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import sys
import h5py
import numpy as np
from . import core
#: default netcdf fillvalues
default_fillvals = {
"S1": "\x00",
"i1": -127,
"u1": 255,
"i2": -32767,
"u2": 65535,
"i4": -2147483647,
"u4": 4294967295,
"i8": -9223372036854775806,
"u8": 18446744073709551614,
"f4": 9.969209968386869e36,
"f8": 9.969209968386869e36,
}
def _get_default_fillvalue(dtype):
kind = np.dtype(dtype).kind
fillvalue = None
if kind in ["u", "i", "f"]:
size = np.dtype(dtype).itemsize
fillvalue = default_fillvals[f"{kind}{size}"]
return fillvalue
def _check_return_dtype_endianess(endian="native"):
little_endian = sys.byteorder == "little"
endianess = "="
if endian == "little":
endianess = little_endian and endianess or "<"
elif endian == "big":
endianess = not little_endian and endianess or ">"
elif endian == "native":
pass
else:
raise ValueError(
f"'endian' keyword argument must be 'little','big' or 'native', got '{endian}'"
)
return endianess
class HasAttributesMixin:
_initialized = False
def getncattr(self, name):
"""Retrieve a netCDF4 attribute."""
return self.attrs[name]
def setncattr(self, name, value):
"""Set a netCDF4 attribute."""
self.attrs[name] = value
def ncattrs(self):
"""Return netCDF4 attribute names."""
return list(self.attrs)
def __getattr__(self, name):
try:
return self.attrs[name]
except KeyError:
raise AttributeError(
f"NetCDF: attribute {type(self).__name__}:{name} not found"
)
def __setattr__(self, name, value):
if self._initialized and name not in self.__dict__:
self.attrs[name] = value
else:
object.__setattr__(self, name, value)
class Variable(core.BaseVariable, HasAttributesMixin):
_cls_name = "h5netcdf.legacyapi.Variable"
def chunking(self):
"""Return variable chunking information.
The chunksize is returned as a sequence with the size for each dimension.
If the dataset is defined to be contiguous (no chunking) the word 'contiguous'
is returned.
"""
chunks = self._h5ds.chunks
if chunks is None:
return "contiguous"
else:
return chunks
def filters(self):
"""Return HDF5 filter parameters dictionary."""
complevel = self._h5ds.compression_opts
return {
"complevel": 0 if complevel is None else complevel,
"fletcher32": self._h5ds.fletcher32,
"shuffle": self._h5ds.shuffle,
"zlib": self._h5ds.compression == "gzip",
}
@property
def dtype(self):
"""Return netCDF4.Variable numpy dtype."""
dt = self._h5ds.dtype
if h5py.check_dtype(vlen=dt) is str:
return str
return dt
class EnumType(core.EnumType):
_cls_name = "h5netcdf.legacyapi.EnumType"
class VLType(core.VLType):
_cls_name = "h5netcdf.legacyapi.VLType"
class CompoundType(core.CompoundType):
_cls_name = "h5netcdf.legacyapi.CompoundType"
class UserType(core.UserType):
_cls_name = "h5netcdf.legacyapi.UserType"
class Group(core.Group, HasAttributesMixin):
_cls_name = "h5netcdf.legacyapi.Group"
_variable_cls = Variable
_enumtype_cls = EnumType
_vltype_cls = VLType
_cmptype_cls = CompoundType
@property
def _group_cls(self):
return Group
createGroup = core.Group.create_group
createEnumType = core.Group.create_enumtype
createVLType = core.Group.create_vltype
createCompoundType = core.Group.create_cmptype
def createDimension(self, name, size):
"""Creates a new dimension with given name and size.
Parameters
----------
name : str
Dimension name
size : int, None
size must be a positive integer or None (unlimited).
Specifying size=0 results in an unlimited dimension too.
Returns
-------
dim : h5netcdf.legacyapi.Dimension
Dimension class instance.
"""
self._dimensions[name] = size
return self._dimensions[name]
def createVariable(
self,
varname,
datatype,
dimensions=(),
zlib=False,
complevel=4,
shuffle=True,
fletcher32=False,
chunksizes=None,
fill_value=None,
endian="native",
):
"""Creates a new variable.
Parameters
----------
varname : str
Name of the new variable. If given as a path, intermediate groups will be created,
if not existent.
datatype : numpy.dtype, str, UserType (Enum, VL, Compound)
Datatype of the new variable.
dimensions : tuple
Tuple containing dimension name strings. Defaults to empty tuple, effectively
creating a scalar variable.
zlib : bool, optional
If ``True``, variable data will be gzip compressed.
complevel : int, optional
Integer between 1 and 9 defining compression level. Defaults to 4.
Ignored if ``zlib=False``.
shuffle : bool, optional
If ``True``, HDF5 shuffle filter will be applied. Defaults to ``True``.
Ignored if ``zlib=False``.
fletcher32 : bool, optional
If ``True``, HDF5 Fletcher32 checksum algorithm is applied. Defaults to ``False``.
chunksizes : tuple, optional
Tuple of integers specifying the chunksizes of each variable dimension.
Discussion on ``h5netcdf`` chunksizes can be found in (:issue:`52`) and (:pull:`127`).
fill_value : scalar, optional
Specify ``_FillValue`` for uninitialized parts of the variable. Defaults to ``None``.
endian : str, optional
Control on-disk storage format.
Can be any of ``little``, ``big`` or ``native`` (default).
Returns
-------
var : h5netcdf.legacyapi.Variable
Variable class instance
"""
if len(dimensions) == 0: # it's a scalar
# rip off chunk and filter options for consistency with netCDF4-python
chunksizes = None
zlib = False
fletcher32 = False
shuffle = False
if datatype is str:
datatype = h5py.special_dtype(vlen=str)
kwds = {}
if zlib:
# only add compression related keyword arguments if relevant (h5py
# chokes otherwise)
kwds["compression"] = "gzip"
kwds["compression_opts"] = complevel
kwds["shuffle"] = shuffle
# control endian-ess
endianess = _check_return_dtype_endianess(endian)
# needs swapping?
if endianess != "=":
# transform to numpy dtype and swap endianess
dtype = np.dtype(datatype)
if dtype.byteorder != "|":
datatype = dtype.newbyteorder("S")
# closer to netCDF4 chunking behavior
kwds["chunking_heuristic"] = "h5netcdf"
return super().create_variable(
varname,
dimensions,
dtype=datatype,
fletcher32=fletcher32,
chunks=chunksizes,
fillvalue=fill_value,
**kwds,
)
class Dimension(core.Dimension):
_cls_name = "h5netcdf.legacyapi.Dimensions"
class Dataset(core.File, Group, HasAttributesMixin):
_cls_name = "h5netcdf.legacyapi.Dataset"
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