group)
def _setup_rechunk(
source,
target_chunks,
max_mem,
target_store,
target_options=None,
temp_store=None,
temp_options=None,
):
if temp_options is None:
temp_options = target_options
target_options = target_options or {}
temp_options = temp_options or {}
if isinstance(source, xarray.Dataset):
if not isinstance(target_chunks, dict):
raise ValueError(
"You must specify ``target-chunks`` as a dict when rechunking a dataset."
)
variables, attrs = encode_dataset_coordinates(source)
attrs = _encode_zarr_attributes(attrs)
if temp_store:
temp_group = zarr.group(temp_store)
else:
temp_group = None
target_group = zarr.group(target_store)
target_group.attrs.update(attrs)
copy_specs = []
for name, variable in variables.items():
# This isn't strictly necessary because a shallow copy
# also occurs in `encode_dataset_coordinates` but do it
# anyways in case the coord encoding function changes
variable = variable.copy()
# Update the array encoding with provided options and apply it;
# note that at this point the `options` may contain any valid property
# applicable for the `encoding` parameter in Dataset.to_zarr other than "chunks"
options = target_options.get(name, {})
if "chunks" in options:
raise ValueError(
f"Chunks must be provided in ``target_chunks`` rather than options (variable={name})"
)
variable.encoding.update(options)
variable = encode_zarr_variable(variable)
# Extract the array encoding to get a default chunking, a step
# which will also ensure that the target chunking is compatible
# with the current chunking (only necessary for on-disk arrays)
variable_encoding = extract_zarr_variable_encoding(
variable, raise_on_invalid=False, name=name)
variable_chunks = target_chunks.get(name,
variable_encoding["chunks"])
# Restrict options to only those that are specific to zarr and
# not managed internally
options = {k: v for k, v in options.items() if k in ZARR_OPTIONS}
_validate_options(options)
# Extract array attributes along with reserved property for
# xarray dimension names
variable_attrs = _encode_zarr_attributes(variable.attrs)
variable_attrs[DIMENSION_KEY] = encode_zarr_attr_value(
variable.dims)
copy_spec = _setup_array_rechunk(
dask.array.asarray(variable),
variable_chunks,
max_mem,
target_group,
target_options=options,
temp_store_or_group=temp_group,
temp_options=options,
name=name,
)
copy_spec.write.array.attrs.update(variable_attrs) # type: ignore
copy_specs.append(copy_spec)
return copy_specs, temp_group, target_group
elif isinstance(source, zarr.hierarchy.Group):
if not isinstance(target_chunks, dict):
raise ValueError(
"You must specify ``target-chunks`` as a dict when rechunking a group."
)
if temp_store:
temp_group = zarr.group(temp_store)
else:
temp_group = None
target_group = zarr.group(target_store)
target_group.attrs.update(source.attrs)
copy_specs = []
for array_name, array_target_chunks in target_chunks.items():
copy_spec = _setup_array_rechunk(
source[array_name],
array_target_chunks,
max_mem,
target_group,
target_options=target_options.get(array_name),
temp_store_or_group=temp_group,
temp_options=temp_options.get(array_name),
name=array_name,
)
copy_specs.append(copy_spec)
return copy_specs, temp_group, target_group
elif isinstance(source, (zarr.core.Array, dask.array.Array)):
copy_spec = _setup_array_rechunk(
source,
target_chunks,
max_mem,
target_store,
target_options=target_options,
temp_store_or_group=temp_store,
temp_options=temp_options,
)
intermediate = copy_spec.intermediate.array
target = copy_spec.write.array
return [copy_spec], intermediate, target
else:
raise ValueError(
f"Source must be a Zarr Array, Zarr Group, Dask Array or Xarray Dataset (not {type(source)})."
)
def _get_zattrs(self):
""" helper method to create zattrs dictionary """
zattrs = {}
for k, v in self._obj.attrs.items():
zattrs[k] = encode_zarr_attr_value(v)
return zattrs
def _extract_dataset_zattrs(dataset: xr.Dataset):
""" helper function to create zattrs dictionary from Dataset global attrs """
zattrs = {}
for k, v in dataset.attrs.items():
zattrs[k] = encode_zarr_attr_value(v)
return zattrs
