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# -*- 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
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