1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238
|
"""
Functions for handling chunked arrays.
"""
from __future__ import annotations
import itertools
from collections.abc import Hashable, Mapping
from functools import lru_cache
from numbers import Number
from typing import TYPE_CHECKING, Any, Literal, TypeVar, Union, overload
from xarray.core import utils
from xarray.core.utils import emit_user_level_warning
from xarray.core.variable import IndexVariable, Variable
from xarray.namedarray.parallelcompat import (
ChunkManagerEntrypoint,
get_chunked_array_type,
guess_chunkmanager,
)
if TYPE_CHECKING:
from xarray.core.dataarray import DataArray
from xarray.core.dataset import Dataset
from xarray.core.types import T_ChunkDim
MissingCoreDimOptions = Literal["raise", "copy", "drop"]
@lru_cache(maxsize=512)
def _get_breaks_cached(
*,
size: int,
chunk_sizes: tuple[int, ...],
preferred_chunk_sizes: int | tuple[int, ...],
) -> int | None:
if isinstance(preferred_chunk_sizes, int) and preferred_chunk_sizes == 1:
# short-circuit for the trivial case
return None
# Determine the stop indices of the preferred chunks, but omit the last stop
# (equal to the dim size). In particular, assume that when a sequence
# expresses the preferred chunks, the sequence sums to the size.
preferred_stops = (
range(preferred_chunk_sizes, size, preferred_chunk_sizes)
if isinstance(preferred_chunk_sizes, int)
else set(itertools.accumulate(preferred_chunk_sizes[:-1]))
)
# Gather any stop indices of the specified chunks that are not a stop index
# of a preferred chunk. Again, omit the last stop, assuming that it equals
# the dim size.
actual_stops = itertools.accumulate(chunk_sizes[:-1])
# This copy is required for parallel iteration
actual_stops_2 = itertools.accumulate(chunk_sizes[:-1])
disagrees = itertools.compress(
actual_stops_2, (a not in preferred_stops for a in actual_stops)
)
try:
return next(disagrees)
except StopIteration:
return None
def _get_chunk(var: Variable, chunks, chunkmanager: ChunkManagerEntrypoint):
"""
Return map from each dim to chunk sizes, accounting for backend's preferred chunks.
"""
if isinstance(var, IndexVariable):
return {}
dims = var.dims
shape = var.shape
# Determine the explicit requested chunks.
preferred_chunks = var.encoding.get("preferred_chunks", {})
preferred_chunk_shape = tuple(
itertools.starmap(preferred_chunks.get, zip(dims, shape, strict=True))
)
if isinstance(chunks, Number) or (chunks == "auto"):
chunks = dict.fromkeys(dims, chunks)
chunk_shape = tuple(
chunks.get(dim, None) or preferred_chunk_sizes
for dim, preferred_chunk_sizes in zip(dims, preferred_chunk_shape, strict=True)
)
chunk_shape = chunkmanager.normalize_chunks(
chunk_shape, shape=shape, dtype=var.dtype, previous_chunks=preferred_chunk_shape
)
# Warn where requested chunks break preferred chunks, provided that the variable
# contains data.
if var.size:
for dim, size, chunk_sizes in zip(dims, shape, chunk_shape, strict=True):
try:
preferred_chunk_sizes = preferred_chunks[dim]
except KeyError:
continue
disagreement = _get_breaks_cached(
size=size,
chunk_sizes=chunk_sizes,
preferred_chunk_sizes=preferred_chunk_sizes,
)
if disagreement:
emit_user_level_warning(
"The specified chunks separate the stored chunks along "
f'dimension "{dim}" starting at index {disagreement}. This could '
"degrade performance. Instead, consider rechunking after loading.",
)
return dict(zip(dims, chunk_shape, strict=True))
def _maybe_chunk(
name: Hashable,
var: Variable,
chunks: Mapping[Any, T_ChunkDim] | None,
token=None,
lock=None,
name_prefix: str = "xarray-",
overwrite_encoded_chunks: bool = False,
inline_array: bool = False,
chunked_array_type: str | ChunkManagerEntrypoint | None = None,
from_array_kwargs=None,
) -> Variable:
from xarray.namedarray.daskmanager import DaskManager
if chunks is not None:
chunks = {dim: chunks[dim] for dim in var.dims if dim in chunks}
if var.ndim:
chunked_array_type = guess_chunkmanager(
chunked_array_type
) # coerce string to ChunkManagerEntrypoint type
if isinstance(chunked_array_type, DaskManager):
from dask.base import tokenize
# when rechunking by different amounts, make sure dask names change
# by providing chunks as an input to tokenize.
# subtle bugs result otherwise. see GH3350
# we use str() for speed, and use the name for the final array name on the next line
token2 = tokenize(token or var._data, str(chunks))
name2 = f"{name_prefix}{name}-{token2}"
from_array_kwargs = utils.consolidate_dask_from_array_kwargs(
from_array_kwargs,
name=name2,
lock=lock,
inline_array=inline_array,
)
var = var.chunk(
chunks,
chunked_array_type=chunked_array_type,
from_array_kwargs=from_array_kwargs,
)
if overwrite_encoded_chunks and var.chunks is not None:
var.encoding["chunks"] = tuple(x[0] for x in var.chunks)
return var
else:
return var
_T = TypeVar("_T", bound=Union["Dataset", "DataArray"])
_U = TypeVar("_U", bound=Union["Dataset", "DataArray"])
_V = TypeVar("_V", bound=Union["Dataset", "DataArray"])
@overload
def unify_chunks(obj: _T, /) -> tuple[_T]: ...
@overload
def unify_chunks(obj1: _T, obj2: _U, /) -> tuple[_T, _U]: ...
@overload
def unify_chunks(obj1: _T, obj2: _U, obj3: _V, /) -> tuple[_T, _U, _V]: ...
@overload
def unify_chunks(*objects: Dataset | DataArray) -> tuple[Dataset | DataArray, ...]: ...
def unify_chunks(*objects: Dataset | DataArray) -> tuple[Dataset | DataArray, ...]:
"""
Given any number of Dataset and/or DataArray objects, returns
new objects with unified chunk size along all chunked dimensions.
Returns
-------
unified (DataArray or Dataset) – Tuple of objects with the same type as
*objects with consistent chunk sizes for all dask-array variables
See Also
--------
dask.array.core.unify_chunks
"""
from xarray.core.dataarray import DataArray
# Convert all objects to datasets
datasets = [
obj._to_temp_dataset() if isinstance(obj, DataArray) else obj.copy()
for obj in objects
]
# Get arguments to pass into dask.array.core.unify_chunks
unify_chunks_args = []
sizes: dict[Hashable, int] = {}
for ds in datasets:
for v in ds._variables.values():
if v.chunks is not None:
# Check that sizes match across different datasets
for dim, size in v.sizes.items():
try:
if sizes[dim] != size:
raise ValueError(
f"Dimension {dim!r} size mismatch: {sizes[dim]} != {size}"
)
except KeyError:
sizes[dim] = size
unify_chunks_args += [v._data, v._dims]
# No dask arrays: Return inputs
if not unify_chunks_args:
return objects
chunkmanager = get_chunked_array_type(*list(unify_chunks_args))
_, chunked_data = chunkmanager.unify_chunks(*unify_chunks_args)
chunked_data_iter = iter(chunked_data)
out: list[Dataset | DataArray] = []
for obj, ds in zip(objects, datasets, strict=True):
for k, v in ds._variables.items():
if v.chunks is not None:
ds._variables[k] = v.copy(data=next(chunked_data_iter))
out.append(obj._from_temp_dataset(ds) if isinstance(obj, DataArray) else ds)
return tuple(out)
|