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from __future__ import annotations
import importlib.util
import os
from collections.abc import (
Callable,
Hashable,
Iterable,
Mapping,
MutableMapping,
Sequence,
)
from functools import partial
from io import IOBase
from itertools import starmap
from numbers import Number
from typing import (
TYPE_CHECKING,
Any,
Final,
Literal,
TypeVar,
Union,
cast,
overload,
)
import numpy as np
from xarray import backends, conventions
from xarray.backends import plugins
from xarray.backends.common import (
AbstractDataStore,
ArrayWriter,
BytesIOProxy,
T_PathFileOrDataStore,
_find_absolute_paths,
_normalize_path,
)
from xarray.backends.locks import _get_scheduler
from xarray.coders import CFDatetimeCoder, CFTimedeltaCoder
from xarray.core import dtypes, indexing
from xarray.core.coordinates import Coordinates
from xarray.core.dataarray import DataArray
from xarray.core.dataset import Dataset
from xarray.core.datatree import DataTree
from xarray.core.indexes import Index
from xarray.core.treenode import group_subtrees
from xarray.core.types import NetcdfWriteModes, ReadBuffer, ZarrWriteModes
from xarray.core.utils import emit_user_level_warning, is_remote_uri
from xarray.namedarray.daskmanager import DaskManager
from xarray.namedarray.parallelcompat import guess_chunkmanager
from xarray.structure.chunks import _get_chunk, _maybe_chunk
from xarray.structure.combine import (
_infer_concat_order_from_positions,
_nested_combine,
combine_by_coords,
)
from xarray.util.deprecation_helpers import (
_COMPAT_DEFAULT,
_COORDS_DEFAULT,
_DATA_VARS_DEFAULT,
_JOIN_DEFAULT,
CombineKwargDefault,
)
if TYPE_CHECKING:
try:
from dask.delayed import Delayed
except ImportError:
Delayed = None # type: ignore[assignment, misc]
from xarray.backends.common import BackendEntrypoint
from xarray.core.types import (
CombineAttrsOptions,
CompatOptions,
ErrorOptionsWithWarn,
JoinOptions,
NestedSequence,
ReadBuffer,
T_Chunks,
ZarrStoreLike,
)
T_NetcdfEngine = Literal["netcdf4", "scipy", "h5netcdf"]
T_Engine = Union[
T_NetcdfEngine,
Literal["pydap", "zarr"], # noqa: PYI051
type[BackendEntrypoint],
str, # no nice typing support for custom backends
None,
]
T_NetcdfTypes = Literal[
"NETCDF4", "NETCDF4_CLASSIC", "NETCDF3_64BIT", "NETCDF3_CLASSIC"
]
DATAARRAY_NAME = "__xarray_dataarray_name__"
DATAARRAY_VARIABLE = "__xarray_dataarray_variable__"
ENGINES = {
"netcdf4": backends.NetCDF4DataStore.open,
"scipy": backends.ScipyDataStore,
"pydap": backends.PydapDataStore.open,
"h5netcdf": backends.H5NetCDFStore.open,
"zarr": backends.ZarrStore.open_group,
}
def _get_default_engine_remote_uri() -> Literal["netcdf4", "pydap"]:
engine: Literal["netcdf4", "pydap"]
try:
import netCDF4 # noqa: F401
engine = "netcdf4"
except ImportError: # pragma: no cover
try:
import pydap # noqa: F401
engine = "pydap"
except ImportError as err:
raise ValueError(
"netCDF4 or pydap is required for accessing remote datasets via OPeNDAP"
) from err
return engine
def _get_default_engine_gz() -> Literal["scipy"]:
try:
import scipy # noqa: F401
engine: Final = "scipy"
except ImportError as err: # pragma: no cover
raise ValueError("scipy is required for accessing .gz files") from err
return engine
def _get_default_engine_netcdf() -> Literal["netcdf4", "h5netcdf", "scipy"]:
candidates: list[tuple[str, str]] = [
("netcdf4", "netCDF4"),
("h5netcdf", "h5netcdf"),
("scipy", "scipy.io.netcdf"),
]
for engine, module_name in candidates:
if importlib.util.find_spec(module_name) is not None:
return cast(Literal["netcdf4", "h5netcdf", "scipy"], engine)
raise ValueError(
"cannot read or write NetCDF files because none of "
"'netCDF4-python', 'h5netcdf', or 'scipy' are installed"
)
def _get_default_engine(path: str, allow_remote: bool = False) -> T_NetcdfEngine:
if allow_remote and is_remote_uri(path):
return _get_default_engine_remote_uri() # type: ignore[return-value]
elif path.endswith(".gz"):
return _get_default_engine_gz()
else:
return _get_default_engine_netcdf()
def _validate_dataset_names(dataset: Dataset) -> None:
"""DataArray.name and Dataset keys must be a string or None"""
def check_name(name: Hashable):
if isinstance(name, str):
if not name:
raise ValueError(
f"Invalid name {name!r} for DataArray or Dataset key: "
"string must be length 1 or greater for "
"serialization to netCDF or zarr files"
)
elif name is not None:
raise TypeError(
f"Invalid name {name!r} for DataArray or Dataset key: "
"must be either a string or None for serialization to netCDF "
"or zarr files"
)
for k in dataset.variables:
check_name(k)
def _validate_attrs(dataset, engine, invalid_netcdf=False):
"""`attrs` must have a string key and a value which is either: a number,
a string, an ndarray, a list/tuple of numbers/strings, or a numpy.bool_.
Notes
-----
A numpy.bool_ is only allowed when using the h5netcdf engine with
`invalid_netcdf=True`.
"""
valid_types = (str, Number, np.ndarray, np.number, list, tuple, bytes)
if invalid_netcdf and engine == "h5netcdf":
valid_types += (np.bool_,)
def check_attr(name, value, valid_types):
if isinstance(name, str):
if not name:
raise ValueError(
f"Invalid name for attr {name!r}: string must be "
"length 1 or greater for serialization to "
"netCDF files"
)
else:
raise TypeError(
f"Invalid name for attr: {name!r} must be a string for "
"serialization to netCDF files"
)
if not isinstance(value, valid_types):
raise TypeError(
f"Invalid value for attr {name!r}: {value!r}. For serialization to "
"netCDF files, its value must be of one of the following types: "
f"{', '.join([vtype.__name__ for vtype in valid_types])}"
)
if isinstance(value, bytes) and engine == "h5netcdf":
try:
value.decode("utf-8")
except UnicodeDecodeError as e:
raise ValueError(
f"Invalid value provided for attribute '{name!r}': {value!r}. "
"Only binary data derived from UTF-8 encoded strings is allowed "
f"for the '{engine}' engine. Consider using the 'netcdf4' engine."
) from e
if b"\x00" in value:
raise ValueError(
f"Invalid value provided for attribute '{name!r}': {value!r}. "
f"Null characters are not permitted for the '{engine}' engine. "
"Consider using the 'netcdf4' engine."
)
# Check attrs on the dataset itself
for k, v in dataset.attrs.items():
check_attr(k, v, valid_types)
# Check attrs on each variable within the dataset
for variable in dataset.variables.values():
for k, v in variable.attrs.items():
check_attr(k, v, valid_types)
def _sanitize_unlimited_dims(dataset, unlimited_dims):
msg_origin = "unlimited_dims-kwarg"
if unlimited_dims is None:
unlimited_dims = dataset.encoding.get("unlimited_dims", None)
msg_origin = "dataset.encoding"
if unlimited_dims is not None:
if isinstance(unlimited_dims, str) or not isinstance(unlimited_dims, Iterable):
unlimited_dims = [unlimited_dims]
else:
unlimited_dims = list(unlimited_dims)
dataset_dims = set(dataset.dims)
unlimited_dims = set(unlimited_dims)
if undeclared_dims := (unlimited_dims - dataset_dims):
msg = (
f"Unlimited dimension(s) {undeclared_dims!r} declared in {msg_origin!r}, "
f"but not part of current dataset dimensions. "
f"Consider removing {undeclared_dims!r} from {msg_origin!r}."
)
raise ValueError(msg)
return unlimited_dims
def _resolve_decoders_kwargs(decode_cf, open_backend_dataset_parameters, **decoders):
for d in list(decoders):
if decode_cf is False and d in open_backend_dataset_parameters:
decoders[d] = False
if decoders[d] is None:
decoders.pop(d)
return decoders
def _get_mtime(filename_or_obj):
# if passed an actual file path, augment the token with
# the file modification time
mtime = None
try:
path = os.fspath(filename_or_obj)
except TypeError:
path = None
if path and not is_remote_uri(path):
mtime = os.path.getmtime(os.path.expanduser(filename_or_obj))
return mtime
def _protect_dataset_variables_inplace(dataset: Dataset, cache: bool) -> None:
for name, variable in dataset.variables.items():
if name not in dataset._indexes:
# no need to protect IndexVariable objects
data: indexing.ExplicitlyIndexedNDArrayMixin
data = indexing.CopyOnWriteArray(variable._data)
if cache:
data = indexing.MemoryCachedArray(data)
variable.data = data
def _protect_datatree_variables_inplace(tree: DataTree, cache: bool) -> None:
for node in tree.subtree:
_protect_dataset_variables_inplace(node, cache)
def _finalize_store(write, store):
"""Finalize this store by explicitly syncing and closing"""
del write # ensure writing is done first
store.close()
def _multi_file_closer(closers):
for closer in closers:
closer()
def load_dataset(filename_or_obj, **kwargs) -> Dataset:
"""Open, load into memory, and close a Dataset from a file or file-like
object.
This is a thin wrapper around :py:meth:`~xarray.open_dataset`. It differs
from `open_dataset` in that it loads the Dataset into memory, closes the
file, and returns the Dataset. In contrast, `open_dataset` keeps the file
handle open and lazy loads its contents. All parameters are passed directly
to `open_dataset`. See that documentation for further details.
Returns
-------
dataset : Dataset
The newly created Dataset.
See Also
--------
open_dataset
"""
if "cache" in kwargs:
raise TypeError("cache has no effect in this context")
with open_dataset(filename_or_obj, **kwargs) as ds:
return ds.load()
def load_dataarray(filename_or_obj, **kwargs):
"""Open, load into memory, and close a DataArray from a file or file-like
object containing a single data variable.
This is a thin wrapper around :py:meth:`~xarray.open_dataarray`. It differs
from `open_dataarray` in that it loads the Dataset into memory, closes the
file, and returns the Dataset. In contrast, `open_dataarray` keeps the file
handle open and lazy loads its contents. All parameters are passed directly
to `open_dataarray`. See that documentation for further details.
Returns
-------
datarray : DataArray
The newly created DataArray.
See Also
--------
open_dataarray
"""
if "cache" in kwargs:
raise TypeError("cache has no effect in this context")
with open_dataarray(filename_or_obj, **kwargs) as da:
return da.load()
def _chunk_ds(
backend_ds,
filename_or_obj,
engine,
chunks,
overwrite_encoded_chunks,
inline_array,
chunked_array_type,
from_array_kwargs,
**extra_tokens,
):
chunkmanager = guess_chunkmanager(chunked_array_type)
# TODO refactor to move this dask-specific logic inside the DaskManager class
if isinstance(chunkmanager, DaskManager):
from dask.base import tokenize
mtime = _get_mtime(filename_or_obj)
token = tokenize(filename_or_obj, mtime, engine, chunks, **extra_tokens)
name_prefix = "open_dataset-"
else:
# not used
token = (None,)
name_prefix = None
variables = {}
for name, var in backend_ds.variables.items():
var_chunks = _get_chunk(var, chunks, chunkmanager)
variables[name] = _maybe_chunk(
name,
var,
var_chunks,
overwrite_encoded_chunks=overwrite_encoded_chunks,
name_prefix=name_prefix,
token=token,
inline_array=inline_array,
chunked_array_type=chunkmanager,
from_array_kwargs=from_array_kwargs.copy(),
)
return backend_ds._replace(variables)
def _maybe_create_default_indexes(ds):
to_index = {
name: coord.variable
for name, coord in ds.coords.items()
if coord.dims == (name,) and name not in ds.xindexes
}
return ds.assign_coords(Coordinates(to_index))
def _dataset_from_backend_dataset(
backend_ds,
filename_or_obj,
engine,
chunks,
cache,
overwrite_encoded_chunks,
inline_array,
chunked_array_type,
from_array_kwargs,
create_default_indexes,
**extra_tokens,
):
if not isinstance(chunks, int | dict) and chunks not in {None, "auto"}:
raise ValueError(
f"chunks must be an int, dict, 'auto', or None. Instead found {chunks}."
)
_protect_dataset_variables_inplace(backend_ds, cache)
if create_default_indexes:
ds = _maybe_create_default_indexes(backend_ds)
else:
ds = backend_ds
if chunks is not None:
ds = _chunk_ds(
ds,
filename_or_obj,
engine,
chunks,
overwrite_encoded_chunks,
inline_array,
chunked_array_type,
from_array_kwargs,
**extra_tokens,
)
ds.set_close(backend_ds._close)
# Ensure source filename always stored in dataset object
if "source" not in ds.encoding:
path = getattr(filename_or_obj, "path", filename_or_obj)
if isinstance(path, str | os.PathLike):
ds.encoding["source"] = _normalize_path(path)
return ds
def _datatree_from_backend_datatree(
backend_tree,
filename_or_obj,
engine,
chunks,
cache,
overwrite_encoded_chunks,
inline_array,
chunked_array_type,
from_array_kwargs,
create_default_indexes,
**extra_tokens,
):
if not isinstance(chunks, int | dict) and chunks not in {None, "auto"}:
raise ValueError(
f"chunks must be an int, dict, 'auto', or None. Instead found {chunks}."
)
_protect_datatree_variables_inplace(backend_tree, cache)
if create_default_indexes:
tree = backend_tree.map_over_datasets(_maybe_create_default_indexes)
else:
tree = backend_tree
if chunks is not None:
tree = DataTree.from_dict(
{
path: _chunk_ds(
node.dataset,
filename_or_obj,
engine,
chunks,
overwrite_encoded_chunks,
inline_array,
chunked_array_type,
from_array_kwargs,
node=path,
**extra_tokens,
)
for path, [node] in group_subtrees(tree)
},
name=tree.name,
)
if create_default_indexes or chunks is not None:
for path, [node] in group_subtrees(backend_tree):
tree[path].set_close(node._close)
# Ensure source filename always stored in dataset object
if "source" not in tree.encoding:
path = getattr(filename_or_obj, "path", filename_or_obj)
if isinstance(path, str | os.PathLike):
tree.encoding["source"] = _normalize_path(path)
return tree
def open_dataset(
filename_or_obj: T_PathFileOrDataStore,
*,
engine: T_Engine = None,
chunks: T_Chunks = None,
cache: bool | None = None,
decode_cf: bool | None = None,
mask_and_scale: bool | Mapping[str, bool] | None = None,
decode_times: bool
| CFDatetimeCoder
| Mapping[str, bool | CFDatetimeCoder]
| None = None,
decode_timedelta: bool
| CFTimedeltaCoder
| Mapping[str, bool | CFTimedeltaCoder]
| None = None,
use_cftime: bool | Mapping[str, bool] | None = None,
concat_characters: bool | Mapping[str, bool] | None = None,
decode_coords: Literal["coordinates", "all"] | bool | None = None,
drop_variables: str | Iterable[str] | None = None,
create_default_indexes: bool = True,
inline_array: bool = False,
chunked_array_type: str | None = None,
from_array_kwargs: dict[str, Any] | None = None,
backend_kwargs: dict[str, Any] | None = None,
**kwargs,
) -> Dataset:
"""Open and decode a dataset from a file or file-like object.
Parameters
----------
filename_or_obj : str, Path, file-like, bytes, memoryview or DataStore
Strings and Path objects are interpreted as a path to a netCDF file
or an OpenDAP URL and opened with python-netCDF4, unless the filename
ends with .gz, in which case the file is gunzipped and opened with
scipy.io.netcdf (only netCDF3 supported). Bytes, memoryview and
file-like objects are opened by scipy.io.netcdf (netCDF3) or h5netcdf
(netCDF4).
engine : {"netcdf4", "scipy", "pydap", "h5netcdf", "zarr", None}\
, installed backend \
or subclass of xarray.backends.BackendEntrypoint, optional
Engine to use when reading files. If not provided, the default engine
is chosen based on available dependencies, with a preference for
"netcdf4". A custom backend class (a subclass of ``BackendEntrypoint``)
can also be used.
chunks : int, dict, 'auto' or None, default: None
If provided, used to load the data into dask arrays.
- ``chunks="auto"`` will use dask ``auto`` chunking taking into account the
engine preferred chunks.
- ``chunks=None`` skips using dask. This uses xarray's internally private
:ref:`lazy indexing classes <internal design.lazy indexing>`,
but data is eagerly loaded into memory as numpy arrays when accessed.
This can be more efficient for smaller arrays or when large arrays are sliced before computation.
- ``chunks=-1`` loads the data with dask using a single chunk for all arrays.
- ``chunks={}`` loads the data with dask using the engine's preferred chunk
size, generally identical to the format's chunk size. If not available, a
single chunk for all arrays.
See dask chunking for more details.
cache : bool, optional
If True, cache data loaded from the underlying datastore in memory as
NumPy arrays when accessed to avoid reading from the underlying data-
store multiple times. Defaults to True unless you specify the `chunks`
argument to use dask, in which case it defaults to False. Does not
change the behavior of coordinates corresponding to dimensions, which
always load their data from disk into a ``pandas.Index``.
decode_cf : bool, optional
Whether to decode these variables, assuming they were saved according
to CF conventions.
mask_and_scale : bool or dict-like, optional
If True, replace array values equal to `_FillValue` with NA and scale
values according to the formula `original_values * scale_factor +
add_offset`, where `_FillValue`, `scale_factor` and `add_offset` are
taken from variable attributes (if they exist). If the `_FillValue` or
`missing_value` attribute contains multiple values a warning will be
issued and all array values matching one of the multiple values will
be replaced by NA. Pass a mapping, e.g. ``{"my_variable": False}``,
to toggle this feature per-variable individually.
This keyword may not be supported by all the backends.
decode_times : bool, CFDatetimeCoder or dict-like, optional
If True, decode times encoded in the standard NetCDF datetime format
into datetime objects. Otherwise, use :py:class:`coders.CFDatetimeCoder` or leave them
encoded as numbers.
Pass a mapping, e.g. ``{"my_variable": False}``,
to toggle this feature per-variable individually.
This keyword may not be supported by all the backends.
decode_timedelta : bool, CFTimedeltaCoder, or dict-like, optional
If True, decode variables and coordinates with time units in
{"days", "hours", "minutes", "seconds", "milliseconds", "microseconds"}
into timedelta objects. If False, leave them encoded as numbers.
If None (default), assume the same value of ``decode_times``; if
``decode_times`` is a :py:class:`coders.CFDatetimeCoder` instance, this
takes the form of a :py:class:`coders.CFTimedeltaCoder` instance with a
matching ``time_unit``.
Pass a mapping, e.g. ``{"my_variable": False}``,
to toggle this feature per-variable individually.
This keyword may not be supported by all the backends.
use_cftime: bool or dict-like, optional
Only relevant if encoded dates come from a standard calendar
(e.g. "gregorian", "proleptic_gregorian", "standard", or not
specified). If None (default), attempt to decode times to
``np.datetime64[ns]`` objects; if this is not possible, decode times to
``cftime.datetime`` objects. If True, always decode times to
``cftime.datetime`` objects, regardless of whether or not they can be
represented using ``np.datetime64[ns]`` objects. If False, always
decode times to ``np.datetime64[ns]`` objects; if this is not possible
raise an error. Pass a mapping, e.g. ``{"my_variable": False}``,
to toggle this feature per-variable individually.
This keyword may not be supported by all the backends.
.. deprecated:: 2025.01.1
Please pass a :py:class:`coders.CFDatetimeCoder` instance initialized with ``use_cftime`` to the ``decode_times`` kwarg instead.
concat_characters : bool or dict-like, optional
If True, concatenate along the last dimension of character arrays to
form string arrays. Dimensions will only be concatenated over (and
removed) if they have no corresponding variable and if they are only
used as the last dimension of character arrays.
Pass a mapping, e.g. ``{"my_variable": False}``,
to toggle this feature per-variable individually.
This keyword may not be supported by all the backends.
decode_coords : bool or {"coordinates", "all"}, optional
Controls which variables are set as coordinate variables:
- "coordinates" or True: Set variables referred to in the
``'coordinates'`` attribute of the datasets or individual variables
as coordinate variables.
- "all": Set variables referred to in ``'grid_mapping'``, ``'bounds'`` and
other attributes as coordinate variables.
Only existing variables can be set as coordinates. Missing variables
will be silently ignored.
drop_variables: str or iterable of str, optional
A variable or list of variables to exclude from being parsed from the
dataset. This may be useful to drop variables with problems or
inconsistent values.
create_default_indexes : bool, default: True
If True, create pandas indexes for :term:`dimension coordinates <dimension coordinate>`,
which loads the coordinate data into memory. Set it to False if you want to avoid loading
data into memory.
Note that backends can still choose to create other indexes. If you want to control that,
please refer to the backend's documentation.
inline_array: bool, default: False
How to include the array in the dask task graph.
By default(``inline_array=False``) the array is included in a task by
itself, and each chunk refers to that task by its key. With
``inline_array=True``, Dask will instead inline the array directly
in the values of the task graph. See :py:func:`dask.array.from_array`.
chunked_array_type: str, optional
Which chunked array type to coerce this datasets' arrays to.
Defaults to 'dask' if installed, else whatever is registered via the `ChunkManagerEnetryPoint` system.
Experimental API that should not be relied upon.
from_array_kwargs: dict
Additional keyword arguments passed on to the `ChunkManagerEntrypoint.from_array` method used to create
chunked arrays, via whichever chunk manager is specified through the `chunked_array_type` kwarg.
For example if :py:func:`dask.array.Array` objects are used for chunking, additional kwargs will be passed
to :py:func:`dask.array.from_array`. Experimental API that should not be relied upon.
backend_kwargs: dict
Additional keyword arguments passed on to the engine open function,
equivalent to `**kwargs`.
**kwargs: dict
Additional keyword arguments passed on to the engine open function.
For example:
- 'group': path to the netCDF4 group in the given file to open given as
a str,supported by "netcdf4", "h5netcdf", "zarr".
- 'lock': resource lock to use when reading data from disk. Only
relevant when using dask or another form of parallelism. By default,
appropriate locks are chosen to safely read and write files with the
currently active dask scheduler. Supported by "netcdf4", "h5netcdf",
"scipy".
See engine open function for kwargs accepted by each specific engine.
Returns
-------
dataset : Dataset
The newly created dataset.
Notes
-----
``open_dataset`` opens the file with read-only access. When you modify
values of a Dataset, even one linked to files on disk, only the in-memory
copy you are manipulating in xarray is modified: the original file on disk
is never touched.
See Also
--------
open_mfdataset
"""
if cache is None:
cache = chunks is None
if backend_kwargs is not None:
kwargs.update(backend_kwargs)
if engine is None:
engine = plugins.guess_engine(filename_or_obj)
if from_array_kwargs is None:
from_array_kwargs = {}
backend = plugins.get_backend(engine)
decoders = _resolve_decoders_kwargs(
decode_cf,
open_backend_dataset_parameters=backend.open_dataset_parameters,
mask_and_scale=mask_and_scale,
decode_times=decode_times,
decode_timedelta=decode_timedelta,
concat_characters=concat_characters,
use_cftime=use_cftime,
decode_coords=decode_coords,
)
overwrite_encoded_chunks = kwargs.pop("overwrite_encoded_chunks", None)
backend_ds = backend.open_dataset(
filename_or_obj,
drop_variables=drop_variables,
**decoders,
**kwargs,
)
ds = _dataset_from_backend_dataset(
backend_ds,
filename_or_obj,
engine,
chunks,
cache,
overwrite_encoded_chunks,
inline_array,
chunked_array_type,
from_array_kwargs,
drop_variables=drop_variables,
create_default_indexes=create_default_indexes,
**decoders,
**kwargs,
)
return ds
def open_dataarray(
filename_or_obj: T_PathFileOrDataStore,
*,
engine: T_Engine = None,
chunks: T_Chunks = None,
cache: bool | None = None,
decode_cf: bool | None = None,
mask_and_scale: bool | None = None,
decode_times: bool
| CFDatetimeCoder
| Mapping[str, bool | CFDatetimeCoder]
| None = None,
decode_timedelta: bool | CFTimedeltaCoder | None = None,
use_cftime: bool | None = None,
concat_characters: bool | None = None,
decode_coords: Literal["coordinates", "all"] | bool | None = None,
drop_variables: str | Iterable[str] | None = None,
create_default_indexes: bool = True,
inline_array: bool = False,
chunked_array_type: str | None = None,
from_array_kwargs: dict[str, Any] | None = None,
backend_kwargs: dict[str, Any] | None = None,
**kwargs,
) -> DataArray:
"""Open an DataArray from a file or file-like object containing a single
data variable.
This is designed to read netCDF files with only one data variable. If
multiple variables are present then a ValueError is raised.
Parameters
----------
filename_or_obj : str, Path, file-like, bytes, memoryview or DataStore
Strings and Path objects are interpreted as a path to a netCDF file
or an OpenDAP URL and opened with python-netCDF4, unless the filename
ends with .gz, in which case the file is gunzipped and opened with
scipy.io.netcdf (only netCDF3 supported). Bytes, memoryview and
file-like objects are opened by scipy.io.netcdf (netCDF3) or h5netcdf
(netCDF4).
engine : {"netcdf4", "scipy", "pydap", "h5netcdf", "zarr", None}\
, installed backend \
or subclass of xarray.backends.BackendEntrypoint, optional
Engine to use when reading files. If not provided, the default engine
is chosen based on available dependencies, with a preference for
"netcdf4".
chunks : int, dict, 'auto' or None, default: None
If provided, used to load the data into dask arrays.
- ``chunks='auto'`` will use dask ``auto`` chunking taking into account the
engine preferred chunks.
- ``chunks=None`` skips using dask. This uses xarray's internally private
:ref:`lazy indexing classes <internal design.lazy indexing>`,
but data is eagerly loaded into memory as numpy arrays when accessed.
This can be more efficient for smaller arrays, though results may vary.
- ``chunks=-1`` loads the data with dask using a single chunk for all arrays.
- ``chunks={}`` loads the data with dask using engine preferred chunks if
exposed by the backend, otherwise with a single chunk for all arrays.
See dask chunking for more details.
cache : bool, optional
If True, cache data loaded from the underlying datastore in memory as
NumPy arrays when accessed to avoid reading from the underlying data-
store multiple times. Defaults to True unless you specify the `chunks`
argument to use dask, in which case it defaults to False. Does not
change the behavior of coordinates corresponding to dimensions, which
always load their data from disk into a ``pandas.Index``.
decode_cf : bool, optional
Whether to decode these variables, assuming they were saved according
to CF conventions.
mask_and_scale : bool, optional
If True, replace array values equal to `_FillValue` with NA and scale
values according to the formula `original_values * scale_factor +
add_offset`, where `_FillValue`, `scale_factor` and `add_offset` are
taken from variable attributes (if they exist). If the `_FillValue` or
`missing_value` attribute contains multiple values a warning will be
issued and all array values matching one of the multiple values will
be replaced by NA. This keyword may not be supported by all the backends.
decode_times : bool, CFDatetimeCoder or dict-like, optional
If True, decode times encoded in the standard NetCDF datetime format
into datetime objects. Otherwise, use :py:class:`coders.CFDatetimeCoder` or
leave them encoded as numbers.
Pass a mapping, e.g. ``{"my_variable": False}``,
to toggle this feature per-variable individually.
This keyword may not be supported by all the backends.
decode_timedelta : bool, optional
If True, decode variables and coordinates with time units in
{"days", "hours", "minutes", "seconds", "milliseconds", "microseconds"}
into timedelta objects. If False, leave them encoded as numbers.
If None (default), assume the same value of ``decode_times``; if
``decode_times`` is a :py:class:`coders.CFDatetimeCoder` instance, this
takes the form of a :py:class:`coders.CFTimedeltaCoder` instance with a
matching ``time_unit``.
This keyword may not be supported by all the backends.
use_cftime: bool, optional
Only relevant if encoded dates come from a standard calendar
(e.g. "gregorian", "proleptic_gregorian", "standard", or not
specified). If None (default), attempt to decode times to
``np.datetime64[ns]`` objects; if this is not possible, decode times to
``cftime.datetime`` objects. If True, always decode times to
``cftime.datetime`` objects, regardless of whether or not they can be
represented using ``np.datetime64[ns]`` objects. If False, always
decode times to ``np.datetime64[ns]`` objects; if this is not possible
raise an error. This keyword may not be supported by all the backends.
.. deprecated:: 2025.01.1
Please pass a :py:class:`coders.CFDatetimeCoder` instance initialized with ``use_cftime`` to the ``decode_times`` kwarg instead.
concat_characters : bool, optional
If True, concatenate along the last dimension of character arrays to
form string arrays. Dimensions will only be concatenated over (and
removed) if they have no corresponding variable and if they are only
used as the last dimension of character arrays.
This keyword may not be supported by all the backends.
decode_coords : bool or {"coordinates", "all"}, optional
Controls which variables are set as coordinate variables:
- "coordinates" or True: Set variables referred to in the
``'coordinates'`` attribute of the datasets or individual variables
as coordinate variables.
- "all": Set variables referred to in ``'grid_mapping'``, ``'bounds'`` and
other attributes as coordinate variables.
Only existing variables can be set as coordinates. Missing variables
will be silently ignored.
drop_variables: str or iterable of str, optional
A variable or list of variables to exclude from being parsed from the
dataset. This may be useful to drop variables with problems or
inconsistent values.
create_default_indexes : bool, default: True
If True, create pandas indexes for :term:`dimension coordinates <dimension coordinate>`,
which loads the coordinate data into memory. Set it to False if you want to avoid loading
data into memory.
Note that backends can still choose to create other indexes. If you want to control that,
please refer to the backend's documentation.
inline_array: bool, default: False
How to include the array in the dask task graph.
By default(``inline_array=False``) the array is included in a task by
itself, and each chunk refers to that task by its key. With
``inline_array=True``, Dask will instead inline the array directly
in the values of the task graph. See :py:func:`dask.array.from_array`.
chunked_array_type: str, optional
Which chunked array type to coerce the underlying data array to.
Defaults to 'dask' if installed, else whatever is registered via the `ChunkManagerEnetryPoint` system.
Experimental API that should not be relied upon.
from_array_kwargs: dict
Additional keyword arguments passed on to the `ChunkManagerEntrypoint.from_array` method used to create
chunked arrays, via whichever chunk manager is specified through the `chunked_array_type` kwarg.
For example if :py:func:`dask.array.Array` objects are used for chunking, additional kwargs will be passed
to :py:func:`dask.array.from_array`. Experimental API that should not be relied upon.
backend_kwargs: dict
Additional keyword arguments passed on to the engine open function,
equivalent to `**kwargs`.
**kwargs: dict
Additional keyword arguments passed on to the engine open function.
For example:
- 'group': path to the netCDF4 group in the given file to open given as
a str,supported by "netcdf4", "h5netcdf", "zarr".
- 'lock': resource lock to use when reading data from disk. Only
relevant when using dask or another form of parallelism. By default,
appropriate locks are chosen to safely read and write files with the
currently active dask scheduler. Supported by "netcdf4", "h5netcdf",
"scipy".
See engine open function for kwargs accepted by each specific engine.
Notes
-----
This is designed to be fully compatible with `DataArray.to_netcdf`. Saving
using `DataArray.to_netcdf` and then loading with this function will
produce an identical result.
All parameters are passed directly to `xarray.open_dataset`. See that
documentation for further details.
See also
--------
open_dataset
"""
dataset = open_dataset(
filename_or_obj,
decode_cf=decode_cf,
mask_and_scale=mask_and_scale,
decode_times=decode_times,
concat_characters=concat_characters,
decode_coords=decode_coords,
engine=engine,
chunks=chunks,
cache=cache,
drop_variables=drop_variables,
create_default_indexes=create_default_indexes,
inline_array=inline_array,
chunked_array_type=chunked_array_type,
from_array_kwargs=from_array_kwargs,
backend_kwargs=backend_kwargs,
use_cftime=use_cftime,
decode_timedelta=decode_timedelta,
**kwargs,
)
if len(dataset.data_vars) != 1:
if len(dataset.data_vars) == 0:
msg = "Given file dataset contains no data variables."
else:
msg = (
"Given file dataset contains more than one data "
"variable. Please read with xarray.open_dataset and "
"then select the variable you want."
)
raise ValueError(msg)
else:
(data_array,) = dataset.data_vars.values()
data_array.set_close(dataset._close)
# Reset names if they were changed during saving
# to ensure that we can 'roundtrip' perfectly
if DATAARRAY_NAME in dataset.attrs:
data_array.name = dataset.attrs[DATAARRAY_NAME]
del dataset.attrs[DATAARRAY_NAME]
if data_array.name == DATAARRAY_VARIABLE:
data_array.name = None
return data_array
def open_datatree(
filename_or_obj: T_PathFileOrDataStore,
*,
engine: T_Engine = None,
chunks: T_Chunks = None,
cache: bool | None = None,
decode_cf: bool | None = None,
mask_and_scale: bool | Mapping[str, bool] | None = None,
decode_times: bool
| CFDatetimeCoder
| Mapping[str, bool | CFDatetimeCoder]
| None = None,
decode_timedelta: bool
| CFTimedeltaCoder
| Mapping[str, bool | CFTimedeltaCoder]
| None = None,
use_cftime: bool | Mapping[str, bool] | None = None,
concat_characters: bool | Mapping[str, bool] | None = None,
decode_coords: Literal["coordinates", "all"] | bool | None = None,
drop_variables: str | Iterable[str] | None = None,
create_default_indexes: bool = True,
inline_array: bool = False,
chunked_array_type: str | None = None,
from_array_kwargs: dict[str, Any] | None = None,
backend_kwargs: dict[str, Any] | None = None,
**kwargs,
) -> DataTree:
"""
Open and decode a DataTree from a file or file-like object, creating one tree node for each group in the file.
Parameters
----------
filename_or_obj : str, Path, file-like, bytes or DataStore
Strings and Path objects are interpreted as a path to a netCDF file or
Zarr store. Bytes and memoryview objects are interpreted as file
contents.
engine : {"netcdf4", "h5netcdf", "zarr", None}, \
installed backend or xarray.backends.BackendEntrypoint, optional
Engine to use when reading files. If not provided, the default engine
is chosen based on available dependencies, with a preference for
"netcdf4". A custom backend class (a subclass of ``BackendEntrypoint``)
can also be used.
chunks : int, dict, 'auto' or None, default: None
If provided, used to load the data into dask arrays.
- ``chunks="auto"`` will use dask ``auto`` chunking taking into account the
engine preferred chunks.
- ``chunks=None`` skips using dask. This uses xarray's internally private
:ref:`lazy indexing classes <internal design.lazy indexing>`,
but data is eagerly loaded into memory as numpy arrays when accessed.
This can be more efficient for smaller arrays, though results may vary.
- ``chunks=-1`` loads the data with dask using a single chunk for all arrays.
- ``chunks={}`` loads the data with dask using the engine's preferred chunk
size, generally identical to the format's chunk size. If not available, a
single chunk for all arrays.
See dask chunking for more details.
cache : bool, optional
If True, cache data loaded from the underlying datastore in memory as
NumPy arrays when accessed to avoid reading from the underlying data-
store multiple times. Defaults to True unless you specify the `chunks`
argument to use dask, in which case it defaults to False. Does not
change the behavior of coordinates corresponding to dimensions, which
always load their data from disk into a ``pandas.Index``.
decode_cf : bool, optional
Whether to decode these variables, assuming they were saved according
to CF conventions.
mask_and_scale : bool or dict-like, optional
If True, replace array values equal to `_FillValue` with NA and scale
values according to the formula `original_values * scale_factor +
add_offset`, where `_FillValue`, `scale_factor` and `add_offset` are
taken from variable attributes (if they exist). If the `_FillValue` or
`missing_value` attribute contains multiple values a warning will be
issued and all array values matching one of the multiple values will
be replaced by NA. Pass a mapping, e.g. ``{"my_variable": False}``,
to toggle this feature per-variable individually.
This keyword may not be supported by all the backends.
decode_times : bool, CFDatetimeCoder or dict-like, optional
If True, decode times encoded in the standard NetCDF datetime format
into datetime objects. Otherwise, use :py:class:`coders.CFDatetimeCoder` or
leave them encoded as numbers.
Pass a mapping, e.g. ``{"my_variable": False}``,
to toggle this feature per-variable individually.
This keyword may not be supported by all the backends.
decode_timedelta : bool or dict-like, optional
If True, decode variables and coordinates with time units in
{"days", "hours", "minutes", "seconds", "milliseconds", "microseconds"}
into timedelta objects. If False, leave them encoded as numbers.
If None (default), assume the same value of ``decode_times``; if
``decode_times`` is a :py:class:`coders.CFDatetimeCoder` instance, this
takes the form of a :py:class:`coders.CFTimedeltaCoder` instance with a
matching ``time_unit``.
Pass a mapping, e.g. ``{"my_variable": False}``,
to toggle this feature per-variable individually.
This keyword may not be supported by all the backends.
use_cftime: bool or dict-like, optional
Only relevant if encoded dates come from a standard calendar
(e.g. "gregorian", "proleptic_gregorian", "standard", or not
specified). If None (default), attempt to decode times to
``np.datetime64[ns]`` objects; if this is not possible, decode times to
``cftime.datetime`` objects. If True, always decode times to
``cftime.datetime`` objects, regardless of whether or not they can be
represented using ``np.datetime64[ns]`` objects. If False, always
decode times to ``np.datetime64[ns]`` objects; if this is not possible
raise an error. Pass a mapping, e.g. ``{"my_variable": False}``,
to toggle this feature per-variable individually.
This keyword may not be supported by all the backends.
.. deprecated:: 2025.01.1
Please pass a :py:class:`coders.CFDatetimeCoder` instance initialized with ``use_cftime`` to the ``decode_times`` kwarg instead.
concat_characters : bool or dict-like, optional
If True, concatenate along the last dimension of character arrays to
form string arrays. Dimensions will only be concatenated over (and
removed) if they have no corresponding variable and if they are only
used as the last dimension of character arrays.
Pass a mapping, e.g. ``{"my_variable": False}``,
to toggle this feature per-variable individually.
This keyword may not be supported by all the backends.
decode_coords : bool or {"coordinates", "all"}, optional
Controls which variables are set as coordinate variables:
- "coordinates" or True: Set variables referred to in the
``'coordinates'`` attribute of the datasets or individual variables
as coordinate variables.
- "all": Set variables referred to in ``'grid_mapping'``, ``'bounds'`` and
other attributes as coordinate variables.
Only existing variables can be set as coordinates. Missing variables
will be silently ignored.
drop_variables: str or iterable of str, optional
A variable or list of variables to exclude from being parsed from the
dataset. This may be useful to drop variables with problems or
inconsistent values.
create_default_indexes : bool, default: True
If True, create pandas indexes for :term:`dimension coordinates <dimension coordinate>`,
which loads the coordinate data into memory. Set it to False if you want to avoid loading
data into memory.
Note that backends can still choose to create other indexes. If you want to control that,
please refer to the backend's documentation.
inline_array: bool, default: False
How to include the array in the dask task graph.
By default(``inline_array=False``) the array is included in a task by
itself, and each chunk refers to that task by its key. With
``inline_array=True``, Dask will instead inline the array directly
in the values of the task graph. See :py:func:`dask.array.from_array`.
chunked_array_type: str, optional
Which chunked array type to coerce this datasets' arrays to.
Defaults to 'dask' if installed, else whatever is registered via the `ChunkManagerEnetryPoint` system.
Experimental API that should not be relied upon.
from_array_kwargs: dict
Additional keyword arguments passed on to the `ChunkManagerEntrypoint.from_array` method used to create
chunked arrays, via whichever chunk manager is specified through the `chunked_array_type` kwarg.
For example if :py:func:`dask.array.Array` objects are used for chunking, additional kwargs will be passed
to :py:func:`dask.array.from_array`. Experimental API that should not be relied upon.
backend_kwargs: dict
Additional keyword arguments passed on to the engine open function,
equivalent to `**kwargs`.
**kwargs: dict
Additional keyword arguments passed on to the engine open function.
For example:
- 'group': path to the group in the given file to open as the root group as
a str.
- 'lock': resource lock to use when reading data from disk. Only
relevant when using dask or another form of parallelism. By default,
appropriate locks are chosen to safely read and write files with the
currently active dask scheduler. Supported by "netcdf4", "h5netcdf",
"scipy".
See engine open function for kwargs accepted by each specific engine.
Returns
-------
tree : DataTree
The newly created datatree.
Notes
-----
``open_datatree`` opens the file with read-only access. When you modify
values of a DataTree, even one linked to files on disk, only the in-memory
copy you are manipulating in xarray is modified: the original file on disk
is never touched.
See Also
--------
xarray.open_groups
xarray.open_dataset
"""
if cache is None:
cache = chunks is None
if backend_kwargs is not None:
kwargs.update(backend_kwargs)
if engine is None:
engine = plugins.guess_engine(filename_or_obj)
if from_array_kwargs is None:
from_array_kwargs = {}
backend = plugins.get_backend(engine)
decoders = _resolve_decoders_kwargs(
decode_cf,
open_backend_dataset_parameters=backend.open_dataset_parameters,
mask_and_scale=mask_and_scale,
decode_times=decode_times,
decode_timedelta=decode_timedelta,
concat_characters=concat_characters,
use_cftime=use_cftime,
decode_coords=decode_coords,
)
overwrite_encoded_chunks = kwargs.pop("overwrite_encoded_chunks", None)
backend_tree = backend.open_datatree(
filename_or_obj,
drop_variables=drop_variables,
**decoders,
**kwargs,
)
tree = _datatree_from_backend_datatree(
backend_tree,
filename_or_obj,
engine,
chunks,
cache,
overwrite_encoded_chunks,
inline_array,
chunked_array_type,
from_array_kwargs,
drop_variables=drop_variables,
create_default_indexes=create_default_indexes,
**decoders,
**kwargs,
)
return tree
def open_groups(
filename_or_obj: T_PathFileOrDataStore,
*,
engine: T_Engine = None,
chunks: T_Chunks = None,
cache: bool | None = None,
decode_cf: bool | None = None,
mask_and_scale: bool | Mapping[str, bool] | None = None,
decode_times: bool
| CFDatetimeCoder
| Mapping[str, bool | CFDatetimeCoder]
| None = None,
decode_timedelta: bool
| CFTimedeltaCoder
| Mapping[str, bool | CFTimedeltaCoder]
| None = None,
use_cftime: bool | Mapping[str, bool] | None = None,
concat_characters: bool | Mapping[str, bool] | None = None,
decode_coords: Literal["coordinates", "all"] | bool | None = None,
drop_variables: str | Iterable[str] | None = None,
create_default_indexes: bool = True,
inline_array: bool = False,
chunked_array_type: str | None = None,
from_array_kwargs: dict[str, Any] | None = None,
backend_kwargs: dict[str, Any] | None = None,
**kwargs,
) -> dict[str, Dataset]:
"""
Open and decode a file or file-like object, creating a dictionary containing one xarray Dataset for each group in the file.
Useful for an HDF file ("netcdf4" or "h5netcdf") containing many groups that are not alignable with their parents
and cannot be opened directly with ``open_datatree``. It is encouraged to use this function to inspect your data,
then make the necessary changes to make the structure coercible to a `DataTree` object before calling `DataTree.from_dict()` and proceeding with your analysis.
Parameters
----------
filename_or_obj : str, Path, file-like, bytes, memoryview or DataStore
Strings and Path objects are interpreted as a path to a netCDF file or
Zarr store. Bytes and memoryview objects are interpreted as file
contents.
engine : {"netcdf4", "h5netcdf", "zarr", None}, \
installed backend or xarray.backends.BackendEntrypoint, optional
Engine to use when reading files. If not provided, the default engine
is chosen based on available dependencies, with a preference for
"netcdf4". A custom backend class (a subclass of ``BackendEntrypoint``)
can also be used.
chunks : int, dict, 'auto' or None, default: None
If provided, used to load the data into dask arrays.
- ``chunks="auto"`` will use dask ``auto`` chunking taking into account the
engine preferred chunks.
- ``chunks=None`` skips using dask. This uses xarray's internally private
:ref:`lazy indexing classes <internal design.lazy indexing>`,
but data is eagerly loaded into memory as numpy arrays when accessed.
This can be more efficient for smaller arrays, though results may vary.
- ``chunks=-1`` loads the data with dask using a single chunk for all arrays.
- ``chunks={}`` loads the data with dask using the engine's preferred chunk
size, generally identical to the format's chunk size. If not available, a
single chunk for all arrays.
See dask chunking for more details.
cache : bool, optional
If True, cache data loaded from the underlying datastore in memory as
NumPy arrays when accessed to avoid reading from the underlying data-
store multiple times. Defaults to True unless you specify the `chunks`
argument to use dask, in which case it defaults to False. Does not
change the behavior of coordinates corresponding to dimensions, which
always load their data from disk into a ``pandas.Index``.
decode_cf : bool, optional
Whether to decode these variables, assuming they were saved according
to CF conventions.
mask_and_scale : bool or dict-like, optional
If True, replace array values equal to `_FillValue` with NA and scale
values according to the formula `original_values * scale_factor +
add_offset`, where `_FillValue`, `scale_factor` and `add_offset` are
taken from variable attributes (if they exist). If the `_FillValue` or
`missing_value` attribute contains multiple values a warning will be
issued and all array values matching one of the multiple values will
be replaced by NA. Pass a mapping, e.g. ``{"my_variable": False}``,
to toggle this feature per-variable individually.
This keyword may not be supported by all the backends.
decode_times : bool, CFDatetimeCoder or dict-like, optional
If True, decode times encoded in the standard NetCDF datetime format
into datetime objects. Otherwise, use :py:class:`coders.CFDatetimeCoder` or
leave them encoded as numbers.
Pass a mapping, e.g. ``{"my_variable": False}``,
to toggle this feature per-variable individually.
This keyword may not be supported by all the backends.
decode_timedelta : bool or dict-like, optional
If True, decode variables and coordinates with time units in
{"days", "hours", "minutes", "seconds", "milliseconds", "microseconds"}
into timedelta objects. If False, leave them encoded as numbers.
If None (default), assume the same value of ``decode_times``; if
``decode_times`` is a :py:class:`coders.CFDatetimeCoder` instance, this
takes the form of a :py:class:`coders.CFTimedeltaCoder` instance with a
matching ``time_unit``.
This keyword may not be supported by all the backends.
use_cftime: bool or dict-like, optional
Only relevant if encoded dates come from a standard calendar
(e.g. "gregorian", "proleptic_gregorian", "standard", or not
specified). If None (default), attempt to decode times to
``np.datetime64[ns]`` objects; if this is not possible, decode times to
``cftime.datetime`` objects. If True, always decode times to
``cftime.datetime`` objects, regardless of whether or not they can be
represented using ``np.datetime64[ns]`` objects. If False, always
decode times to ``np.datetime64[ns]`` objects; if this is not possible
raise an error. Pass a mapping, e.g. ``{"my_variable": False}``,
to toggle this feature per-variable individually.
This keyword may not be supported by all the backends.
.. deprecated:: 2025.01.1
Please pass a :py:class:`coders.CFDatetimeCoder` instance initialized with ``use_cftime`` to the ``decode_times`` kwarg instead.
concat_characters : bool or dict-like, optional
If True, concatenate along the last dimension of character arrays to
form string arrays. Dimensions will only be concatenated over (and
removed) if they have no corresponding variable and if they are only
used as the last dimension of character arrays.
Pass a mapping, e.g. ``{"my_variable": False}``,
to toggle this feature per-variable individually.
This keyword may not be supported by all the backends.
decode_coords : bool or {"coordinates", "all"}, optional
Controls which variables are set as coordinate variables:
- "coordinates" or True: Set variables referred to in the
``'coordinates'`` attribute of the datasets or individual variables
as coordinate variables.
- "all": Set variables referred to in ``'grid_mapping'``, ``'bounds'`` and
other attributes as coordinate variables.
Only existing variables can be set as coordinates. Missing variables
will be silently ignored.
drop_variables: str or iterable of str, optional
A variable or list of variables to exclude from being parsed from the
dataset. This may be useful to drop variables with problems or
inconsistent values.
create_default_indexes : bool, default: True
If True, create pandas indexes for :term:`dimension coordinates <dimension coordinate>`,
which loads the coordinate data into memory. Set it to False if you want to avoid loading
data into memory.
Note that backends can still choose to create other indexes. If you want to control that,
please refer to the backend's documentation.
inline_array: bool, default: False
How to include the array in the dask task graph.
By default(``inline_array=False``) the array is included in a task by
itself, and each chunk refers to that task by its key. With
``inline_array=True``, Dask will instead inline the array directly
in the values of the task graph. See :py:func:`dask.array.from_array`.
chunked_array_type: str, optional
Which chunked array type to coerce this datasets' arrays to.
Defaults to 'dask' if installed, else whatever is registered via the `ChunkManagerEnetryPoint` system.
Experimental API that should not be relied upon.
from_array_kwargs: dict
Additional keyword arguments passed on to the `ChunkManagerEntrypoint.from_array` method used to create
chunked arrays, via whichever chunk manager is specified through the `chunked_array_type` kwarg.
For example if :py:func:`dask.array.Array` objects are used for chunking, additional kwargs will be passed
to :py:func:`dask.array.from_array`. Experimental API that should not be relied upon.
backend_kwargs: dict
Additional keyword arguments passed on to the engine open function,
equivalent to `**kwargs`.
**kwargs: dict
Additional keyword arguments passed on to the engine open function.
For example:
- 'group': path to the group in the given file to open as the root group as
a str.
- 'lock': resource lock to use when reading data from disk. Only
relevant when using dask or another form of parallelism. By default,
appropriate locks are chosen to safely read and write files with the
currently active dask scheduler. Supported by "netcdf4", "h5netcdf",
"scipy".
See engine open function for kwargs accepted by each specific engine.
Returns
-------
groups : dict of str to xarray.Dataset
The groups as Dataset objects
Notes
-----
``open_groups`` opens the file with read-only access. When you modify
values of a Dataset, even one linked to files on disk, only the in-memory
copy you are manipulating in xarray is modified: the original file on disk
is never touched.
See Also
--------
xarray.open_datatree
xarray.open_dataset
xarray.DataTree.from_dict
"""
if cache is None:
cache = chunks is None
if backend_kwargs is not None:
kwargs.update(backend_kwargs)
if engine is None:
engine = plugins.guess_engine(filename_or_obj)
if from_array_kwargs is None:
from_array_kwargs = {}
backend = plugins.get_backend(engine)
decoders = _resolve_decoders_kwargs(
decode_cf,
open_backend_dataset_parameters=(),
mask_and_scale=mask_and_scale,
decode_times=decode_times,
decode_timedelta=decode_timedelta,
concat_characters=concat_characters,
use_cftime=use_cftime,
decode_coords=decode_coords,
)
overwrite_encoded_chunks = kwargs.pop("overwrite_encoded_chunks", None)
backend_groups = backend.open_groups_as_dict(
filename_or_obj,
drop_variables=drop_variables,
**decoders,
**kwargs,
)
groups = {
name: _dataset_from_backend_dataset(
backend_ds,
filename_or_obj,
engine,
chunks,
cache,
overwrite_encoded_chunks,
inline_array,
chunked_array_type,
from_array_kwargs,
drop_variables=drop_variables,
create_default_indexes=create_default_indexes,
**decoders,
**kwargs,
)
for name, backend_ds in backend_groups.items()
}
return groups
_FLike = TypeVar("_FLike", bound=Union[str, ReadBuffer])
def _remove_path(
paths: NestedSequence[_FLike], paths_to_remove: set[_FLike]
) -> NestedSequence[_FLike]:
# Initialize an empty list to store the result
result: list[Union[_FLike, NestedSequence[_FLike]]] = []
for item in paths:
if isinstance(item, list):
# If the current item is a list, recursively call remove_elements on it
nested_result = _remove_path(item, paths_to_remove)
if nested_result: # Only add non-empty lists to avoid adding empty lists
result.append(nested_result)
elif item not in paths_to_remove:
# Add the item to the result if it is not in the set of elements to remove
result.append(item)
return result
def open_mfdataset(
paths: str
| os.PathLike
| ReadBuffer
| NestedSequence[str | os.PathLike | ReadBuffer],
chunks: T_Chunks = None,
concat_dim: (
str
| DataArray
| Index
| Sequence[str]
| Sequence[DataArray]
| Sequence[Index]
| None
) = None,
compat: CompatOptions | CombineKwargDefault = _COMPAT_DEFAULT,
preprocess: Callable[[Dataset], Dataset] | None = None,
engine: T_Engine = None,
data_vars: Literal["all", "minimal", "different"]
| None
| list[str]
| CombineKwargDefault = _DATA_VARS_DEFAULT,
coords=_COORDS_DEFAULT,
combine: Literal["by_coords", "nested"] = "by_coords",
parallel: bool = False,
join: JoinOptions | CombineKwargDefault = _JOIN_DEFAULT,
attrs_file: str | os.PathLike | None = None,
combine_attrs: CombineAttrsOptions = "override",
errors: ErrorOptionsWithWarn = "raise",
**kwargs,
) -> Dataset:
"""Open multiple files as a single dataset.
If combine='by_coords' then the function ``combine_by_coords`` is used to combine
the datasets into one before returning the result, and if combine='nested' then
``combine_nested`` is used. The filepaths must be structured according to which
combining function is used, the details of which are given in the documentation for
``combine_by_coords`` and ``combine_nested``. By default ``combine='by_coords'``
will be used. Requires dask to be installed. See documentation for
details on dask [1]_. Global attributes from the ``attrs_file`` are used
for the combined dataset.
Parameters
----------
paths : str or nested sequence of paths
Either a string glob in the form ``"path/to/my/files/*.nc"`` or an explicit list of
files to open. Paths can be given as strings or as pathlib Paths. If
concatenation along more than one dimension is desired, then ``paths`` must be a
nested list-of-lists (see ``combine_nested`` for details). (A string glob will
be expanded to a 1-dimensional list.)
chunks : int, dict, 'auto' or None, optional
Dictionary with keys given by dimension names and values given by chunk sizes.
In general, these should divide the dimensions of each dataset. If int, chunk
each dimension by ``chunks``. By default, chunks will be chosen to load entire
input files into memory at once. This has a major impact on performance: please
see the full documentation for more details [2]_. This argument is evaluated
on a per-file basis, so chunk sizes that span multiple files will be ignored.
concat_dim : str, DataArray, Index or a Sequence of these or None, optional
Dimensions to concatenate files along. You only need to provide this argument
if ``combine='nested'``, and if any of the dimensions along which you want to
concatenate is not a dimension in the original datasets, e.g., if you want to
stack a collection of 2D arrays along a third dimension. Set
``concat_dim=[..., None, ...]`` explicitly to disable concatenation along a
particular dimension. Default is None, which for a 1D list of filepaths is
equivalent to opening the files separately and then merging them with
``xarray.merge``.
combine : {"by_coords", "nested"}, optional
Whether ``xarray.combine_by_coords`` or ``xarray.combine_nested`` is used to
combine all the data. Default is to use ``xarray.combine_by_coords``.
compat : {"identical", "equals", "broadcast_equals", \
"no_conflicts", "override"}, default: "no_conflicts"
String indicating how to compare variables of the same name for
potential conflicts when merging:
* "broadcast_equals": all values must be equal when variables are
broadcast against each other to ensure common dimensions.
* "equals": all values and dimensions must be the same.
* "identical": all values, dimensions and attributes must be the
same.
* "no_conflicts": only values which are not null in both datasets
must be equal. The returned dataset then contains the combination
of all non-null values.
* "override": skip comparing and pick variable from first dataset
preprocess : callable, optional
If provided, call this function on each dataset prior to concatenation.
You can find the file-name from which each dataset was loaded in
``ds.encoding["source"]``.
engine : {"netcdf4", "scipy", "pydap", "h5netcdf", "zarr", None}\
, installed backend \
or subclass of xarray.backends.BackendEntrypoint, optional
Engine to use when reading files. If not provided, the default engine
is chosen based on available dependencies, with a preference for
"netcdf4".
data_vars : {"minimal", "different", "all"} or list of str, default: "all"
These data variables will be concatenated together:
* "minimal": Only data variables in which the dimension already
appears are included.
* "different": Data variables which are not equal (ignoring
attributes) across all datasets are also concatenated (as well as
all for which dimension already appears). Beware: this option may
load the data payload of data variables into memory if they are not
already loaded.
* "all": All data variables will be concatenated.
* list of str: The listed data variables will be concatenated, in
addition to the "minimal" data variables.
coords : {"minimal", "different", "all"} or list of str, optional
These coordinate variables will be concatenated together:
* "minimal": Only coordinates in which the dimension already appears
are included.
* "different": Coordinates which are not equal (ignoring attributes)
across all datasets are also concatenated (as well as all for which
dimension already appears). Beware: this option may load the data
payload of coordinate variables into memory if they are not already
loaded.
* "all": All coordinate variables will be concatenated, except
those corresponding to other dimensions.
* list of str: The listed coordinate variables will be concatenated,
in addition the "minimal" coordinates.
parallel : bool, default: False
If True, the open and preprocess steps of this function will be
performed in parallel using ``dask.delayed``. Default is False.
join : {"outer", "inner", "left", "right", "exact", "override"}, default: "outer"
String indicating how to combine differing indexes
(excluding concat_dim) in objects
- "outer": use the union of object indexes
- "inner": use the intersection of object indexes
- "left": use indexes from the first object with each dimension
- "right": use indexes from the last object with each dimension
- "exact": instead of aligning, raise `ValueError` when indexes to be
aligned are not equal
- "override": if indexes are of same size, rewrite indexes to be
those of the first object with that dimension. Indexes for the same
dimension must have the same size in all objects.
attrs_file : str or path-like, optional
Path of the file used to read global attributes from.
By default global attributes are read from the first file provided,
with wildcard matches sorted by filename.
combine_attrs : {"drop", "identical", "no_conflicts", "drop_conflicts", \
"override"} or callable, default: "override"
A callable or a string indicating how to combine attrs of the objects being
merged:
- "drop": empty attrs on returned Dataset.
- "identical": all attrs must be the same on every object.
- "no_conflicts": attrs from all objects are combined, any that have
the same name must also have the same value.
- "drop_conflicts": attrs from all objects are combined, any that have
the same name but different values are dropped.
- "override": skip comparing and copy attrs from the first dataset to
the result.
If a callable, it must expect a sequence of ``attrs`` dicts and a context object
as its only parameters.
errors : {"raise", "warn", "ignore"}, default: "raise"
String indicating how to handle errors in opening dataset.
- "raise": invalid dataset will raise an exception.
- "warn": a warning will be issued for each invalid dataset.
- "ignore": invalid dataset will be ignored.
**kwargs : optional
Additional arguments passed on to :py:func:`xarray.open_dataset`. For an
overview of some of the possible options, see the documentation of
:py:func:`xarray.open_dataset`
Returns
-------
xarray.Dataset
Notes
-----
``open_mfdataset`` opens files with read-only access. When you modify values
of a Dataset, even one linked to files on disk, only the in-memory copy you
are manipulating in xarray is modified: the original file on disk is never
touched.
See Also
--------
combine_by_coords
combine_nested
open_dataset
Examples
--------
A user might want to pass additional arguments into ``preprocess`` when
applying some operation to many individual files that are being opened. One route
to do this is through the use of ``functools.partial``.
>>> from functools import partial
>>> def _preprocess(x, lon_bnds, lat_bnds):
... return x.sel(lon=slice(*lon_bnds), lat=slice(*lat_bnds))
...
>>> lon_bnds, lat_bnds = (-110, -105), (40, 45)
>>> partial_func = partial(_preprocess, lon_bnds=lon_bnds, lat_bnds=lat_bnds)
>>> ds = xr.open_mfdataset(
... "file_*.nc", concat_dim="time", preprocess=partial_func
... ) # doctest: +SKIP
It is also possible to use any argument to ``open_dataset`` together
with ``open_mfdataset``, such as for example ``drop_variables``:
>>> ds = xr.open_mfdataset(
... "file.nc", drop_variables=["varname_1", "varname_2"] # any list of vars
... ) # doctest: +SKIP
References
----------
.. [1] https://docs.xarray.dev/en/stable/dask.html
.. [2] https://docs.xarray.dev/en/stable/dask.html#chunking-and-performance
"""
paths = _find_absolute_paths(paths, engine=engine, **kwargs)
if not paths:
raise OSError("no files to open")
paths1d: list[str | ReadBuffer]
if combine == "nested":
if isinstance(concat_dim, str | DataArray) or concat_dim is None:
concat_dim = [concat_dim] # type: ignore[assignment]
# This creates a flat list which is easier to iterate over, whilst
# encoding the originally-supplied structure as "ids".
# The "ids" are not used at all if combine='by_coords`.
combined_ids_paths = _infer_concat_order_from_positions(paths)
ids, paths1d = (
list(combined_ids_paths.keys()),
list(combined_ids_paths.values()),
)
elif concat_dim is not None:
raise ValueError(
"When combine='by_coords', passing a value for `concat_dim` has no "
"effect. To manually combine along a specific dimension you should "
"instead specify combine='nested' along with a value for `concat_dim`.",
)
else:
paths1d = paths # type: ignore[assignment]
open_kwargs = dict(engine=engine, chunks=chunks or {}, **kwargs)
if parallel:
import dask
# wrap the open_dataset, getattr, and preprocess with delayed
open_ = dask.delayed(open_dataset)
getattr_ = dask.delayed(getattr)
if preprocess is not None:
preprocess = dask.delayed(preprocess)
else:
open_ = open_dataset
getattr_ = getattr
if errors not in ("raise", "warn", "ignore"):
raise ValueError(
f"'errors' must be 'raise', 'warn' or 'ignore', got '{errors}'"
)
datasets = []
invalid_paths = set()
for p in paths1d:
try:
ds = open_(p, **open_kwargs)
datasets.append(ds)
except Exception as e:
if errors == "raise":
raise
elif errors == "warn":
emit_user_level_warning(f"Could not open {p} due to {e}. Ignoring.")
# remove invalid paths
invalid_paths.add(p)
if invalid_paths:
paths = _remove_path(paths, invalid_paths)
if combine == "nested":
# Create new ids and paths based on removed items
combined_ids_paths = _infer_concat_order_from_positions(paths)
ids = list(combined_ids_paths.keys())
closers = [getattr_(ds, "_close") for ds in datasets]
if preprocess is not None:
datasets = [preprocess(ds) for ds in datasets]
if parallel:
# calling compute here will return the datasets/file_objs lists,
# the underlying datasets will still be stored as dask arrays
datasets, closers = dask.compute(datasets, closers)
# Combine all datasets, closing them in case of a ValueError
try:
if combine == "nested":
# Combined nested list by successive concat and merge operations
# along each dimension, using structure given by "ids"
combined = _nested_combine(
datasets,
concat_dims=concat_dim,
compat=compat,
data_vars=data_vars,
coords=coords,
ids=ids,
join=join,
combine_attrs=combine_attrs,
fill_value=dtypes.NA,
)
elif combine == "by_coords":
# Redo ordering from coordinates, ignoring how they were ordered
# previously
combined = combine_by_coords(
datasets,
compat=compat,
data_vars=data_vars,
coords=coords,
join=join,
combine_attrs=combine_attrs,
)
else:
raise ValueError(
f"{combine} is an invalid option for the keyword argument ``combine``"
)
except ValueError:
for ds in datasets:
ds.close()
raise
combined.set_close(partial(_multi_file_closer, closers))
# read global attributes from the attrs_file or from the first dataset
if attrs_file is not None:
if isinstance(attrs_file, os.PathLike):
attrs_file = cast(str, os.fspath(attrs_file))
combined.attrs = datasets[paths1d.index(attrs_file)].attrs
return combined
WRITEABLE_STORES: dict[T_NetcdfEngine, Callable] = {
"netcdf4": backends.NetCDF4DataStore.open,
"scipy": backends.ScipyDataStore,
"h5netcdf": backends.H5NetCDFStore.open,
}
# multifile=True returns writer and datastore
@overload
def to_netcdf(
dataset: Dataset,
path_or_file: str | os.PathLike | None = None,
mode: NetcdfWriteModes = "w",
format: T_NetcdfTypes | None = None,
group: str | None = None,
engine: T_NetcdfEngine | None = None,
encoding: Mapping[Hashable, Mapping[str, Any]] | None = None,
unlimited_dims: Iterable[Hashable] | None = None,
compute: bool = True,
*,
multifile: Literal[True],
invalid_netcdf: bool = False,
auto_complex: bool | None = None,
) -> tuple[ArrayWriter, AbstractDataStore]: ...
# path=None writes to bytes or memoryview, depending on store
@overload
def to_netcdf(
dataset: Dataset,
path_or_file: None = None,
mode: NetcdfWriteModes = "w",
format: T_NetcdfTypes | None = None,
group: str | None = None,
engine: T_NetcdfEngine | None = None,
encoding: Mapping[Hashable, Mapping[str, Any]] | None = None,
unlimited_dims: Iterable[Hashable] | None = None,
compute: bool = True,
multifile: Literal[False] = False,
invalid_netcdf: bool = False,
auto_complex: bool | None = None,
) -> bytes | memoryview: ...
# compute=False returns dask.Delayed
@overload
def to_netcdf(
dataset: Dataset,
path_or_file: str | os.PathLike,
mode: NetcdfWriteModes = "w",
format: T_NetcdfTypes | None = None,
group: str | None = None,
engine: T_NetcdfEngine | None = None,
encoding: Mapping[Hashable, Mapping[str, Any]] | None = None,
unlimited_dims: Iterable[Hashable] | None = None,
*,
compute: Literal[False],
multifile: Literal[False] = False,
invalid_netcdf: bool = False,
auto_complex: bool | None = None,
) -> Delayed: ...
# default return None
@overload
def to_netcdf(
dataset: Dataset,
path_or_file: str | os.PathLike | IOBase,
mode: NetcdfWriteModes = "w",
format: T_NetcdfTypes | None = None,
group: str | None = None,
engine: T_NetcdfEngine | None = None,
encoding: Mapping[Hashable, Mapping[str, Any]] | None = None,
unlimited_dims: Iterable[Hashable] | None = None,
compute: Literal[True] = True,
multifile: Literal[False] = False,
invalid_netcdf: bool = False,
auto_complex: bool | None = None,
) -> None: ...
# if compute cannot be evaluated at type check time
# we may get back either Delayed or None
@overload
def to_netcdf(
dataset: Dataset,
path_or_file: str | os.PathLike,
mode: NetcdfWriteModes = "w",
format: T_NetcdfTypes | None = None,
group: str | None = None,
engine: T_NetcdfEngine | None = None,
encoding: Mapping[Hashable, Mapping[str, Any]] | None = None,
unlimited_dims: Iterable[Hashable] | None = None,
compute: bool = False,
multifile: Literal[False] = False,
invalid_netcdf: bool = False,
auto_complex: bool | None = None,
) -> Delayed | None: ...
# if multifile cannot be evaluated at type check time
# we may get back either writer and datastore or Delayed or None
@overload
def to_netcdf(
dataset: Dataset,
path_or_file: str | os.PathLike,
mode: NetcdfWriteModes = "w",
format: T_NetcdfTypes | None = None,
group: str | None = None,
engine: T_NetcdfEngine | None = None,
encoding: Mapping[Hashable, Mapping[str, Any]] | None = None,
unlimited_dims: Iterable[Hashable] | None = None,
compute: bool = False,
multifile: bool = False,
invalid_netcdf: bool = False,
auto_complex: bool | None = None,
) -> tuple[ArrayWriter, AbstractDataStore] | Delayed | None: ...
# Any
@overload
def to_netcdf(
dataset: Dataset,
path_or_file: str | os.PathLike | IOBase | None,
mode: NetcdfWriteModes = "w",
format: T_NetcdfTypes | None = None,
group: str | None = None,
engine: T_NetcdfEngine | None = None,
encoding: Mapping[Hashable, Mapping[str, Any]] | None = None,
unlimited_dims: Iterable[Hashable] | None = None,
compute: bool = False,
multifile: bool = False,
invalid_netcdf: bool = False,
auto_complex: bool | None = None,
) -> tuple[ArrayWriter, AbstractDataStore] | bytes | memoryview | Delayed | None: ...
def to_netcdf(
dataset: Dataset,
path_or_file: str | os.PathLike | IOBase | None = None,
mode: NetcdfWriteModes = "w",
format: T_NetcdfTypes | None = None,
group: str | None = None,
engine: T_NetcdfEngine | None = None,
encoding: Mapping[Hashable, Mapping[str, Any]] | None = None,
unlimited_dims: Iterable[Hashable] | None = None,
compute: bool = True,
multifile: bool = False,
invalid_netcdf: bool = False,
auto_complex: bool | None = None,
) -> tuple[ArrayWriter, AbstractDataStore] | bytes | memoryview | Delayed | None:
"""This function creates an appropriate datastore for writing a dataset to
disk as a netCDF file
See `Dataset.to_netcdf` for full API docs.
The ``multifile`` argument is only for the private use of save_mfdataset.
"""
if isinstance(path_or_file, os.PathLike):
path_or_file = os.fspath(path_or_file)
if encoding is None:
encoding = {}
if isinstance(path_or_file, str):
if engine is None:
engine = _get_default_engine(path_or_file)
path_or_file = _normalize_path(path_or_file)
else:
# writing to bytes/memoryview or a file-like object
if engine is None:
# TODO: only use 'scipy' if format is None or a netCDF3 format
engine = "scipy"
elif engine not in ("scipy", "h5netcdf"):
raise ValueError(
"invalid engine for creating bytes/memoryview or writing to a "
f"file-like object with to_netcdf: {engine!r}. Only "
"engine=None, engine='scipy' and engine='h5netcdf' is "
"supported."
)
if not compute:
raise NotImplementedError(
"to_netcdf() with compute=False is not yet implemented when "
"returning bytes"
)
# validate Dataset keys, DataArray names, and attr keys/values
_validate_dataset_names(dataset)
_validate_attrs(dataset, engine, invalid_netcdf)
# sanitize unlimited_dims
unlimited_dims = _sanitize_unlimited_dims(dataset, unlimited_dims)
try:
store_open = WRITEABLE_STORES[engine]
except KeyError as err:
raise ValueError(f"unrecognized engine for to_netcdf: {engine!r}") from err
if format is not None:
format = format.upper() # type: ignore[assignment]
# handle scheduler specific logic
scheduler = _get_scheduler()
have_chunks = any(v.chunks is not None for v in dataset.variables.values())
autoclose = have_chunks and scheduler in ["distributed", "multiprocessing"]
if autoclose and engine == "scipy":
raise NotImplementedError(
f"Writing netCDF files with the {engine} backend "
f"is not currently supported with dask's {scheduler} scheduler"
)
if path_or_file is None:
target = BytesIOProxy()
else:
target = path_or_file # type: ignore[assignment]
kwargs = dict(autoclose=True) if autoclose else {}
if invalid_netcdf:
if engine == "h5netcdf":
kwargs["invalid_netcdf"] = invalid_netcdf
else:
raise ValueError(
f"unrecognized option 'invalid_netcdf' for engine {engine}"
)
if auto_complex is not None:
kwargs["auto_complex"] = auto_complex
store = store_open(target, mode, format, group, **kwargs)
writer = ArrayWriter()
# TODO: figure out how to refactor this logic (here and in save_mfdataset)
# to avoid this mess of conditionals
try:
# TODO: allow this work (setting up the file for writing array data)
# to be parallelized with dask
dump_to_store(
dataset, store, writer, encoding=encoding, unlimited_dims=unlimited_dims
)
if autoclose:
store.close()
if multifile:
return writer, store
writes = writer.sync(compute=compute)
finally:
if not multifile and compute: # type: ignore[redundant-expr]
store.close()
if path_or_file is None:
assert isinstance(target, BytesIOProxy) # created in this function
return target.getvalue_or_getbuffer()
if not compute:
import dask
return dask.delayed(_finalize_store)(writes, store)
return None
def dump_to_store(
dataset, store, writer=None, encoder=None, encoding=None, unlimited_dims=None
):
"""Store dataset contents to a backends.*DataStore object."""
if writer is None:
writer = ArrayWriter()
if encoding is None:
encoding = {}
variables, attrs = conventions.encode_dataset_coordinates(dataset)
check_encoding = set()
for k, enc in encoding.items():
# no need to shallow copy the variable again; that already happened
# in encode_dataset_coordinates
variables[k].encoding = enc
check_encoding.add(k)
if encoder:
variables, attrs = encoder(variables, attrs)
store.store(variables, attrs, check_encoding, writer, unlimited_dims=unlimited_dims)
def save_mfdataset(
datasets,
paths,
mode="w",
format=None,
groups=None,
engine=None,
compute=True,
**kwargs,
):
"""Write multiple datasets to disk as netCDF files simultaneously.
This function is intended for use with datasets consisting of dask.array
objects, in which case it can write the multiple datasets to disk
simultaneously using a shared thread pool.
When not using dask, it is no different than calling ``to_netcdf``
repeatedly.
Parameters
----------
datasets : list of Dataset
List of datasets to save.
paths : list of str or list of path-like objects
List of paths to which to save each corresponding dataset.
mode : {"w", "a"}, optional
Write ("w") or append ("a") mode. If mode="w", any existing file at
these locations will be overwritten.
format : {"NETCDF4", "NETCDF4_CLASSIC", "NETCDF3_64BIT", \
"NETCDF3_CLASSIC"}, optional
File format for the resulting netCDF file:
* NETCDF4: Data is stored in an HDF5 file, using netCDF4 API
features.
* NETCDF4_CLASSIC: Data is stored in an HDF5 file, using only
netCDF 3 compatible API features.
* NETCDF3_64BIT: 64-bit offset version of the netCDF 3 file format,
which fully supports 2+ GB files, but is only compatible with
clients linked against netCDF version 3.6.0 or later.
* NETCDF3_CLASSIC: The classic netCDF 3 file format. It does not
handle 2+ GB files very well.
All formats are supported by the netCDF4-python library.
scipy.io.netcdf only supports the last two formats.
The default format is NETCDF4 if you are saving a file to disk and
have the netCDF4-python library available. Otherwise, xarray falls
back to using scipy to write netCDF files and defaults to the
NETCDF3_64BIT format (scipy does not support netCDF4).
groups : list of str, optional
Paths to the netCDF4 group in each corresponding file to which to save
datasets (only works for format="NETCDF4"). The groups will be created
if necessary.
engine : {"netcdf4", "scipy", "h5netcdf"}, optional
Engine to use when writing netCDF files. If not provided, the
default engine is chosen based on available dependencies, with a
preference for "netcdf4" if writing to a file on disk.
See `Dataset.to_netcdf` for additional information.
compute : bool
If true compute immediately, otherwise return a
``dask.delayed.Delayed`` object that can be computed later.
**kwargs : dict, optional
Additional arguments are passed along to ``to_netcdf``.
Examples
--------
Save a dataset into one netCDF per year of data:
>>> ds = xr.Dataset(
... {"a": ("time", np.linspace(0, 1, 48))},
... coords={"time": pd.date_range("2010-01-01", freq="ME", periods=48)},
... )
>>> ds
<xarray.Dataset> Size: 768B
Dimensions: (time: 48)
Coordinates:
* time (time) datetime64[ns] 384B 2010-01-31 2010-02-28 ... 2013-12-31
Data variables:
a (time) float64 384B 0.0 0.02128 0.04255 ... 0.9574 0.9787 1.0
>>> years, datasets = zip(*ds.groupby("time.year"))
>>> paths = [f"{y}.nc" for y in years]
>>> xr.save_mfdataset(datasets, paths)
"""
if mode == "w" and len(set(paths)) < len(paths):
raise ValueError(
"cannot use mode='w' when writing multiple datasets to the same path"
)
for obj in datasets:
if not isinstance(obj, Dataset):
raise TypeError(
"save_mfdataset only supports writing Dataset "
f"objects, received type {type(obj)}"
)
if groups is None:
groups = [None] * len(datasets)
if len({len(datasets), len(paths), len(groups)}) > 1:
raise ValueError(
"must supply lists of the same length for the "
"datasets, paths and groups arguments to "
"save_mfdataset"
)
writers, stores = zip(
*[
to_netcdf(
ds,
path,
mode,
format,
group,
engine,
compute=compute,
multifile=True,
**kwargs,
)
for ds, path, group in zip(datasets, paths, groups, strict=True)
],
strict=True,
)
try:
writes = [w.sync(compute=compute) for w in writers]
finally:
if compute:
for store in stores:
store.close()
if not compute:
import dask
return dask.delayed(
list(
starmap(dask.delayed(_finalize_store), zip(writes, stores, strict=True))
)
)
# compute=True returns ZarrStore
@overload
def to_zarr(
dataset: Dataset,
store: ZarrStoreLike | None = None,
chunk_store: MutableMapping | str | os.PathLike | None = None,
mode: ZarrWriteModes | None = None,
synchronizer=None,
group: str | None = None,
encoding: Mapping | None = None,
*,
compute: Literal[True] = True,
consolidated: bool | None = None,
append_dim: Hashable | None = None,
region: Mapping[str, slice | Literal["auto"]] | Literal["auto"] | None = None,
safe_chunks: bool = True,
align_chunks: bool = False,
storage_options: dict[str, str] | None = None,
zarr_version: int | None = None,
write_empty_chunks: bool | None = None,
chunkmanager_store_kwargs: dict[str, Any] | None = None,
) -> backends.ZarrStore: ...
# compute=False returns dask.Delayed
@overload
def to_zarr(
dataset: Dataset,
store: ZarrStoreLike | None = None,
chunk_store: MutableMapping | str | os.PathLike | None = None,
mode: ZarrWriteModes | None = None,
synchronizer=None,
group: str | None = None,
encoding: Mapping | None = None,
*,
compute: Literal[False],
consolidated: bool | None = None,
append_dim: Hashable | None = None,
region: Mapping[str, slice | Literal["auto"]] | Literal["auto"] | None = None,
safe_chunks: bool = True,
align_chunks: bool = False,
storage_options: dict[str, str] | None = None,
zarr_version: int | None = None,
write_empty_chunks: bool | None = None,
chunkmanager_store_kwargs: dict[str, Any] | None = None,
) -> Delayed: ...
def to_zarr(
dataset: Dataset,
store: ZarrStoreLike | None = None,
chunk_store: MutableMapping | str | os.PathLike | None = None,
mode: ZarrWriteModes | None = None,
synchronizer=None,
group: str | None = None,
encoding: Mapping | None = None,
*,
compute: bool = True,
consolidated: bool | None = None,
append_dim: Hashable | None = None,
region: Mapping[str, slice | Literal["auto"]] | Literal["auto"] | None = None,
safe_chunks: bool = True,
align_chunks: bool = False,
storage_options: dict[str, str] | None = None,
zarr_version: int | None = None,
zarr_format: int | None = None,
write_empty_chunks: bool | None = None,
chunkmanager_store_kwargs: dict[str, Any] | None = None,
) -> backends.ZarrStore | Delayed:
"""This function creates an appropriate datastore for writing a dataset to
a zarr ztore
See `Dataset.to_zarr` for full API docs.
"""
from xarray.backends.zarr import _choose_default_mode, _get_mappers
# validate Dataset keys, DataArray names
_validate_dataset_names(dataset)
# Load empty arrays to avoid bug saving zero length dimensions (Issue #5741)
# TODO: delete when min dask>=2023.12.1
# https://github.com/dask/dask/pull/10506
for v in dataset.variables.values():
if v.size == 0:
v.load()
if encoding is None:
encoding = {}
kwargs, mapper, chunk_mapper = _get_mappers(
storage_options=storage_options, store=store, chunk_store=chunk_store
)
mode = _choose_default_mode(mode=mode, append_dim=append_dim, region=region)
if mode == "r+":
already_consolidated = consolidated
consolidate_on_close = False
else:
already_consolidated = False
consolidate_on_close = consolidated or consolidated is None
zstore = backends.ZarrStore.open_group(
store=mapper,
mode=mode,
synchronizer=synchronizer,
group=group,
consolidated=already_consolidated,
consolidate_on_close=consolidate_on_close,
chunk_store=chunk_mapper,
append_dim=append_dim,
write_region=region,
safe_chunks=safe_chunks,
align_chunks=align_chunks,
zarr_version=zarr_version,
zarr_format=zarr_format,
write_empty=write_empty_chunks,
**kwargs,
)
dataset = zstore._validate_and_autodetect_region(
dataset,
)
zstore._validate_encoding(encoding)
writer = ArrayWriter()
# TODO: figure out how to properly handle unlimited_dims
dump_to_store(dataset, zstore, writer, encoding=encoding)
writes = writer.sync(
compute=compute, chunkmanager_store_kwargs=chunkmanager_store_kwargs
)
if compute:
_finalize_store(writes, zstore)
else:
import dask
return dask.delayed(_finalize_store)(writes, zstore)
return zstore
|