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import os
import warnings
from glob import glob
from io import BytesIO
from numbers import Number
from pathlib import Path
from typing import (
TYPE_CHECKING,
Callable,
Dict,
Hashable,
Iterable,
Mapping,
MutableMapping,
Tuple,
Union,
)
import numpy as np
from .. import backends, coding, conventions
from ..core import indexing
from ..core.combine import (
_infer_concat_order_from_positions,
_nested_combine,
combine_by_coords,
)
from ..core.dataarray import DataArray
from ..core.dataset import Dataset, _maybe_chunk
from ..core.utils import close_on_error, is_grib_path, is_remote_uri
from .common import AbstractDataStore, ArrayWriter
from .locks import _get_scheduler
if TYPE_CHECKING:
try:
from dask.delayed import Delayed
except ImportError:
Delayed = None
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,
"pynio": backends.NioDataStore,
"pseudonetcdf": backends.PseudoNetCDFDataStore.open,
"cfgrib": backends.CfGribDataStore,
"zarr": backends.ZarrStore.open_group,
}
def _get_default_engine_remote_uri():
try:
import netCDF4 # noqa: F401
engine = "netcdf4"
except ImportError: # pragma: no cover
try:
import pydap # noqa: F401
engine = "pydap"
except ImportError:
raise ValueError(
"netCDF4 or pydap is required for accessing "
"remote datasets via OPeNDAP"
)
return engine
def _get_default_engine_grib():
msgs = []
try:
import Nio # noqa: F401
msgs += ["set engine='pynio' to access GRIB files with PyNIO"]
except ImportError: # pragma: no cover
pass
try:
import cfgrib # noqa: F401
msgs += ["set engine='cfgrib' to access GRIB files with cfgrib"]
except ImportError: # pragma: no cover
pass
if msgs:
raise ValueError(" or\n".join(msgs))
else:
raise ValueError("PyNIO or cfgrib is required for accessing GRIB files")
def _get_default_engine_gz():
try:
import scipy # noqa: F401
engine = "scipy"
except ImportError: # pragma: no cover
raise ValueError("scipy is required for accessing .gz files")
return engine
def _get_default_engine_netcdf():
try:
import netCDF4 # noqa: F401
engine = "netcdf4"
except ImportError: # pragma: no cover
try:
import scipy.io.netcdf # noqa: F401
engine = "scipy"
except ImportError:
raise ValueError(
"cannot read or write netCDF files without "
"netCDF4-python or scipy installed"
)
return engine
def _get_engine_from_magic_number(filename_or_obj):
# check byte header to determine file type
if isinstance(filename_or_obj, bytes):
magic_number = filename_or_obj[:8]
else:
if filename_or_obj.tell() != 0:
raise ValueError(
"file-like object read/write pointer not at zero "
"please close and reopen, or use a context manager"
)
magic_number = filename_or_obj.read(8)
filename_or_obj.seek(0)
if magic_number.startswith(b"CDF"):
engine = "scipy"
elif magic_number.startswith(b"\211HDF\r\n\032\n"):
engine = "h5netcdf"
else:
raise ValueError(
f"{magic_number} is not the signature of any supported file format "
"did you mean to pass a string for a path instead?"
)
return engine
def _get_default_engine(path, allow_remote=False):
if allow_remote and is_remote_uri(path):
engine = _get_default_engine_remote_uri()
elif is_grib_path(path):
engine = _get_default_engine_grib()
elif path.endswith(".gz"):
engine = _get_default_engine_gz()
else:
engine = _get_default_engine_netcdf()
return engine
def _autodetect_engine(filename_or_obj):
if isinstance(filename_or_obj, str):
engine = _get_default_engine(filename_or_obj, allow_remote=True)
else:
engine = _get_engine_from_magic_number(filename_or_obj)
return engine
def _get_backend_cls(engine, engines=ENGINES):
"""Select open_dataset method based on current engine"""
try:
return engines[engine]
except KeyError:
raise ValueError(
"unrecognized engine for open_dataset: {}\n"
"must be one of: {}".format(engine, list(ENGINES))
)
def _normalize_path(path):
if isinstance(path, Path):
path = str(path)
if isinstance(path, str) and not is_remote_uri(path):
path = os.path.abspath(os.path.expanduser(path))
return path
def _validate_dataset_names(dataset):
"""DataArray.name and Dataset keys must be a string or None"""
def check_name(name):
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 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 "
"files"
)
for k in dataset.variables:
check_name(k)
def _validate_attrs(dataset):
"""`attrs` must have a string key and a value which is either: a number,
a string, an ndarray or a list/tuple of numbers/strings.
"""
def check_attr(name, value):
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, (str, Number, np.ndarray, np.number, list, tuple)):
raise TypeError(
f"Invalid value for attr {name!r}: {value!r} must be a number, "
"a string, an ndarray or a list/tuple of "
"numbers/strings for serialization to netCDF "
"files"
)
# Check attrs on the dataset itself
for k, v in dataset.attrs.items():
check_attr(k, v)
# 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)
def _protect_dataset_variables_inplace(dataset, cache):
for name, variable in dataset.variables.items():
if name not in variable.dims:
# no need to protect IndexVariable objects
data = indexing.CopyOnWriteArray(variable._data)
if cache:
data = indexing.MemoryCachedArray(data)
variable.data = data
def _finalize_store(write, store):
""" Finalize this store by explicitly syncing and closing"""
del write # ensure writing is done first
store.close()
def load_dataset(filename_or_obj, **kwargs):
"""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 open_dataset(
filename_or_obj,
group=None,
decode_cf=True,
mask_and_scale=None,
decode_times=True,
autoclose=None,
concat_characters=True,
decode_coords=True,
engine=None,
chunks=None,
lock=None,
cache=None,
drop_variables=None,
backend_kwargs=None,
use_cftime=None,
decode_timedelta=None,
):
"""Open and decode a dataset from a file or file-like object.
Parameters
----------
filename_or_obj : str, Path, file-like 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). Byte-strings or file-like
objects are opened by scipy.io.netcdf (netCDF3) or h5py (netCDF4/HDF).
group : str, optional
Path to the netCDF4 group in the given file to open (only works for
netCDF4 files).
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. mask_and_scale defaults to True except for the
pseudonetcdf backend.
decode_times : bool, optional
If True, decode times encoded in the standard NetCDF datetime format
into datetime objects. Otherwise, leave them encoded as numbers.
autoclose : bool, optional
If True, automatically close files to avoid OS Error of too many files
being open. However, this option doesn't work with streams, e.g.,
BytesIO.
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.
decode_coords : bool, optional
If True, decode the 'coordinates' attribute to identify coordinates in
the resulting dataset.
engine : {"netcdf4", "scipy", "pydap", "h5netcdf", "pynio", "cfgrib", \
"pseudonetcdf", "zarr"}, 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 or dict, optional
If chunks is provided, it is used to load the new dataset into dask
arrays. ``chunks={}`` loads the dataset with dask using a single
chunk for all arrays. When using ``engine="zarr"``, setting
``chunks='auto'`` will create dask chunks based on the variable's zarr
chunks.
lock : False or lock-like, optional
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.
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``.
drop_variables: str or iterable, 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.
backend_kwargs: dict, optional
A dictionary of keyword arguments to pass on to the backend. This
may be useful when backend options would improve performance or
allow user control of dataset processing.
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.
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_time.
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 os.environ.get("XARRAY_BACKEND_API", "v1") == "v2":
kwargs = locals().copy()
from . import apiv2, plugins
if engine in plugins.ENGINES:
return apiv2.open_dataset(**kwargs)
if autoclose is not None:
warnings.warn(
"The autoclose argument is no longer used by "
"xarray.open_dataset() and is now ignored; it will be removed in "
"a future version of xarray. If necessary, you can control the "
"maximum number of simultaneous open files with "
"xarray.set_options(file_cache_maxsize=...).",
FutureWarning,
stacklevel=2,
)
if mask_and_scale is None:
mask_and_scale = not engine == "pseudonetcdf"
if not decode_cf:
mask_and_scale = False
decode_times = False
concat_characters = False
decode_coords = False
decode_timedelta = False
if cache is None:
cache = chunks is None
if backend_kwargs is None:
backend_kwargs = {}
def maybe_decode_store(store, chunks):
ds = conventions.decode_cf(
store,
mask_and_scale=mask_and_scale,
decode_times=decode_times,
concat_characters=concat_characters,
decode_coords=decode_coords,
drop_variables=drop_variables,
use_cftime=use_cftime,
decode_timedelta=decode_timedelta,
)
_protect_dataset_variables_inplace(ds, cache)
if chunks is not None and engine != "zarr":
from dask.base import tokenize
# if passed an actual file path, augment the token with
# the file modification time
if isinstance(filename_or_obj, str) and not is_remote_uri(filename_or_obj):
mtime = os.path.getmtime(filename_or_obj)
else:
mtime = None
token = tokenize(
filename_or_obj,
mtime,
group,
decode_cf,
mask_and_scale,
decode_times,
concat_characters,
decode_coords,
engine,
chunks,
drop_variables,
use_cftime,
decode_timedelta,
)
name_prefix = "open_dataset-%s" % token
ds2 = ds.chunk(chunks, name_prefix=name_prefix, token=token)
elif engine == "zarr":
# adapted from Dataset.Chunk() and taken from open_zarr
if not (isinstance(chunks, (int, dict)) or chunks is None):
if chunks != "auto":
raise ValueError(
"chunks must be an int, dict, 'auto', or None. "
"Instead found %s. " % chunks
)
if chunks == "auto":
try:
import dask.array # noqa
except ImportError:
chunks = None
# auto chunking needs to be here and not in ZarrStore because
# the variable chunks does not survive decode_cf
# return trivial case
if chunks is None:
return ds
if isinstance(chunks, int):
chunks = dict.fromkeys(ds.dims, chunks)
variables = {
k: _maybe_chunk(
k,
v,
store.get_chunk(k, v, chunks),
overwrite_encoded_chunks=overwrite_encoded_chunks,
)
for k, v in ds.variables.items()
}
ds2 = ds._replace(variables)
else:
ds2 = ds
ds2._file_obj = ds._file_obj
return ds2
filename_or_obj = _normalize_path(filename_or_obj)
if isinstance(filename_or_obj, AbstractDataStore):
store = filename_or_obj
else:
if engine is None:
engine = _autodetect_engine(filename_or_obj)
extra_kwargs = {}
if group is not None:
extra_kwargs["group"] = group
if lock is not None:
extra_kwargs["lock"] = lock
if engine == "zarr":
backend_kwargs = backend_kwargs.copy()
overwrite_encoded_chunks = backend_kwargs.pop(
"overwrite_encoded_chunks", None
)
opener = _get_backend_cls(engine)
store = opener(filename_or_obj, **extra_kwargs, **backend_kwargs)
with close_on_error(store):
ds = maybe_decode_store(store, chunks)
# Ensure source filename always stored in dataset object (GH issue #2550)
if "source" not in ds.encoding:
if isinstance(filename_or_obj, str):
ds.encoding["source"] = filename_or_obj
return ds
def open_dataarray(
filename_or_obj,
group=None,
decode_cf=True,
mask_and_scale=None,
decode_times=True,
autoclose=None,
concat_characters=True,
decode_coords=True,
engine=None,
chunks=None,
lock=None,
cache=None,
drop_variables=None,
backend_kwargs=None,
use_cftime=None,
decode_timedelta=None,
):
"""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 or DataStore
Strings and Paths 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). Byte-strings or file-like
objects are opened by scipy.io.netcdf (netCDF3) or h5py (netCDF4/HDF).
group : str, optional
Path to the netCDF4 group in the given file to open (only works for
netCDF4 files).
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. mask_and_scale defaults to True except for the
pseudonetcdf backend.
decode_times : bool, optional
If True, decode times encoded in the standard NetCDF datetime format
into datetime objects. Otherwise, leave them encoded as numbers.
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.
decode_coords : bool, optional
If True, decode the 'coordinates' attribute to identify coordinates in
the resulting dataset.
engine : {"netcdf4", "scipy", "pydap", "h5netcdf", "pynio", "cfgrib"}, \
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 or dict, optional
If chunks is provided, it used to load the new dataset into dask
arrays.
lock : False or lock-like, optional
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.
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``.
drop_variables: str or iterable, 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.
backend_kwargs: dict, optional
A dictionary of keyword arguments to pass on to the backend. This
may be useful when backend options would improve performance or
allow user control of dataset processing.
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.
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_time.
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,
group=group,
decode_cf=decode_cf,
mask_and_scale=mask_and_scale,
decode_times=decode_times,
autoclose=autoclose,
concat_characters=concat_characters,
decode_coords=decode_coords,
engine=engine,
chunks=chunks,
lock=lock,
cache=cache,
drop_variables=drop_variables,
backend_kwargs=backend_kwargs,
use_cftime=use_cftime,
decode_timedelta=decode_timedelta,
)
if len(dataset.data_vars) != 1:
raise ValueError(
"Given file dataset contains more than one data "
"variable. Please read with xarray.open_dataset and "
"then select the variable you want."
)
else:
(data_array,) = dataset.data_vars.values()
data_array._file_obj = dataset._file_obj
# 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
class _MultiFileCloser:
__slots__ = ("file_objs",)
def __init__(self, file_objs):
self.file_objs = file_objs
def close(self):
for f in self.file_objs:
f.close()
def open_mfdataset(
paths,
chunks=None,
concat_dim=None,
compat="no_conflicts",
preprocess=None,
engine=None,
lock=None,
data_vars="all",
coords="different",
combine="by_coords",
autoclose=None,
parallel=False,
join="outer",
attrs_file=None,
**kwargs,
):
"""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 sequence
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 or dict, 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]_.
concat_dim : str, or list of str, DataArray, Index or None, optional
Dimensions to concatenate files along. You only need to provide this argument
if ``combine='by_coords'``, 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"}, optional
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", "pynio", "cfgrib", "zarr"}, \
optional
Engine to use when reading files. If not provided, the default engine
is chosen based on available dependencies, with a preference for
"netcdf4".
lock : False or lock-like, optional
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.
data_vars : {"minimal", "different", "all"} or list of str, optional
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, optional
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"}, optional
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 pathlib.Path, 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.
**kwargs : optional
Additional arguments passed on to :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
References
----------
.. [1] http://xarray.pydata.org/en/stable/dask.html
.. [2] http://xarray.pydata.org/en/stable/dask.html#chunking-and-performance
"""
if isinstance(paths, str):
if is_remote_uri(paths):
raise ValueError(
"cannot do wild-card matching for paths that are remote URLs: "
"{!r}. Instead, supply paths as an explicit list of strings.".format(
paths
)
)
paths = sorted(glob(paths))
else:
paths = [str(p) if isinstance(p, Path) else p for p in paths]
if not paths:
raise OSError("no files to open")
# If combine='by_coords' then this is unnecessary, but quick.
# If combine='nested' then this creates a flat list which is easier to
# iterate over, while saving the originally-supplied structure as "ids"
if combine == "nested":
if isinstance(concat_dim, (str, DataArray)) or concat_dim is None:
concat_dim = [concat_dim]
combined_ids_paths = _infer_concat_order_from_positions(paths)
ids, paths = (list(combined_ids_paths.keys()), list(combined_ids_paths.values()))
open_kwargs = dict(
engine=engine, chunks=chunks or {}, lock=lock, autoclose=autoclose, **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
datasets = [open_(p, **open_kwargs) for p in paths]
file_objs = [getattr_(ds, "_file_obj") 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, file_objs = dask.compute(datasets, file_objs)
# 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="drop",
)
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="drop",
)
else:
raise ValueError(
"{} is an invalid option for the keyword argument"
" ``combine``".format(combine)
)
except ValueError:
for ds in datasets:
ds.close()
raise
combined._file_obj = _MultiFileCloser(file_objs)
# read global attributes from the attrs_file or from the first dataset
if attrs_file is not None:
if isinstance(attrs_file, Path):
attrs_file = str(attrs_file)
combined.attrs = datasets[paths.index(attrs_file)].attrs
else:
combined.attrs = datasets[0].attrs
return combined
WRITEABLE_STORES: Dict[str, Callable] = {
"netcdf4": backends.NetCDF4DataStore.open,
"scipy": backends.ScipyDataStore,
"h5netcdf": backends.H5NetCDFStore.open,
}
def to_netcdf(
dataset: Dataset,
path_or_file=None,
mode: str = "w",
format: str = None,
group: str = None,
engine: str = None,
encoding: Mapping = None,
unlimited_dims: Iterable[Hashable] = None,
compute: bool = True,
multifile: bool = False,
invalid_netcdf: bool = False,
) -> Union[Tuple[ArrayWriter, AbstractDataStore], bytes, "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, Path):
path_or_file = str(path_or_file)
if encoding is None:
encoding = {}
if path_or_file is None:
if engine is None:
engine = "scipy"
elif engine != "scipy":
raise ValueError(
"invalid engine for creating bytes with "
"to_netcdf: %r. Only the default engine "
"or engine='scipy' is supported" % engine
)
if not compute:
raise NotImplementedError(
"to_netcdf() with compute=False is not yet implemented when "
"returning bytes"
)
elif 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: # file-like object
engine = "scipy"
# validate Dataset keys, DataArray names, and attr keys/values
_validate_dataset_names(dataset)
_validate_attrs(dataset)
try:
store_open = WRITEABLE_STORES[engine]
except KeyError:
raise ValueError("unrecognized engine for to_netcdf: %r" % engine)
if format is not None:
format = format.upper()
# handle scheduler specific logic
scheduler = _get_scheduler()
have_chunks = any(v.chunks for v in dataset.variables.values())
autoclose = have_chunks and scheduler in ["distributed", "multiprocessing"]
if autoclose and engine == "scipy":
raise NotImplementedError(
"Writing netCDF files with the %s backend "
"is not currently supported with dask's %s "
"scheduler" % (engine, scheduler)
)
target = path_or_file if path_or_file is not None else BytesIO()
kwargs = dict(autoclose=True) if autoclose else {}
if invalid_netcdf:
if engine == "h5netcdf":
kwargs["invalid_netcdf"] = invalid_netcdf
else:
raise ValueError(
"unrecognized option 'invalid_netcdf' for engine %s" % engine
)
store = store_open(target, mode, format, group, **kwargs)
if unlimited_dims is None:
unlimited_dims = dataset.encoding.get("unlimited_dims", None)
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)
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)
if path_or_file is None:
store.sync()
return target.getvalue()
finally:
if not multifile and compute:
store.close()
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
):
"""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
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.
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="M", periods=48)},
... )
>>> ds
<xarray.Dataset>
Dimensions: (time: 48)
Coordinates:
* time (time) datetime64[ns] 2010-01-31 2010-02-28 ... 2013-12-31
Data variables:
a (time) float64 0.0 0.02128 0.04255 0.06383 ... 0.9574 0.9787 1.0
>>> years, datasets = zip(*ds.groupby("time.year"))
>>> paths = ["%s.nc" % y 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 "
"objects, received type %s" % 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
)
for ds, path, group in zip(datasets, paths, groups)
]
)
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(
[dask.delayed(_finalize_store)(w, s) for w, s in zip(writes, stores)]
)
def _validate_datatypes_for_zarr_append(dataset):
"""DataArray.name and Dataset keys must be a string or None"""
def check_dtype(var):
if (
not np.issubdtype(var.dtype, np.number)
and not np.issubdtype(var.dtype, np.datetime64)
and not np.issubdtype(var.dtype, np.bool_)
and not coding.strings.is_unicode_dtype(var.dtype)
and not var.dtype == object
):
# and not re.match('^bytes[1-9]+$', var.dtype.name)):
raise ValueError(
"Invalid dtype for data variable: {} "
"dtype must be a subtype of number, "
"datetime, bool, a fixed sized string, "
"a fixed size unicode string or an "
"object".format(var)
)
for k in dataset.data_vars.values():
check_dtype(k)
def _validate_append_dim_and_encoding(
ds_to_append, store, append_dim, region, encoding, **open_kwargs
):
try:
ds = backends.zarr.open_zarr(store, **open_kwargs)
except ValueError: # store empty
return
if append_dim:
if append_dim not in ds.dims:
raise ValueError(
f"append_dim={append_dim!r} does not match any existing "
f"dataset dimensions {ds.dims}"
)
if region is not None and append_dim in region:
raise ValueError(
f"cannot list the same dimension in both ``append_dim`` and "
f"``region`` with to_zarr(), got {append_dim} in both"
)
if region is not None:
if not isinstance(region, dict):
raise TypeError(f"``region`` must be a dict, got {type(region)}")
for k, v in region.items():
if k not in ds_to_append.dims:
raise ValueError(
f"all keys in ``region`` are not in Dataset dimensions, got "
f"{list(region)} and {list(ds_to_append.dims)}"
)
if not isinstance(v, slice):
raise TypeError(
"all values in ``region`` must be slice objects, got "
f"region={region}"
)
if v.step not in {1, None}:
raise ValueError(
"step on all slices in ``region`` must be 1 or None, got "
f"region={region}"
)
non_matching_vars = [
k
for k, v in ds_to_append.variables.items()
if not set(region).intersection(v.dims)
]
if non_matching_vars:
raise ValueError(
f"when setting `region` explicitly in to_zarr(), all "
f"variables in the dataset to write must have at least "
f"one dimension in common with the region's dimensions "
f"{list(region.keys())}, but that is not "
f"the case for some variables here. To drop these variables "
f"from this dataset before exporting to zarr, write: "
f".drop({non_matching_vars!r})"
)
for var_name, new_var in ds_to_append.variables.items():
if var_name in ds.variables:
existing_var = ds.variables[var_name]
if new_var.dims != existing_var.dims:
raise ValueError(
f"variable {var_name!r} already exists with different "
f"dimension names {existing_var.dims} != "
f"{new_var.dims}, but changing variable "
f"dimensions is not supported by to_zarr()."
)
existing_sizes = {}
for dim, size in existing_var.sizes.items():
if region is not None and dim in region:
start, stop, stride = region[dim].indices(size)
assert stride == 1 # region was already validated above
size = stop - start
if dim != append_dim:
existing_sizes[dim] = size
new_sizes = {
dim: size for dim, size in new_var.sizes.items() if dim != append_dim
}
if existing_sizes != new_sizes:
raise ValueError(
f"variable {var_name!r} already exists with different "
f"dimension sizes: {existing_sizes} != {new_sizes}. "
f"to_zarr() only supports changing dimension sizes when "
f"explicitly appending, but append_dim={append_dim!r}."
)
if var_name in encoding.keys():
raise ValueError(
f"variable {var_name!r} already exists, but encoding was provided"
)
def to_zarr(
dataset: Dataset,
store: Union[MutableMapping, str, Path] = None,
chunk_store=None,
mode: str = None,
synchronizer=None,
group: str = None,
encoding: Mapping = None,
compute: bool = True,
consolidated: bool = False,
append_dim: Hashable = None,
region: Mapping[str, slice] = None,
):
"""This function creates an appropriate datastore for writing a dataset to
a zarr ztore
See `Dataset.to_zarr` for full API docs.
"""
if isinstance(store, Path):
store = str(store)
if isinstance(chunk_store, Path):
chunk_store = str(store)
if encoding is None:
encoding = {}
if mode is None:
if append_dim is not None or region is not None:
mode = "a"
else:
mode = "w-"
if mode != "a" and append_dim is not None:
raise ValueError("cannot set append_dim unless mode='a' or mode=None")
if mode != "a" and region is not None:
raise ValueError("cannot set region unless mode='a' or mode=None")
if mode not in ["w", "w-", "a"]:
# TODO: figure out how to handle 'r+'
raise ValueError(
"The only supported options for mode are 'w', "
f"'w-' and 'a', but mode={mode!r}"
)
if consolidated and region is not None:
raise ValueError(
"cannot use consolidated=True when the region argument is set. "
"Instead, set consolidated=True when writing to zarr with "
"compute=False before writing data."
)
if isinstance(store, Path):
store = str(store)
# validate Dataset keys, DataArray names, and attr keys/values
_validate_dataset_names(dataset)
_validate_attrs(dataset)
if mode == "a":
_validate_datatypes_for_zarr_append(dataset)
_validate_append_dim_and_encoding(
dataset,
store,
append_dim,
group=group,
consolidated=consolidated,
region=region,
encoding=encoding,
)
zstore = backends.ZarrStore.open_group(
store=store,
mode=mode,
synchronizer=synchronizer,
group=group,
consolidate_on_close=consolidated,
chunk_store=chunk_store,
append_dim=append_dim,
write_region=region,
)
writer = ArrayWriter()
# TODO: figure out how to properly handle unlimited_dims
dump_to_store(dataset, zstore, writer, encoding=encoding)
writes = writer.sync(compute=compute)
if compute:
_finalize_store(writes, zstore)
else:
import dask
return dask.delayed(_finalize_store)(writes, zstore)
return zstore
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