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from io import BytesIO
import numpy as np
from ..core.indexing import NumpyIndexingAdapter
from ..core.utils import Frozen, FrozenDict
from ..core.variable import Variable
from .common import BackendArray, WritableCFDataStore
from .file_manager import CachingFileManager, DummyFileManager
from .locks import ensure_lock, get_write_lock
from .netcdf3 import encode_nc3_attr_value, encode_nc3_variable, is_valid_nc3_name
def _decode_string(s):
if isinstance(s, bytes):
return s.decode("utf-8", "replace")
return s
def _decode_attrs(d):
# don't decode _FillValue from bytes -> unicode, because we want to ensure
# that its type matches the data exactly
return {k: v if k == "_FillValue" else _decode_string(v) for (k, v) in d.items()}
class ScipyArrayWrapper(BackendArray):
def __init__(self, variable_name, datastore):
self.datastore = datastore
self.variable_name = variable_name
array = self.get_variable().data
self.shape = array.shape
self.dtype = np.dtype(array.dtype.kind + str(array.dtype.itemsize))
def get_variable(self, needs_lock=True):
ds = self.datastore._manager.acquire(needs_lock)
return ds.variables[self.variable_name]
def __getitem__(self, key):
data = NumpyIndexingAdapter(self.get_variable().data)[key]
# Copy data if the source file is mmapped. This makes things consistent
# with the netCDF4 library by ensuring we can safely read arrays even
# after closing associated files.
copy = self.datastore.ds.use_mmap
return np.array(data, dtype=self.dtype, copy=copy)
def __setitem__(self, key, value):
with self.datastore.lock:
data = self.get_variable(needs_lock=False)
try:
data[key] = value
except TypeError:
if key is Ellipsis:
# workaround for GH: scipy/scipy#6880
data[:] = value
else:
raise
def _open_scipy_netcdf(filename, mode, mmap, version):
import gzip
import scipy.io
# if the string ends with .gz, then gunzip and open as netcdf file
if isinstance(filename, str) and filename.endswith(".gz"):
try:
return scipy.io.netcdf_file(
gzip.open(filename), mode=mode, mmap=mmap, version=version
)
except TypeError as e:
# TODO: gzipped loading only works with NetCDF3 files.
if "is not a valid NetCDF 3 file" in e.message:
raise ValueError("gzipped file loading only supports NetCDF 3 files.")
else:
raise
if isinstance(filename, bytes) and filename.startswith(b"CDF"):
# it's a NetCDF3 bytestring
filename = BytesIO(filename)
try:
return scipy.io.netcdf_file(filename, mode=mode, mmap=mmap, version=version)
except TypeError as e: # netcdf3 message is obscure in this case
errmsg = e.args[0]
if "is not a valid NetCDF 3 file" in errmsg:
msg = """
If this is a NetCDF4 file, you may need to install the
netcdf4 library, e.g.,
$ pip install netcdf4
"""
errmsg += msg
raise TypeError(errmsg)
else:
raise
class ScipyDataStore(WritableCFDataStore):
"""Store for reading and writing data via scipy.io.netcdf.
This store has the advantage of being able to be initialized with a
StringIO object, allow for serialization without writing to disk.
It only supports the NetCDF3 file-format.
"""
def __init__(
self, filename_or_obj, mode="r", format=None, group=None, mmap=None, lock=None
):
if group is not None:
raise ValueError("cannot save to a group with the scipy.io.netcdf backend")
if format is None or format == "NETCDF3_64BIT":
version = 2
elif format == "NETCDF3_CLASSIC":
version = 1
else:
raise ValueError("invalid format for scipy.io.netcdf backend: %r" % format)
if lock is None and mode != "r" and isinstance(filename_or_obj, str):
lock = get_write_lock(filename_or_obj)
self.lock = ensure_lock(lock)
if isinstance(filename_or_obj, str):
manager = CachingFileManager(
_open_scipy_netcdf,
filename_or_obj,
mode=mode,
lock=lock,
kwargs=dict(mmap=mmap, version=version),
)
else:
scipy_dataset = _open_scipy_netcdf(
filename_or_obj, mode=mode, mmap=mmap, version=version
)
manager = DummyFileManager(scipy_dataset)
self._manager = manager
@property
def ds(self):
return self._manager.acquire()
def open_store_variable(self, name, var):
return Variable(
var.dimensions,
ScipyArrayWrapper(name, self),
_decode_attrs(var._attributes),
)
def get_variables(self):
return FrozenDict(
(k, self.open_store_variable(k, v)) for k, v in self.ds.variables.items()
)
def get_attrs(self):
return Frozen(_decode_attrs(self.ds._attributes))
def get_dimensions(self):
return Frozen(self.ds.dimensions)
def get_encoding(self):
encoding = {}
encoding["unlimited_dims"] = {
k for k, v in self.ds.dimensions.items() if v is None
}
return encoding
def set_dimension(self, name, length, is_unlimited=False):
if name in self.ds.dimensions:
raise ValueError(
"%s does not support modifying dimensions" % type(self).__name__
)
dim_length = length if not is_unlimited else None
self.ds.createDimension(name, dim_length)
def _validate_attr_key(self, key):
if not is_valid_nc3_name(key):
raise ValueError("Not a valid attribute name")
def set_attribute(self, key, value):
self._validate_attr_key(key)
value = encode_nc3_attr_value(value)
setattr(self.ds, key, value)
def encode_variable(self, variable):
variable = encode_nc3_variable(variable)
return variable
def prepare_variable(
self, name, variable, check_encoding=False, unlimited_dims=None
):
if check_encoding and variable.encoding:
if variable.encoding != {"_FillValue": None}:
raise ValueError(
"unexpected encoding for scipy backend: %r"
% list(variable.encoding)
)
data = variable.data
# nb. this still creates a numpy array in all memory, even though we
# don't write the data yet; scipy.io.netcdf does not not support
# incremental writes.
if name not in self.ds.variables:
self.ds.createVariable(name, data.dtype, variable.dims)
scipy_var = self.ds.variables[name]
for k, v in variable.attrs.items():
self._validate_attr_key(k)
setattr(scipy_var, k, v)
target = ScipyArrayWrapper(name, self)
return target, data
def sync(self):
self.ds.sync()
def close(self):
self._manager.close()
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