import logging
import time
import traceback
import warnings
from collections.abc import Mapping
import numpy as np
from ..conventions import cf_encoder
from ..core import indexing
from ..core.pycompat import dask_array_type
from ..core.utils import FrozenDict, NdimSizeLenMixin
# Create a logger object, but don't add any handlers. Leave that to user code.
logger = logging.getLogger(__name__)
NONE_VAR_NAME = "__values__"
def _encode_variable_name(name):
if name is None:
name = NONE_VAR_NAME
return name
def _decode_variable_name(name):
if name == NONE_VAR_NAME:
name = None
return name
def find_root_and_group(ds):
"""Find the root and group name of a netCDF4/h5netcdf dataset."""
hierarchy = ()
while ds.parent is not None:
hierarchy = (ds.name.split("/")[-1],) + hierarchy
ds = ds.parent
group = "/" + "/".join(hierarchy)
return ds, group
def robust_getitem(array, key, catch=Exception, max_retries=6, initial_delay=500):
"""
Robustly index an array, using retry logic with exponential backoff if any
of the errors ``catch`` are raised. The initial_delay is measured in ms.
With the default settings, the maximum delay will be in the range of 32-64
seconds.
"""
assert max_retries >= 0
for n in range(max_retries + 1):
try:
return array[key]
except catch:
if n == max_retries:
raise
base_delay = initial_delay * 2 ** n
next_delay = base_delay + np.random.randint(base_delay)
msg = (
"getitem failed, waiting %s ms before trying again "
"(%s tries remaining). Full traceback: %s"
% (next_delay, max_retries - n, traceback.format_exc())
)
logger.debug(msg)
time.sleep(1e-3 * next_delay)
class BackendArray(NdimSizeLenMixin, indexing.ExplicitlyIndexed):
__slots__ = ()
def __array__(self, dtype=None):
key = indexing.BasicIndexer((slice(None),) * self.ndim)
return np.asarray(self[key], dtype=dtype)
class AbstractDataStore(Mapping):
__slots__ = ()
def __iter__(self):
return iter(self.variables)
def __getitem__(self, key):
return self.variables[key]
def __len__(self):
return len(self.variables)
def get_dimensions(self): # pragma: no cover
raise NotImplementedError()
def get_attrs(self): # pragma: no cover
raise NotImplementedError()
def get_variables(self): # pragma: no cover
raise NotImplementedError()
def get_encoding(self):
return {}
def load(self):
"""
This loads the variables and attributes simultaneously.
A centralized loading function makes it easier to create
data stores that do automatic encoding/decoding.
For example::
class SuffixAppendingDataStore(AbstractDataStore):
def load(self):
variables, attributes = AbstractDataStore.load(self)
variables = {'%s_suffix' % k: v
for k, v in variables.items()}
attributes = {'%s_suffix' % k: v
for k, v in attributes.items()}
return variables, attributes
This function will be called anytime variables or attributes
are requested, so care should be taken to make sure its fast.
"""
variables = FrozenDict(
(_decode_variable_name(k), v) for k, v in self.get_variables().items()
)
attributes = FrozenDict(self.get_attrs())
return variables, attributes
@property
def variables(self): # pragma: no cover
warnings.warn(
"The ``variables`` property has been deprecated and "
"will be removed in xarray v0.11.",
FutureWarning,
stacklevel=2,
)
variables, _ = self.load()
return variables
@property
def attrs(self): # pragma: no cover
warnings.warn(
"The ``attrs`` property has been deprecated and "
"will be removed in xarray v0.11.",
FutureWarning,
stacklevel=2,
)
_, attrs = self.load()
return attrs
@property
def dimensions(self): # pragma: no cover
warnings.warn(
"The ``dimensions`` property has been deprecated and "
"will be removed in xarray v0.11.",
FutureWarning,
stacklevel=2,
)
return self.get_dimensions()
def close(self):
pass
def __enter__(self):
return self
def __exit__(self, exception_type, exception_value, traceback):
self.close()
class ArrayWriter:
__slots__ = ("sources", "targets", "regions", "lock")
def __init__(self, lock=None):
self.sources = []
self.targets = []
self.regions = []
self.lock = lock
def add(self, source, target, region=None):
if isinstance(source, dask_array_type):
self.sources.append(source)
self.targets.append(target)
self.regions.append(region)
else:
if region:
target[region] = source
else:
target[...] = source
def sync(self, compute=True):
if self.sources:
import dask.array as da
# TODO: consider wrapping targets with dask.delayed, if this makes
# for any discernable difference in perforance, e.g.,
# targets = [dask.delayed(t) for t in self.targets]
delayed_store = da.store(
self.sources,
self.targets,
lock=self.lock,
compute=compute,
flush=True,
regions=self.regions,
)
self.sources = []
self.targets = []
self.regions = []
return delayed_store
class AbstractWritableDataStore(AbstractDataStore):
__slots__ = ()
def encode(self, variables, attributes):
"""
Encode the variables and attributes in this store
Parameters
----------
variables : dict-like
Dictionary of key/value (variable name / xr.Variable) pairs
attributes : dict-like
Dictionary of key/value (attribute name / attribute) pairs
Returns
-------
variables : dict-like
attributes : dict-like
"""
variables = {k: self.encode_variable(v) for k, v in variables.items()}
attributes = {k: self.encode_attribute(v) for k, v in attributes.items()}
return variables, attributes
def encode_variable(self, v):
"""encode one variable"""
return v
def encode_attribute(self, a):
"""encode one attribute"""
return a
def set_dimension(self, dim, length): # pragma: no cover
raise NotImplementedError()
def set_attribute(self, k, v): # pragma: no cover
raise NotImplementedError()
def set_variable(self, k, v): # pragma: no cover
raise NotImplementedError()
def store_dataset(self, dataset):
"""
in stores, variables are all variables AND coordinates
in xarray.Dataset variables are variables NOT coordinates,
so here we pass the whole dataset in instead of doing
dataset.variables
"""
self.store(dataset, dataset.attrs)
def store(
self,
variables,
attributes,
check_encoding_set=frozenset(),
writer=None,
unlimited_dims=None,
):
"""
Top level method for putting data on this store, this method:
- encodes variables/attributes
- sets dimensions
- sets variables
Parameters
----------
variables : dict-like
Dictionary of key/value (variable name / xr.Variable) pairs
attributes : dict-like
Dictionary of key/value (attribute name / attribute) pairs
check_encoding_set : list-like
List of variables that should be checked for invalid encoding
values
writer : ArrayWriter
unlimited_dims : list-like
List of dimension names that should be treated as unlimited
dimensions.
"""
if writer is None:
writer = ArrayWriter()
variables, attributes = self.encode(variables, attributes)
self.set_attributes(attributes)
self.set_dimensions(variables, unlimited_dims=unlimited_dims)
self.set_variables(
variables, check_encoding_set, writer, unlimited_dims=unlimited_dims
)
def set_attributes(self, attributes):
"""
This provides a centralized method to set the dataset attributes on the
data store.
Parameters
----------
attributes : dict-like
Dictionary of key/value (attribute name / attribute) pairs
"""
for k, v in attributes.items():
self.set_attribute(k, v)
def set_variables(self, variables, check_encoding_set, writer, unlimited_dims=None):
"""
This provides a centralized method to set the variables on the data
store.
Parameters
----------
variables : dict-like
Dictionary of key/value (variable name / xr.Variable) pairs
check_encoding_set : list-like
List of variables that should be checked for invalid encoding
values
writer : ArrayWriter
unlimited_dims : list-like
List of dimension names that should be treated as unlimited
dimensions.
"""
for vn, v in variables.items():
name = _encode_variable_name(vn)
check = vn in check_encoding_set
target, source = self.prepare_variable(
name, v, check, unlimited_dims=unlimited_dims
)
writer.add(source, target)
def set_dimensions(self, variables, unlimited_dims=None):
"""
This provides a centralized method to set the dimensions on the data
store.
Parameters
----------
variables : dict-like
Dictionary of key/value (variable name / xr.Variable) pairs
unlimited_dims : list-like
List of dimension names that should be treated as unlimited
dimensions.
"""
if unlimited_dims is None:
unlimited_dims = set()
existing_dims = self.get_dimensions()
dims = {}
for v in unlimited_dims: # put unlimited_dims first
dims[v] = None
for v in variables.values():
dims.update(dict(zip(v.dims, v.shape)))
for dim, length in dims.items():
if dim in existing_dims and length != existing_dims[dim]:
raise ValueError(
"Unable to update size for existing dimension"
"%r (%d != %d)" % (dim, length, existing_dims[dim])
)
elif dim not in existing_dims:
is_unlimited = dim in unlimited_dims
self.set_dimension(dim, length, is_unlimited)
class WritableCFDataStore(AbstractWritableDataStore):
__slots__ = ()
def encode(self, variables, attributes):
# All NetCDF files get CF encoded by default, without this attempting
# to write times, for example, would fail.
variables, attributes = cf_encoder(variables, attributes)
variables = {k: self.encode_variable(v) for k, v in variables.items()}
attributes = {k: self.encode_attribute(v) for k, v in attributes.items()}
return variables, attributes