File: common.py

package info (click to toggle)
python-xarray 2023.01.0-1.1
  • links: PTS, VCS
  • area: main
  • in suites: bookworm
  • size: 8,980 kB
  • sloc: python: 86,209; makefile: 232; sh: 47
file content (430 lines) | stat: -rw-r--r-- 13,556 bytes parent folder | download
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
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
from __future__ import annotations

import logging
import os
import time
import traceback
from typing import TYPE_CHECKING, Any, ClassVar, Iterable

import numpy as np

from xarray.conventions import cf_encoder
from xarray.core import indexing
from xarray.core.pycompat import is_duck_dask_array
from xarray.core.utils import FrozenDict, NdimSizeLenMixin, is_remote_uri

if TYPE_CHECKING:
    from io import BufferedIOBase

# Create a logger object, but don't add any handlers. Leave that to user code.
logger = logging.getLogger(__name__)


NONE_VAR_NAME = "__values__"


def _normalize_path(path):
    if isinstance(path, os.PathLike):
        path = os.fspath(path)

    if isinstance(path, str) and not is_remote_uri(path):
        path = os.path.abspath(os.path.expanduser(path))

    return path


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 = (
                f"getitem failed, waiting {next_delay} ms before trying again "
                f"({max_retries - n} tries remaining). Full traceback: {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:
    __slots__ = ()

    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

    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 is_duck_dask_array(source):
            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 discernible 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"
                    f"{dim!r} ({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


class BackendEntrypoint:
    """
    ``BackendEntrypoint`` is a class container and it is the main interface
    for the backend plugins, see :ref:`RST backend_entrypoint`.
    It shall implement:

    - ``open_dataset`` method: it shall implement reading from file, variables
      decoding and it returns an instance of :py:class:`~xarray.Dataset`.
      It shall take in input at least ``filename_or_obj`` argument and
      ``drop_variables`` keyword argument.
      For more details see :ref:`RST open_dataset`.
    - ``guess_can_open`` method: it shall return ``True`` if the backend is able to open
      ``filename_or_obj``, ``False`` otherwise. The implementation of this
      method is not mandatory.

    Attributes
    ----------

    available : bool, default: True
        Indicate wether this backend is available given the installed packages.
        The setting of this attribute is not mandatory.
    open_dataset_parameters : tuple, default: None
        A list of ``open_dataset`` method parameters.
        The setting of this attribute is not mandatory.
    description : str, default: ""
        A short string describing the engine.
        The setting of this attribute is not mandatory.
    url : str, default: ""
        A string with the URL to the backend's documentation.
        The setting of this attribute is not mandatory.
    """

    available: ClassVar[bool] = True

    open_dataset_parameters: ClassVar[tuple | None] = None
    description: ClassVar[str] = ""
    url: ClassVar[str] = ""

    def __repr__(self) -> str:
        txt = f"<{type(self).__name__}>"
        if self.description:
            txt += f"\n  {self.description}"
        if self.url:
            txt += f"\n  Learn more at {self.url}"
        return txt

    def open_dataset(
        self,
        filename_or_obj: str | os.PathLike[Any] | BufferedIOBase | AbstractDataStore,
        drop_variables: str | Iterable[str] | None = None,
        **kwargs: Any,
    ):
        """
        Backend open_dataset method used by Xarray in :py:func:`~xarray.open_dataset`.
        """

        raise NotImplementedError

    def guess_can_open(
        self,
        filename_or_obj: str | os.PathLike[Any] | BufferedIOBase | AbstractDataStore,
    ):
        """
        Backend open_dataset method used by Xarray in :py:func:`~xarray.open_dataset`.
        """

        return False


BACKEND_ENTRYPOINTS: dict[str, type[BackendEntrypoint]] = {}