File: mixin.py

package info (click to toggle)
python-mne 0.19.1%2Bdfsg-1
  • links: PTS, VCS
  • area: main
  • in suites: bullseye
  • size: 100,440 kB
  • sloc: python: 120,243; pascal: 1,861; makefile: 225; sh: 15
file content (464 lines) | stat: -rw-r--r-- 16,702 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
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
# -*- coding: utf-8 -*-
"""Some utility functions."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
#
# License: BSD (3-clause)


from copy import deepcopy
import logging
import json
from collections import OrderedDict

import numpy as np

from .check import _check_pandas_installed, _check_preload, _validate_type
from ._logging import warn, verbose
from .numerics import object_size, object_hash


logger = logging.getLogger('mne')  # one selection here used across mne-python
logger.propagate = False  # don't propagate (in case of multiple imports)


class SizeMixin(object):
    """Estimate MNE object sizes."""

    def __eq__(self, other):
        """Compare self to other.

        Parameters
        ----------
        other : object
            The object to compare to.

        Returns
        -------
        eq : bool
            True if the two objects are equal.
        """
        return isinstance(other, type(self)) and hash(self) == hash(other)

    @property
    def _size(self):
        """Estimate the object size."""
        try:
            size = object_size(self.info)
        except Exception:
            warn('Could not get size for self.info')
            return -1
        if hasattr(self, 'data'):
            size += object_size(self.data)
        elif hasattr(self, '_data'):
            size += object_size(self._data)
        return size

    def __hash__(self):
        """Hash the object.

        Returns
        -------
        hash : int
            The hash
        """
        from ..evoked import Evoked
        from ..epochs import BaseEpochs
        from ..io.base import BaseRaw
        if isinstance(self, Evoked):
            return object_hash(dict(info=self.info, data=self.data))
        elif isinstance(self, (BaseEpochs, BaseRaw)):
            _check_preload(self, "Hashing ")
            return object_hash(dict(info=self.info, data=self._data))
        else:
            raise RuntimeError('Hashing unknown object type: %s' % type(self))


class GetEpochsMixin(object):
    """Class to add epoch selection and metadata to certain classes."""

    def __getitem__(self, item):
        """Return an Epochs object with a copied subset of epochs.

        Parameters
        ----------
        item : slice, array-like, str, or list
            See below for use cases.

        Returns
        -------
        epochs : instance of Epochs
            See below for use cases.

        Notes
        -----
        Epochs can be accessed as ``epochs[...]`` in several ways:

            1. ``epochs[idx]``: Return ``Epochs`` object with a subset of
               epochs (supports single index and python-style slicing).

            2. ``epochs['name']``: Return ``Epochs`` object with a copy of the
               subset of epochs corresponding to an experimental condition as
               specified by 'name'.

               If conditions are tagged by names separated by '/' (e.g.
               'audio/left', 'audio/right'), and 'name' is not in itself an
               event key, this selects every event whose condition contains
               the 'name' tag (e.g., 'left' matches 'audio/left' and
               'visual/left'; but not 'audio_left'). Note that tags selection
               is insensitive to order: tags like 'auditory/left' and
               'left/auditory' will be treated the same way when accessed.

            3. ``epochs[['name_1', 'name_2', ... ]]``: Return ``Epochs`` object
               with a copy of the subset of epochs corresponding to multiple
               experimental conditions as specified by
               ``'name_1', 'name_2', ...`` .

               If conditions are separated by '/', selects every item
               containing every list tag (e.g. ['audio', 'left'] selects
               'audio/left' and 'audio/center/left', but not 'audio/right').

            4. ``epochs['pandas query']``: Return ``Epochs`` object with a
               copy of the subset of epochs (and matching metadata) that match
               ``pandas query`` called with ``self.metadata.eval``, e.g.::

                   epochs["col_a > 2 and col_b == 'foo'"]

               This is only called if Pandas is installed and ``self.metadata``
               is a :class:`pandas.DataFrame`.

               .. versionadded:: 0.16
        """
        return self._getitem(item)

    def _getitem(self, item, reason='IGNORED', copy=True, drop_event_id=True,
                 select_data=True, return_indices=False):
        """
        Select epochs from current object.

        Parameters
        ----------
        item: slice, array-like, str, or list
            see `__getitem__` for details.
        reason: str
            entry in `drop_log` for unselected epochs
        copy: bool
            return a copy of the current object
        drop_event_id: bool
            remove non-existing event-ids after selection
        select_data: bool
            apply selection to data
            (use `select_data=False` if subclasses do not have a
             valid `_data` field, or data has already been subselected)
        return_indices: bool
            return the indices of selected epochs from the original object
            in addition to the new `Epochs` objects
        Returns
        -------
        `Epochs` or tuple(Epochs, np.ndarray) if `return_indices` is True
            subset of epochs (and optionally array with kept epoch indices)
        """
        data = self._data
        del self._data
        inst = self.copy() if copy else self
        self._data = inst._data = data
        del self

        if isinstance(item, str):
            item = [item]

        # Convert string to indices
        if isinstance(item, (list, tuple)) and len(item) > 0 and \
                isinstance(item[0], str):
            select = inst._keys_to_idx(item)
        elif isinstance(item, slice):
            select = item
        else:
            select = np.atleast_1d(item)
            if len(select) == 0:
                select = np.array([], int)
        has_selection = hasattr(inst, 'selection')
        if has_selection:
            key_selection = inst.selection[select]
            if reason is not None:
                for k in np.setdiff1d(inst.selection, key_selection):
                    inst.drop_log[k] = [reason]
            inst.selection = key_selection

        inst.events = np.atleast_2d(inst.events[select])
        if inst.metadata is not None:
            pd = _check_pandas_installed(strict=False)
            if pd is not False:
                metadata = inst.metadata.iloc[select]
                if has_selection:
                    metadata.index = inst.selection
            else:
                metadata = np.array(inst.metadata, 'object')[select].tolist()

            # will reset the index for us
            GetEpochsMixin.metadata.fset(inst, metadata, verbose=False)
        if inst.preload and select_data:
            # ensure that each Epochs instance owns its own data so we can
            # resize later if necessary
            inst._data = np.require(inst._data[select], requirements=['O'])
        if drop_event_id:
            # update event id to reflect new content of inst
            inst.event_id = {k: v for k, v in inst.event_id.items()
                             if v in inst.events[:, 2]}

        if return_indices:
            return inst, select
        else:
            return inst

    def _keys_to_idx(self, keys):
        """Find entries in event dict."""
        keys = keys if isinstance(keys, (list, tuple)) else [keys]
        try:
            # Assume it's a condition name
            return np.where(np.any(
                np.array([self.events[:, 2] == self.event_id[k]
                          for k in _hid_match(self.event_id, keys)]),
                axis=0))[0]
        except KeyError as err:
            # Could we in principle use metadata with these Epochs and keys?
            if (len(keys) != 1 or self.metadata is None):
                # If not, raise original error
                raise
            msg = str(err.args[0])  # message for KeyError
            pd = _check_pandas_installed(strict=False)
            # See if the query can be done
            if pd is not False:
                self._check_metadata()
                try:
                    # Try metadata
                    mask = self.metadata.eval(keys[0], engine='python').values
                except Exception as exp:
                    msg += (' The epochs.metadata Pandas query did not '
                            'yield any results: %s' % (exp.args[0],))
                else:
                    return np.where(mask)[0]
            else:
                # If not, warn this might be a problem
                msg += (' The epochs.metadata Pandas query could not '
                        'be performed, consider installing Pandas.')
            raise KeyError(msg)

    def __len__(self):
        """Return the number of epochs.

        Returns
        -------
        n_epochs : int
            The number of remaining epochs.

        Notes
        -----
        This function only works if bad epochs have been dropped.

        Examples
        --------
        This can be used as::

            >>> epochs.drop_bad()  # doctest: +SKIP
            >>> len(epochs)  # doctest: +SKIP
            43
            >>> len(epochs.events)  # doctest: +SKIP
            43

        """
        from ..epochs import BaseEpochs
        if isinstance(self, BaseEpochs) and not self._bad_dropped:
            raise RuntimeError('Since bad epochs have not been dropped, the '
                               'length of the Epochs is not known. Load the '
                               'Epochs with preload=True, or call '
                               'Epochs.drop_bad(). To find the number '
                               'of events in the Epochs, use '
                               'len(Epochs.events).')
        return len(self.events)

    def __iter__(self):
        """Facilitate iteration over epochs.

        This method resets the object iteration state to the first epoch.

        Notes
        -----
        This enables the use of this Python pattern::

            >>> for epoch in epochs:  # doctest: +SKIP
            >>>     print(epoch)  # doctest: +SKIP

        Where ``epoch`` is given by successive outputs of
        :meth:`mne.Epochs.next`.
        """
        self._current = 0
        return self

    def __next__(self, return_event_id=False):
        """Iterate over epoch data.

        Parameters
        ----------
        return_event_id : bool
            If True, return both the epoch data and an event_id.

        Returns
        -------
        epoch : array of shape (n_channels, n_times)
            The epoch data.
        event_id : int
            The event id. Only returned if ``return_event_id`` is ``True``.
        """
        if self.preload:
            if self._current >= len(self._data):
                raise StopIteration  # signal the end
            epoch = self._data[self._current]
            self._current += 1
        else:
            is_good = False
            while not is_good:
                if self._current >= len(self.events):
                    raise StopIteration  # signal the end properly
                epoch_noproj = self._get_epoch_from_raw(self._current)
                epoch_noproj = self._detrend_offset_decim(epoch_noproj)
                epoch = self._project_epoch(epoch_noproj)
                self._current += 1
                is_good, _ = self._is_good_epoch(epoch)
            # If delayed-ssp mode, pass 'virgin' data after rejection decision.
            if self._do_delayed_proj:
                epoch = epoch_noproj

        if not return_event_id:
            return epoch
        else:
            return epoch, self.events[self._current - 1][-1]

    next = __next__  # originally for Python2, now b/c public

    def _check_metadata(self, metadata=None, reset_index=False):
        """Check metadata consistency."""
        # reset_index=False will not copy!
        metadata = self.metadata if hasattr(self, '_metadata') and \
            metadata is None else metadata
        if metadata is not None:
            pd = _check_pandas_installed(strict=False)
            if pd is not False:
                _validate_type(metadata, types=pd.DataFrame,
                               item_name='metadata')
                if len(metadata) != len(self.events):
                    raise ValueError('metadata must have the same number of '
                                     'rows (%d) as events (%d)'
                                     % (len(metadata), len(self.events)))
                if reset_index:
                    if hasattr(self, 'selection'):
                        # makes a copy
                        metadata = metadata.reset_index(drop=True)
                        metadata.index = self.selection
                    else:
                        metadata = deepcopy(metadata)
            else:
                _validate_type(metadata, types=list,
                               item_name='metadata')
                if reset_index:
                    metadata = deepcopy(metadata)
        return metadata

    @property
    def metadata(self):
        """Get the metadata."""
        return self._metadata

    @metadata.setter
    @verbose
    def metadata(self, metadata, verbose=None):
        metadata = self._check_metadata(metadata, reset_index=True)
        if metadata is not None:
            if _check_pandas_installed(strict=False):
                n_col = metadata.shape[1]
            else:
                n_col = len(metadata[0])
            n_col = ' with %d columns' % n_col
        else:
            n_col = ''
        if hasattr(self, '_metadata') and self._metadata is not None:
            action = 'Removing' if metadata is None else 'Replacing'
            action += ' existing'
        else:
            action = 'Not setting' if metadata is None else 'Adding'
        logger.info('%s metadata%s' % (action, n_col))
        self._metadata = metadata


def _prepare_write_metadata(metadata):
    """Convert metadata to JSON for saving."""
    if metadata is not None:
        if not isinstance(metadata, list):
            metadata = metadata.to_json(orient='records')
        else:  # Pandas DataFrame
            metadata = json.dumps(metadata)
        assert isinstance(metadata, str)
    return metadata


def _prepare_read_metadata(metadata):
    """Convert saved metadata back from JSON."""
    if metadata is not None:
        pd = _check_pandas_installed(strict=False)
        # use json.loads because this preserves ordering
        # (which is necessary for round-trip equivalence)
        metadata = json.loads(metadata, object_pairs_hook=OrderedDict)
        assert isinstance(metadata, list)
        if pd is not False:
            metadata = pd.DataFrame.from_records(metadata)
            assert isinstance(metadata, pd.DataFrame)
    return metadata


def _hid_match(event_id, keys):
    """Match event IDs using HID selection.

    Parameters
    ----------
    event_id : dict
        The event ID dictionary.
    keys : list | str
        The event ID or subset (for HID), or list of such items.

    Returns
    -------
    use_keys : list
        The full keys that fit the selection criteria.
    """
    # form the hierarchical event ID mapping
    use_keys = []
    for key in keys:
        if not isinstance(key, str):
            raise KeyError('keys must be strings, got %s (%s)'
                           % (type(key), key))
        use_keys.extend(k for k in event_id.keys()
                        if set(key.split('/')).issubset(k.split('/')))
    if len(use_keys) == 0:
        raise KeyError('Event "{}" is not in Epochs. Event_ids must be one of '
                       '"{}"'.format(key, ', '.join(event_id.keys())))
    use_keys = list(set(use_keys))  # deduplicate if necessary
    return use_keys


class _FakeNoPandas(object):  # noqa: D101
    def __enter__(self):  # noqa: D105

        def _check(strict=True):
            if strict:
                raise RuntimeError('Pandas not installed')
            else:
                return False

        import mne
        self._old_check = _check_pandas_installed
        mne.epochs._check_pandas_installed = _check
        mne.utils.mixin._check_pandas_installed = _check

    def __exit__(self, *args):  # noqa: D105
        import mne
        mne.epochs._check_pandas_installed = self._old_check
        mne.utils.mixin._check_pandas_installed = self._old_check