# Authors: Christoph Dinh <chdinh@nmr.mgh.harvard.edu>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
# Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Denis Engemann <denis.engemann@gmail.com>
#
# License: BSD (3-clause)
import time
import copy
import numpy as np
from mne import pick_channels
from mne.io.pick import _picks_to_idx
from mne.utils import logger, verbose, fill_doc, warn
from mne.epochs import BaseEpochs
from mne.event import _find_events
[docs]
@fill_doc
class RtEpochs(BaseEpochs):
"""Realtime Epochs.
Can receive epochs in real time from an RtClient.
For example, to get some epochs from a running mne_rt_server on
'localhost', you could use::
client = mne_realtime.RtClient('localhost')
event_id, tmin, tmax = 1, -0.2, 0.5
epochs = mne_realtime.RtEpochs(client, event_id, tmin, tmax)
epochs.start() # start the measurement and start receiving epochs
evoked_1 = epochs.average() # computed over all epochs
evoked_2 = epochs[-5:].average() # computed over the last 5 epochs
Parameters
----------
client : instance of mne_realtime.RtClient
The realtime client.
event_id : int | list of int
The id of the event to consider. If int, only events with the
ID specified by event_id are considered. Multiple event ID's
can be specified using a list.
tmin : float
Start time before event.
tmax : float
End time after event.
stim_channel : string or list of string
Name of the stim channel or all the stim channels affected by
the trigger.
sleep_time : float
Time in seconds to wait between checking for new epochs when epochs
are requested and the receive queue is empty.
baseline : None (default) or tuple of length 2
The time interval to apply baseline correction.
If None do not apply it. If baseline is (a, b)
the interval is between "a (s)" and "b (s)".
If a is None the beginning of the data is used
and if b is None then b is set to the end of the interval.
If baseline is equal to (None, None) all the time
interval is used.
%(picks_all)s
reject : dict | None
Rejection parameters based on peak-to-peak amplitude.
Valid keys are 'grad' | 'mag' | 'eeg' | 'eog' | 'ecg'.
If reject is None then no rejection is done. Example::
reject = dict(grad=4000e-13, # T / m (gradiometers)
mag=4e-12, # T (magnetometers)
eeg=40e-6, # V (EEG channels)
eog=250e-6 # V (EOG channels))
flat : dict | None
Rejection parameters based on flatness of signal.
Valid keys are 'grad' | 'mag' | 'eeg' | 'eog' | 'ecg', and values
are floats that set the minimum acceptable peak-to-peak amplitude.
If flat is None then no rejection is done.
proj : bool, optional
Apply SSP projection vectors
decim : int
Factor by which to downsample the data from the raw file upon import.
Warning: This simply selects every nth sample, data is not filtered
here. If data is not properly filtered, aliasing artifacts may occur.
reject_tmin : scalar | None
Start of the time window used to reject epochs (with the default None,
the window will start with tmin).
reject_tmax : scalar | None
End of the time window used to reject epochs (with the default None,
the window will end with tmax).
detrend : int | None
If 0 or 1, the data channels (MEG and EEG) will be detrended when
loaded. 0 is a constant (DC) detrend, 1 is a linear detrend. None
is no detrending. Note that detrending is performed before baseline
correction. If no DC offset is preferred (zeroth order detrending),
either turn off baseline correction, as this may introduce a DC
shift, or set baseline correction to use the entire time interval
(will yield equivalent results but be slower).
isi_max : float
The maximum time in seconds between epochs. If no epoch
arrives in the next isi_max seconds the RtEpochs stops.
find_events : dict
The arguments to the real-time `find_events` method as a dictionary.
If `find_events` is None, then default values are used.
Example (also default values)::
find_events = dict(output='onset', consecutive='increasing',
min_duration=0, mask=0, mask_type='not_and',
verbose='ERROR')
See :func:`mne.find_events` for detailed explanation of these options.
%(verbose)s Defaults to client.verbose.
Attributes
----------
info : dict
Measurement info.
event_id : dict
Names of of conditions corresponding to event_ids.
ch_names : list of string
List of channels' names.
events : array, shape (n_events, 3)
The events associated with the epochs currently in the queue.
%(verbose)s
Notes
-----
- Calling `next()` on an `RtEpochs` object (as internally done when
iterating over the object) is blocking, i.e., waits for at most `isi_max`
seconds for a new epoch to be received.
- Calling `get_data()` on an `RtEpochs` object immediately returns the
epochs received so far (without waiting for new epochs).
"""
@verbose
def __init__(self, client, event_id, tmin, tmax, stim_channel='STI 014',
sleep_time=0.1, baseline=(None, 0), picks=None,
reject=None, flat=None, proj=True,
decim=1, reject_tmin=None, reject_tmax=None, detrend=None,
isi_max=2., find_events=None, verbose=None): # noqa: D102
info = client.get_measurement_info()
# the measurement info of the data as we receive it
self._client_info = copy.deepcopy(info)
verbose = client.verbose if verbose is None else verbose
# FIFO queues for received epochs and events
# need to be initialized to validate invariants in base constructor
self._epoch_queue = list()
self._events = list()
self._selection = list()
# Number of good and bad epochs received
self._n_good = 0
self._n_bad = 0
# call BaseEpochs constructor
super(RtEpochs, self).__init__(
info, None, None, event_id, tmin, tmax, baseline, picks=picks,
reject=reject, flat=flat, decim=decim,
reject_tmin=reject_tmin, reject_tmax=reject_tmax, detrend=detrend,
verbose=verbose, proj=True)
self._bad_dropped = True
self._client = client
if not isinstance(stim_channel, list):
stim_channel = [stim_channel]
stim_picks = pick_channels(self._client_info['ch_names'],
include=stim_channel, exclude=[])
if len(stim_picks) == 0:
raise ValueError('No stim channel found to extract event '
'triggers.')
self._stim_picks = stim_picks
# find_events default options
self._find_events_kwargs = dict(output='onset',
consecutive='increasing',
min_duration=0, mask=0,
mask_type='not_and',
verbose='ERROR')
# update default options if dictionary is provided
if find_events is not None:
self._find_events_kwargs.update(find_events)
min_samples = (self._find_events_kwargs['min_duration'] *
self.info['sfreq'])
self._find_events_kwargs.pop('min_duration', None)
self._find_events_kwargs['min_samples'] = min_samples
self._sleep_time = sleep_time
# add calibration factors
cals = np.zeros(self._client_info['nchan'])
for k in range(self._client_info['nchan']):
cals[k] = (self._client_info['chs'][k]['range'] *
self._client_info['chs'][k]['cal'])
self._cals = cals[:, None]
# variables needed for receiving raw buffers
self._last_buffer = None
self._first_samp = 0
self._event_backlog = list()
self._started = False
self._last_time = time.time()
self.isi_max = isi_max
@property
def events(self):
"""The events associated with the epochs currently in the queue."""
return np.array(self._events)
@events.setter
def events(self, new_events):
"""
Update the internal event list.
Parameters
----------
new_events : array of int, shape (n_events, 3)
new events
"""
self._events = [tuple(new_events[i, :])
for i in range(len(new_events))]
@property
def selection(self):
"""Array of integers of the current selection."""
return np.asarray(self._selection, dtype=int)
@selection.setter
def selection(self, new_selection):
"""
Update the internal selection list.
Parameters
----------
new_selection : iterable of epoch indices
"""
self._selection = list(new_selection)
[docs]
def copy(self):
"""Return copy of Epochs instance."""
client = self._client
del self._client
new = super(RtEpochs, self).copy()
self._client = client
new._client = client
return new
def _getitem(self, item, reason='IGNORED', copy=True, drop_event_id=True,
select_data=True, return_indices=False):
epochs, select = super(RtEpochs, self)._getitem(
item=item, reason=reason, copy=copy, drop_event_id=drop_event_id,
select_data=False, return_indices=True)
# try to be compatible with numpy indexing
new_queue = list()
for kept_idx in np.arange(len(epochs._epoch_queue), dtype=int)[select]:
new_queue.append(epochs._epoch_queue[kept_idx])
epochs._epoch_queue = new_queue
epochs._n_good = len(epochs._epoch_queue)
return epochs
[docs]
def start(self):
"""Start receiving epochs.
The measurement will be started if it has not already been started.
"""
if not self._started:
# register the callback
self._client.register_receive_callback(self._process_raw_buffer)
# start the measurement and the receive thread
nchan = self._client_info['nchan']
self._client.start_receive_thread(nchan)
self._started = True
self._last_time = np.inf # init delay counter. Will stop iters
[docs]
def stop(self, stop_receive_thread=True, stop_measurement=False):
"""Stop receiving epochs.
Parameters
----------
stop_receive_thread : bool
Stop the receive thread. Note: Other RtEpochs instances will also
stop receiving epochs when the receive thread is stopped. The
receive thread will always be stopped if stop_measurement is True.
stop_measurement : bool
Also stop the measurement. Note: Other clients attached to the
server will also stop receiving data.
"""
if self._started:
self._client.unregister_receive_callback(self._process_raw_buffer)
self._started = False
if stop_receive_thread or stop_measurement:
self._client.stop_receive_thread(stop_measurement=stop_measurement)
@verbose
def __next__(self, return_event_id=False, verbose=None):
"""Make iteration over epochs easy.
Parameters
----------
return_event_id : bool
If True, return both an epoch and and event_id.
verbose: bool, str, int, or None
If not None, override default verbose level (see
:func:`mne.verbose`. Defaults to self.verbose.
Returns
-------
epoch : instance of Epochs
The epoch.
event_id : int
The event id. Only returned if ``return_event_id`` is ``True``.
"""
first = True
while True:
current_time = time.time()
if len(self._epoch_queue) > self._current:
epoch = self._epoch_queue[self._current]
event_id = self._events[self._current][-1]
self._current += 1
self._last_time = current_time
return (epoch, event_id) if return_event_id else epoch
if current_time > (self._last_time + self.isi_max):
logger.info('Time of %s seconds exceeded.' % self.isi_max)
raise StopIteration # signal the end properly
if self._started:
if first:
logger.info('Waiting for epoch %d' % (self._current + 1))
first = False
time.sleep(self._sleep_time)
else:
raise RuntimeError('Not enough epochs in queue and currently '
'not receiving epochs, cannot get epochs!')
next = __next__
@verbose
def _get_data(self, out=True, picks=None, item=None, *, units=None,
tmin=None, tmax=None, copy=True, verbose=None):
if not out:
return
unused = dict(tmin=tmin, units=units, tmax=tmax)
for key, value in unused.items():
if value is not None:
warn(f'the {key} argument is currently not supported and '
'will be ignored')
item = slice(None) if item is None else item
select = self._item_to_select(item) # indices or slice
use_idx = np.arange(len(self._events))[select]
if picks is None:
picks = slice(None)
else:
picks = _picks_to_idx(self.info, picks, none='all', exclude=())
return np.array([self._epoch_queue[idx][picks] for idx in use_idx])
def _process_raw_buffer(self, raw_buffer):
"""Process raw buffer (callback from RtClient).
Note: Do not print log messages during regular use. It will be printed
asynchronously which is annoying when working in an interactive shell.
Parameters
----------
raw_buffer : array of float, shape=(nchan, n_times)
The raw buffer.
"""
sfreq = self.info['sfreq']
n_samp = len(self._raw_times)
# relative start and stop positions in samples
tmin_samp = int(round(sfreq * self.tmin))
tmax_samp = tmin_samp + n_samp
last_samp = self._first_samp + raw_buffer.shape[1] - 1
# apply calibration without inplace modification
raw_buffer = self._cals * raw_buffer
# detect events
data = np.abs(raw_buffer[self._stim_picks]).astype(np.int64)
# if there is a previous buffer check the last samples from it too
if self._last_buffer is not None:
prev_data = self._last_buffer[
self._stim_picks, -raw_buffer.shape[1]:].astype(np.int64)
data = np.concatenate((prev_data, data), axis=1)
data = np.atleast_2d(data)
buff_events = _find_events(data,
self._first_samp - raw_buffer.shape[1],
**self._find_events_kwargs)
else:
data = np.atleast_2d(data)
buff_events = _find_events(data, self._first_samp,
**self._find_events_kwargs)
events = self._event_backlog
# remove events before the last epoch processed
min_event_samp = self._first_samp - \
int(self._find_events_kwargs['min_samples'])
if len(self._event_backlog) > 0:
backlog_samps = np.array(self._event_backlog)[:, 0]
min_event_samp = backlog_samps[-1] + 1
if buff_events.shape[0] > 0:
valid_events_idx = buff_events[:, 0] >= min_event_samp
buff_events = buff_events[valid_events_idx]
# add events from this buffer to the list of events
# processed so far
for event_id in self.event_id.values():
idx = np.where(buff_events[:, -1] == event_id)[0]
events.extend(zip(list(buff_events[idx, 0]),
list(buff_events[idx, -1])))
events.sort()
event_backlog = list()
for event_samp, event_id in events:
epoch = None
if (event_samp + tmin_samp >= self._first_samp and
event_samp + tmax_samp <= last_samp):
# easy case: whole epoch is in this buffer
start = event_samp + tmin_samp - self._first_samp
stop = event_samp + tmax_samp - self._first_samp
epoch = raw_buffer[:, start:stop]
elif (event_samp + tmin_samp < self._first_samp and
event_samp + tmax_samp <= last_samp):
# have to use some samples from previous buffer
if self._last_buffer is None:
continue
n_last = self._first_samp - (event_samp + tmin_samp)
n_this = n_samp - n_last
epoch = np.c_[self._last_buffer[:, -n_last:],
raw_buffer[:, :n_this]]
elif event_samp + tmax_samp > last_samp:
# we need samples from the future
# we will process this epoch with the next buffer
event_backlog.append((event_samp, event_id))
else:
raise RuntimeError('Unhandled case..')
if epoch is not None:
self._append_epoch_to_queue(epoch, event_samp, event_id)
# set things up for processing of next buffer
self._event_backlog = event_backlog
n_buffer = raw_buffer.shape[1]
if self._last_buffer is None:
self._last_buffer = raw_buffer
elif self._last_buffer.shape[1] <= n_samp + n_buffer:
self._last_buffer = np.c_[self._last_buffer, raw_buffer]
else:
# do not increase size of _last_buffer any further
self._last_buffer[:, :-n_buffer] = self._last_buffer[:, n_buffer:]
self._last_buffer[:, -n_buffer:] = raw_buffer
self._first_samp = self._first_samp + n_buffer
def _append_epoch_to_queue(self, epoch, event_samp, event_id):
"""Append a (raw) epoch to queue.
Note: Do not print log messages during regular use. It will be printed
asynchronously which is annyoing when working in an interactive shell.
Parameters
----------
epoch : array of float, shape=(nchan, n_times)
The raw epoch (only calibration has been applied) over all
channels.
event_samp : int
The time in samples when the epoch occurred.
event_id : int
The event ID of the epoch.
"""
# select the channels
epoch = epoch[self.picks, :]
# Detrend, baseline correct, decimate
kwargs = dict()
try: # Needed on MNE 0.23+
kwargs['picks'] = self._detrend_picks
except AttributeError:
pass
epoch = self._detrend_offset_decim(epoch, verbose='ERROR', **kwargs)
# apply SSP
epoch = self._project_epoch(epoch)
# Decide if this is a good epoch
is_good, offending_reasons = self._is_good_epoch(epoch,
verbose='ERROR')
if is_good:
self._epoch_queue.append(epoch)
self._events.append((event_samp, 0, event_id))
self.drop_log = self.drop_log + (tuple(),)
self._selection.append(len(self.drop_log) - 1)
self._n_good += 1
else:
self.drop_log = self.drop_log + (tuple(offending_reasons),)
self._n_bad += 1
[docs]
@verbose
def decimate(self, decim, offset=0, verbose=None):
"""Decimate the epochs.
.. note:: No filtering is performed. To avoid aliasing, ensure
your data are properly lowpassed.
Parameters
----------
decim : int
The amount to decimate data.
offset : int
Apply an offset to where the decimation starts relative to the
sample corresponding to t=0. The offset is in samples at the
current sampling rate.
.. versionadded:: 0.12
%(verbose)s
Returns
-------
epochs : instance of Epochs
The decimated Epochs object.
See Also
--------
mne.Evoked.decimate
mne.Epochs.resample
mne.io.Raw.resample
Notes
-----
Decimation can be done multiple times. For example,
``epochs.decimate(2).decimate(2)`` will be the same as
``epochs.decimate(4)``.
If `decim` is 1, this method does not copy the underlying data.
.. versionadded:: 0.10.0
"""
super(RtEpochs, self).decimate(decim, offset, verbose=verbose)
for i in range(len(self._epoch_queue)):
self._epoch_queue[i] = self._epoch_queue[i][:, self._decim_slice]
return self
def __repr__(self): # noqa: D105
s = 'good / bad epochs received: %d / %d, epochs in queue: %d, '\
% (self._n_good, self._n_bad, len(self._epoch_queue))
s += ', tmin : %s (s)' % self.tmin
s += ', tmax : %s (s)' % self.tmax
s += ', baseline : %s' % str(self.baseline)
return '<RtEpochs | %s>' % s
