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compressedarray.py
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compressedarray.py
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import numpy as np
from .array import Array
class DeprecationError(Exception):
"""Deprecation error."""
pass
class CompressedArray(Array):
"""Mixin class for a container of an underlying compressed array.
.. versionadded:: (cfdm) 1.7.0
"""
def __new__(cls, *args, **kwargs):
"""Store subarray classes.
A child class must define its subarray classes in the
`_Subarray` dictionary.
.. versionadded:: (cfdm) 1.10.0.0
"""
instance = super().__new__(cls)
instance._Subarray = {}
return instance
def __init__(
self,
compressed_array=None,
shape=None,
size=None,
ndim=None,
compressed_dimension=None,
compressed_dimensions=None,
compression_type=None,
source=None,
copy=True,
):
"""**Initialisation**
:Parameters:
compressed_array: array_like
The compressed array.
shape: `tuple`
The uncompressed array dimension sizes.
compressed_dimensions: `dict`
Mapping of dimensions of the compressed array to their
corresponding dimensions in the uncompressed
array. Compressed array dimensions that are not
compressed must be omitted from the mapping.
*Parameter example:*
``{0: (0, 1)}``
*Parameter example:*
``{0: (0, 1, 2)}``
*Parameter example:*
``{2: (2, 3)}``
*Parameter example:*
``{1: (1,)}``
*Parameter example:*
``{0: (0,), 2: (2,)}``
.. versionadded:: (cfdm) 1.10.0.0
compression_type: `str`
The type of compression.
kwargs: optional
Further named parameters and their values needed to define
the compressed array.
compressed_dimension: Deprecated at version 1.10.0.0
Use the *compressed_dimensions* parameter instead.
{{init source: optional}}
.. versionadded:: (cfdm) 1.10.0.0
copy: `bool`, optional
If True (the default) then deep copy input parameters
prior to initialisation. If False then arguments are
not deep copied.
.. versionadded:: (cfdm) 1.10.0.0
size: `int`
Deprecated at version 1.10.0.0. If set will be
ignored.
Number of elements in the uncompressed array.
ndim: `int`
Deprecated at version 1.10.0.0. If set will be
ignored.
The number of uncompressed array dimensions
"""
if compressed_dimension is not None:
raise DeprecationError(
"The 'compressed_dimension' keyword was deprecated at "
"version 1.10.0.0. "
"Use the 'compressed_dimensions' keyword instead."
) # pragma: no cover
super().__init__(source=source, copy=copy)
if source is not None:
try:
compressed_array = source._get_compressed_Array(None)
except AttributeError:
compressed_array = None
try:
compression_type = source.get_compression_type()
except AttributeError:
compression_type = None
try:
compressed_dimensions = source.compressed_dimensions()
except AttributeError:
compressed_dimensions = {}
try:
shape = source.shape
except AttributeError:
shape = None
elif compressed_dimensions is None:
compressed_dimensions = {}
else:
compressed_dimensions = compressed_dimensions.copy()
self._set_component(
"compressed_dimensions", compressed_dimensions, copy=False
)
if compressed_array is not None:
self._set_compressed_Array(compressed_array, copy=copy)
if shape is not None:
self._set_component("shape", shape, copy=False)
if compression_type:
self._set_component(
"compression_type", compression_type, copy=False
)
def __getitem__(self, indices):
"""Return a subspace of the uncompressed data.
x.__getitem__(indices) <==> x[indices]
Returns a subspace of the uncompressed array as an independent
numpy array.
.. versionadded:: (cfdm) 1.11.0.0
"""
# ------------------------------------------------------------
# Method: Uncompress the entire array and then subspace it
# ------------------------------------------------------------
# Initialise the un-sliced uncompressed array
u = np.ma.masked_all(self.shape, dtype=self.dtype)
Subarray = self.get_Subarray()
subarray_kwargs = {
**self.conformed_data(),
**self.subarray_parameters(),
}
for u_indices, u_shape, c_indices, _ in zip(*self.subarrays()):
subarray = Subarray(
indices=c_indices,
shape=u_shape,
**subarray_kwargs,
)
u[u_indices] = subarray[...]
if indices is Ellipsis:
return u
return self.get_subspace(u, indices, copy=True)
def _first_or_last_element(self, indices):
"""Return the first or last element of the compressed array.
This method will return the first or last element of the
compressed array without performing any decompression.
First and last elements are only recognised by exact *indices*
matches to:
* ``(slice(0, 1, 1),) * self.ndim``
* ``(slice(-1, None, 1),) * self.ndim``
Any other value of indices will raise an `IndexError`. For
instance, note that ``slice(0, 1, 1)`` is not an exact match
to ``slice(0, 1)``.
.. versionadded:: (cfdm) 1.10.0.0
.. seealso:: `__getitem__`
:Parameters:
indices:
Indices to the uncompressed array.
:Returns:
`numpy.ndarray`
The first or last element. If the *indices* do not
acceptably select the first or last element then an
`IndexError` is raised.
"""
ndim = self.ndim
for index in (slice(0, 1, 1), slice(-1, None, 1)):
if indices == (index,) * ndim:
data = self.source()
return np.asanyarray(data[(index,) * data.ndim])
# Indices do not acceptably select the first nor last element
raise IndexError()
def _get_compressed_Array(self, default=ValueError()):
"""Return the compressed array.
:Parameters:
default: optional
Return the value of the *default* parameter if the array
has not been set. If set to an `Exception` instance then
it will be raised instead.
:Returns:
The compressed Array instance.
**Examples**
>>> c = d._get_compressed_Array()
"""
return self._get_component("compressed_Array", default)
def _set_compressed_Array(self, array, copy=True):
"""Set the compressed array.
.. versionadded:: (cfdm) 1.7.0
:Parameters:
array: subclass of `cfdm.data.Array`
The compressed data to be inserted.
:Returns:
`None`
**Examples**
>>> d._set_compressed_Array(a)
"""
if copy:
array = array.copy()
self._set_component("compressed_Array", array, copy=False)
@property
def array(self):
"""Returns a numpy array containing the uncompressed data.
:Returns:
`numpy.ndarray`
The uncompressed array.
**Examples**
>>> n = a.array
>>> isinstance(n, numpy.ndarray)
True
"""
return self[...]
@property
def dtype(self):
"""Data-type of the uncompressed data."""
raise NotImplementedError(
f"Must implement {self.__class__.__name__}.dtype"
) # pragma: no cover
@property
def shape(self):
"""Shape of the uncompressed data."""
return self._get_component("shape")
@property
def compressed_array(self):
"""Returns an independent numpy array with the compressed data.
:Returns:
`numpy.ndarray`
The compressed array.
**Examples**
>>> n = a.compressed_array
>>> isinstance(n, numpy.ndarray)
True
"""
ca = self._get_compressed_Array(None)
if ca is None:
raise ValueError("There is no underlying compressed array")
return ca.array
def get_compressed_axes(self):
"""Return axes that are compressed in the underlying array.
:Returns:
`list`
The compressed axes described by their integer
positions in the uncompressed array.
**Examples**
>>> c.ndim
4
>>> c.compressed_array.ndim
3
>>> c.compressed_axes()
[1, 2]
"""
return sorted(
{x for y in self.compressed_dimensions().values() for x in y}
)
def get_compressed_dimension(self, default=ValueError()):
"""Returns the compressed dimension's position in the array.
.. versionadded:: (cfdm) 1.7.0
.. seealso:: `get_compressed_axes`, `get_compression_type`
:Parameters:
default: optional
Return the value of the *default* parameter if the
underlying array is not compressed. If set to an
`Exception` instance then it will be raised instead.
:Returns:
`int`
The position of the compressed dimension in the compressed
array. If the underlying is not compressed then *default*
is returned, if provided.
**Examples**
>>> i = d.get_compressed_dimension()
"""
compressed_dimensions = self.compressed_dimensions()
if len(compressed_dimensions) != 1:
raise ValueError(
"Can't get unique compressed dimension when there "
f"is not exactly one of them: {self.compressed_dimensions()}"
)
return tuple(compressed_dimensions)[0]
def compressed_dimensions(self):
"""Mapping of compressed to uncompressed dimensions.
A dictionary key is a position of a dimension in the
compressed data, with a value of the positions of the
corresponding dimensions in the uncompressed data. Compressed
array dimensions that are not compressed are omitted from the
mapping.
.. versionadded:: (cfdm) 1.10.0.0
.. seealso:: `get_compressed_axes`, `get_compression_type`
:Returns:
`dict`
The mapping of dimensions of the compressed array to
their corresponding dimensions in the uncompressed
array. Compressed array dimensions that are not
compressed are omitted from the mapping.
"""
c = self._get_component("compressed_dimensions")
if not c:
raise ValueError("No compressed dimensions have been defined")
return self._get_component("compressed_dimensions").copy()
def conformed_data(self):
"""The data as required by the decompression algorithm.
.. versionadded:: (cfdm) 1.10.0.0
:Returns:
`dict`
The compressed data, with the key ``'data'``.
"""
return {"data": self.source().copy()}
def get_filenames(self):
"""Return the names of any files containing the compressed data.
.. versionadded:: (cfdm) 1.10.0.2
:Returns:
`set`
The file names in normalised, absolute form. If the
data are all in memory then an empty `set` is
returned.
"""
data = self._get_compressed_Array(None)
if data is None:
return set()
try:
return data.get_filenames()
except AttributeError:
return set()
def get_Subarray(self):
"""Return the Subarray class.
.. versionadded:: (cfdm) 1.10.0.0
:Returns:
`Subarray`
The class for representing subarrays.
"""
return self._Subarray[self.get_compression_type()]
def source(self, default=ValueError()):
"""Return the underlying array object.
:Parameters:
default: optional
Return the value of the *default* parameter if the array
has not been set. If set to an `Exception` instance then
it will be raised instead.
:Returns:
subclass of `Array`
The underlying array object.
**Examples**
>>> array
<RaggedContiguousArray(2, 4): >
>>> array.source()
<Data(5): [280.0, ..., 279.5]>
"""
return self._get_compressed_Array(default=default)
def subarray_parameters(self):
"""Non-data parameters required by the `Subarray` class.
.. versionadded:: (cfdm) 1.11.0.0
:Returns:
`dict`
The parameters as a dictionary value, with key
``'compressed_dimensions'``.
"""
return {"compressed_dimensions": self.compressed_dimensions()}
def subarray_shapes(self, shapes):
"""Create the subarray shapes along each uncompressed dimension.
.. versionadded:: (cfdm) 1.10.0.0
.. seealso:: `subarray`
:Parameters:
{{subarray_shapes chunks: `int`, sequence, `dict`, or `str`, optional}}
:Returns:
`list`
The subarray shapes along each uncompressed
dimension.
"""
raise NotImplementedError(
f"Must implement {self.__class__.__name__}.subarray_shapes"
) # pragma: no cover
def subarrays(self, shapes=-1):
"""Return descriptors for every subarray.
Theses descriptors are used during subarray decompression.
.. versionadded:: (cfdm) 1.10.0.0
:Parameters:
{{subarrays chunks: ``-1`` or sequence, optional}}
:Returns:
sequence of iterable
Each iterable iterates over a particular descriptor
from each subarray.
"""
raise NotImplementedError(
f"Must implement {self.__class__.__name__}.subarrays"
) # pragma: no cover
def to_memory(self):
"""Bring data on disk into memory.
There is no change to data that is already in memory.
.. versionadded:: (cfdm) 1.10.0.0
:Returns:
`{{class}}`
A copy of the array with all of its data in memory.
"""
a = self.copy()
try:
a._set_compressed_Array(a.source().to_memory(), copy=False)
except AttributeError:
pass
return a