# mne.Epochs¶

class mne.Epochs(raw, events, event_id=None, tmin=-0.2, tmax=0.5, baseline=(None, 0), picks=None, preload=False, reject=None, flat=None, proj=True, decim=1, reject_tmin=None, reject_tmax=None, detrend=None, on_missing='error', reject_by_annotation=True, metadata=None, verbose=None)[source]

Epochs extracted from a Raw instance.

Parameters
rawRaw object

An instance of Raw.

eventsarray of int, shape (n_events, 3)

The events typically returned by the read_events function. If some events don’t match the events of interest as specified by event_id, they will be marked as ‘IGNORED’ in the drop log.

event_id

The id of the event to consider. If dict, the keys can later be used to access associated events. Example: dict(auditory=1, visual=3). If int, a dict will be created with the id as string. If a list, all events with the IDs specified in the list are used. If None, all events will be used with and a dict is created with string integer names corresponding to the event id integers.

tminfloat

Start time before event. If nothing is provided, defaults to -0.2

tmaxfloat

End time after event. If nothing is provided, defaults to 0.5

baselineNone or tuple of length 2 (default (None, 0))

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. Correction is applied by computing mean of the baseline period and subtracting it from the data. The baseline (a, b) includes both endpoints, i.e. all timepoints t such that a <= t <= b.

picks

Channels to include. Slices and lists of integers will be interpreted as channel indices. In lists, channel type strings (e.g., ['meg', 'eeg']) will pick channels of those types, channel name strings (e.g., ['MEG0111', 'MEG2623'] will pick the given channels. Can also be the string values “all” to pick all channels, or “data” to pick data channels. None (default) will pick all channels.

Load all epochs from disk when creating the object or wait before accessing each epoch (more memory efficient but can be slower).

reject

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

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.

projbool | ‘delayed’

Apply SSP projection vectors. If proj is ‘delayed’ and reject is not None the single epochs will be projected before the rejection decision, but used in unprojected state if they are kept. This way deciding which projection vectors are good can be postponed to the evoked stage without resulting in lower epoch counts and without producing results different from early SSP application given comparable parameters. Note that in this case baselining, detrending and temporal decimation will be postponed. If proj is False no projections will be applied which is the recommended value if SSPs are not used for cleaning the data.

decimint

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

Start of the time window used to reject epochs (with the default None, the window will start with tmin).

reject_tmax

End of the time window used to reject epochs (with the default None, the window will end with tmax).

detrend

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).

on_missingstr

What to do if one or several event ids are not found in the recording. Valid keys are ‘error’ | ‘warning’ | ‘ignore’ Default is ‘error’. If on_missing is ‘warning’ it will proceed but warn, if ‘ignore’ it will proceed silently. Note. If none of the event ids are found in the data, an error will be automatically generated irrespective of this parameter.

reject_by_annotationbool

Whether to reject based on annotations. If True (default), epochs overlapping with segments whose description begins with 'bad' are rejected. If False, no rejection based on annotations is performed.

metadatainstance of pandas.DataFrame | None

A pandas.DataFrame specifying more complex metadata about events. If given, len(metadata) must equal len(events). The DataFrame may have values of type (str | int | float). If metadata is given, then pandas-style queries may be used to select subsets of data, see mne.Epochs.__getitem__(). When a subset of the epochs is created in this (or any other supported) manner, the metadata object is subsetted in the same manner. MNE will modify the row indices to match epochs.selection.

New in version 0.16.

verbose

If not None, override default verbose level (see mne.verbose() and Logging documentation for more).

Notes

When accessing data, Epochs are detrended, baseline-corrected, and decimated, then projectors are (optionally) applied.

For indexing and slicing using epochs[...], see mne.Epochs.__getitem__().

All methods for iteration over objects (using mne.Epochs.__iter__(), mne.Epochs.iter_evoked() or mne.Epochs.next()) use the same internal state.

Attributes

 ch_names Channel names. filename The filename. times Time vector in seconds.
 info (instance of Info) Measurement info. event_id (dict) Names of conditions corresponding to event_ids. selection (array) List of indices of selected events (not dropped or ignored etc.). For example, if the original event array had 4 events and the second event has been dropped, this attribute would be np.array([0, 2, 3]). preload (bool) Indicates whether epochs are in memory. drop_log (list of list) A list of the same length as the event array used to initialize the Epochs object. If the i-th original event is still part of the selection, drop_log[i] will be an empty list; otherwise it will be a list of the reasons the event is not longer in the selection, e.g.: ‘IGNORED’ if it isn’t part of the current subset defined by the user; ‘NO_DATA’ or ‘TOO_SHORT’ if epoch didn’t contain enough data; names of channels that exceeded the amplitude threshold; ‘EQUALIZED_COUNTS’ (see equalize_event_counts); or ‘USER’ for user-defined reasons (see drop method). verbose (bool, str, int, or None) If not None, override default verbose level (see mne.verbose() and Logging documentation for more).

Methods

 __contains__(self, ch_type) Check channel type membership. __getitem__(self, item) Return an Epochs object with a copied subset of epochs. __hash__(self) Hash the object. __iter__(self) Facilitate iteration over epochs. __len__(self) Return the number of epochs. add_channels(self, add_list[, force_update_info]) Append new channels to the instance. add_proj(self, projs[, remove_existing, verbose]) Add SSP projection vectors. anonymize(self) Anonymize measurement information in place. apply_baseline(self[, baseline, verbose]) Baseline correct epochs. apply_hilbert(self[, picks, envelope, …]) Compute analytic signal or envelope for a subset of channels. apply_proj(self) Apply the signal space projection (SSP) operators to the data. average(self[, picks, method]) Compute an average over epochs. copy(self) Return copy of Epochs instance. crop(self[, tmin, tmax]) Crop a time interval from the epochs. decimate(self, decim[, offset, verbose]) Decimate the epochs. del_proj(self[, idx]) Remove SSP projection vector. drop(self, indices[, reason, verbose]) Drop epochs based on indices or boolean mask. drop_bad(self[, reject, flat, verbose]) Drop bad epochs without retaining the epochs data. drop_channels(self, ch_names) Drop channel(s). drop_log_stats(self[, ignore]) Compute the channel stats based on a drop_log from Epochs. equalize_event_counts(self, event_ids[, method]) Equalize the number of trials in each condition. filter(self, l_freq, h_freq[, picks, …]) Filter a subset of channels. get_data(self[, picks]) Get all epochs as a 3D array. interpolate_bads(self[, reset_bads, mode, …]) Interpolate bad MEG and EEG channels. iter_evoked(self) Iterate over epochs as a sequence of Evoked objects. load_data(self) Load the data if not already preloaded. next(self[, return_event_id]) Iterate over epoch data. pick(self, picks[, exclude]) Pick a subset of channels. pick_channels(self, ch_names) Pick some channels. pick_types(self[, meg, eeg, stim, eog, ecg, …]) Pick some channels by type and names. plot(self[, picks, scalings, n_epochs, …]) Visualize epochs. plot_drop_log(self[, threshold, n_max_plot, …]) Show the channel stats based on a drop_log from Epochs. plot_image(self[, picks, sigma, vmin, vmax, …]) Plot Event Related Potential / Fields image. plot_projs_topomap(self[, ch_type, layout, axes]) Plot SSP vector. plot_psd(self[, fmin, fmax, tmin, tmax, …]) Plot the power spectral density across epochs. plot_psd_topomap(self[, bands, vmin, vmax, …]) Plot the topomap of the power spectral density across epochs. plot_sensors(self[, kind, ch_type, title, …]) Plot sensor positions. plot_topo_image(self[, layout, sigma, vmin, …]) Plot Event Related Potential / Fields image on topographies. rename_channels(self, mapping) Rename channels. reorder_channels(self, ch_names) Reorder channels. resample(self, sfreq[, npad, window, …]) Resample data. save(self, fname[, split_size, fmt, …]) Save epochs in a fif file. savgol_filter(self, h_freq[, verbose]) Filter the data using Savitzky-Golay polynomial method. set_channel_types(self, mapping) Define the sensor type of channels. set_eeg_reference(self[, ref_channels, …]) Specify which reference to use for EEG data. set_montage(self, montage[, set_dig, verbose]) Set EEG sensor configuration and head digitization. shift_time(self, tshift[, relative]) Shift time scale in epoched data. standard_error(self[, picks]) Compute standard error over epochs. subtract_evoked(self[, evoked]) Subtract an evoked response from each epoch. time_as_index(self, times[, use_rounding]) Convert time to indices. to_data_frame(self[, picks, index, …]) Export data in tabular structure as a pandas DataFrame.
__contains__(self, ch_type)[source]

Check channel type membership.

Parameters
ch_typestr

Channel type to check for. Can be e.g. ‘meg’, ‘eeg’, ‘stim’, etc.

Returns
inbool

Whether or not the instance contains the given channel type.

Examples

Channel type membership can be tested as:

>>> 'meg' in inst
True
>>> 'seeg' in inst
False

__getitem__(self, item)[source]

Return an Epochs object with a copied subset of epochs.

Parameters
item

See below for use cases.

Returns
epochsinstance 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 pandas.DataFrame.

New in version 0.16.

__hash__(self)[source]

Hash the object.

Returns
hashint

The hash

__iter__(self)[source]

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:
>>>     print(epoch)


Where epoch is given by successive outputs of mne.Epochs.next().

__len__(self)[source]

Return the number of epochs.

Returns
n_epochsint

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()
>>> len(epochs)
43
>>> len(epochs.events)
43

add_channels(self, add_list, force_update_info=False)[source]

Append new channels to the instance.

Parameters
add_listlist

A list of objects to append to self. Must contain all the same type as the current object

force_update_infobool

If True, force the info for objects to be appended to match the values in self. This should generally only be used when adding stim channels for which important metadata won’t be overwritten.

New in version 0.12.

Returns
instinstance of Raw, Epochs, or Evoked

The modified instance.

Notes

If self is a Raw instance that has been preloaded into a numpy.memmap instance, the memmap will be resized.

add_proj(self, projs, remove_existing=False, verbose=None)[source]

Parameters
projslist

List with projection vectors.

remove_existingbool

Remove the projection vectors currently in the file.

verbose

If not None, override default verbose level (see mne.verbose() and Logging documentation for more). Defaults to self.verbose.

Returns
selfinstance of Raw | Epochs | Evoked

The data container.

anonymize(self)[source]

Anonymize measurement information in place.

Reset ‘subject_info’, ‘meas_date’, ‘file_id’, and ‘meas_id’ keys if they exist in info.

Returns
infoinstance of Info

Measurement information for the dataset.

Notes

Operates in place.

New in version 0.13.0.

apply_baseline(self, baseline=(None, 0), verbose=None)[source]

Baseline correct epochs.

Parameters
baselinetuple 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. Correction is applied by computing mean of the baseline period and subtracting it from the data. The baseline (a, b) includes both endpoints, i.e. all timepoints t such that a <= t <= b.

verbose

If not None, override default verbose level (see mne.verbose() and Logging documentation for more). Defaults to self.verbose.

Returns
epochsinstance of Epochs

The baseline-corrected Epochs object.

Notes

Baseline correction can be done multiple times.

New in version 0.10.0.

apply_hilbert(self, picks=None, envelope=False, n_jobs=1, n_fft='auto', verbose=None)[source]

Compute analytic signal or envelope for a subset of channels.

Parameters
picks

Channels to include. Slices and lists of integers will be interpreted as channel indices. In lists, channel type strings (e.g., ['meg', 'eeg']) will pick channels of those types, channel name strings (e.g., ['MEG0111', 'MEG2623'] will pick the given channels. Can also be the string values “all” to pick all channels, or “data” to pick data channels. None (default) will pick all data channels(excluding reference MEG channels).

envelopebool (default: False)

Compute the envelope signal of each channel. See Notes.

n_jobs: int

Number of jobs to run in parallel.

n_fft

Points to use in the FFT for Hilbert transformation. The signal will be padded with zeros before computing Hilbert, then cut back to original length. If None, n == self.n_times. If ‘auto’, the next highest fast FFT length will be use.

verbose

If not None, override default verbose level (see mne.verbose() and Logging documentation for more). Defaults to self.verbose.

Returns
selfinstance of Raw, Epochs, or Evoked

The raw object with transformed data.

Notes

Parameters

If envelope=False, the analytic signal for the channels defined in picks is computed and the data of the Raw object is converted to a complex representation (the analytic signal is complex valued).

If envelope=True, the absolute value of the analytic signal for the channels defined in picks is computed, resulting in the envelope signal.

If envelope=False, more memory is required since the original raw data as well as the analytic signal have temporarily to be stored in memory. If n_jobs > 1, more memory is required as len(picks) * n_times additional time points need to be temporaily stored in memory.

Also note that the n_fft parameter will allow you to pad the signal with zeros before performing the Hilbert transform. This padding is cut off, but it may result in a slightly different result (particularly around the edges). Use at your own risk.

Analytic signal

The analytic signal “x_a(t)” of “x(t)” is:

x_a = F^{-1}(F(x) 2U) = x + i y


where “F” is the Fourier transform, “U” the unit step function, and “y” the Hilbert transform of “x”. One usage of the analytic signal is the computation of the envelope signal, which is given by “e(t) = abs(x_a(t))”. Due to the linearity of Hilbert transform and the MNE inverse solution, the enevlope in source space can be obtained by computing the analytic signal in sensor space, applying the MNE inverse, and computing the envelope in source space.

apply_proj(self)[source]

Apply the signal space projection (SSP) operators to the data.

Returns
selfinstance of Raw | Epochs | Evoked

The instance.

Notes

Once the projectors have been applied, they can no longer be removed. It is usually not recommended to apply the projectors at too early stages, as they are applied automatically later on (e.g. when computing inverse solutions). Hint: using the copy method individual projection vectors can be tested without affecting the original data. With evoked data, consider the following example:

projs_a = mne.read_proj('proj_a.fif')
# add the first, copy, apply and see ...
# add the second, copy, apply and see ...
# drop the first and see again
evoked.copy().del_proj(0).apply_proj().plot()
evoked.apply_proj()  # finally keep both

average(self, picks=None, method='mean')[source]

Compute an average over epochs.

Parameters
picks

Channels to include. Slices and lists of integers will be interpreted as channel indices. In lists, channel type strings (e.g., ['meg', 'eeg']) will pick channels of those types, channel name strings (e.g., ['MEG0111', 'MEG2623'] will pick the given channels. Can also be the string values “all” to pick all channels, or “data” to pick data channels. None (default) will pick all data channels.

method

How to combine the data. If “mean”/”median”, the mean/median are returned. Otherwise, must be a callable which, when passed an array of shape (n_epochs, n_channels, n_time) returns an array of shape (n_channels, n_time). Note that due to file type limitations, the kind for all these will be “average”.

Returns
evokedinstance of Evoked | dict of Evoked

The averaged epochs.

Notes

Computes an average of all epochs in the instance, even if they correspond to different conditions. To average by condition, do epochs[condition].average() for each condition separately.

When picks is None and epochs contain only ICA channels, no channels are selected, resulting in an error. This is because ICA channels are not considered data channels (they are of misc type) and only data channels are selected when picks is None.

The method parameter allows e.g. robust averaging. For example, one could do:

>>> from scipy.stats import trim_mean  # doctest:+SKIP
>>> trim = lambda x: trim_mean(x, 0.1, axis=0)  # doctest:+SKIP
>>> epochs.average(method=trim)  # doctest:+SKIP


This would compute the trimmed mean.

property ch_names

Channel names.

property compensation_grade

copy(self)[source]

Return copy of Epochs instance.

crop(self, tmin=None, tmax=None)[source]

Crop a time interval from the epochs.

Parameters
tmin

Start time of selection in seconds.

tmax

End time of selection in seconds.

Returns
epochsinstance of Epochs

The cropped epochs.

Notes

Unlike Python slices, MNE time intervals include both their end points; crop(tmin, tmax) returns the interval tmin <= t <= tmax.

Note that the object is modified in place.

decimate(self, decim, offset=0, verbose=None)[source]

Decimate the epochs.

Note

No filtering is performed. To avoid aliasing, ensure your data are properly lowpassed.

Parameters
decimint

The amount to decimate data.

offsetint

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.

New in version 0.12.

verbose

If not None, override default verbose level (see mne.verbose() and Logging documentation for more). Defaults to self.verbose.

Returns
epochsinstance of Epochs

The decimated Epochs object.

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.

New in version 0.10.0.

del_proj(self, idx='all')[source]

Remove SSP projection vector.

Note: The projection vector can only be removed if it is inactive

(has not been applied to the data).

Parameters
idx

Index of the projector to remove. Can also be “all” (default) to remove all projectors.

Returns
selfinstance of Raw | Epochs | Evoked
drop(self, indices, reason='USER', verbose=None)[source]

Drop epochs based on indices or boolean mask.

Note

The indices refer to the current set of undropped epochs rather than the complete set of dropped and undropped epochs. They are therefore not necessarily consistent with any external indices (e.g., behavioral logs). To drop epochs based on external criteria, do not use the preload=True flag when constructing an Epochs object, and call this method before calling the mne.Epochs.drop_bad() or mne.Epochs.load_data() methods.

Parameters
indices

Set epochs to remove by specifying indices to remove or a boolean mask to apply (where True values get removed). Events are correspondingly modified.

reasonstr

Reason for dropping the epochs (‘ECG’, ‘timeout’, ‘blink’ etc). Default: ‘USER’.

verbose

If not None, override default verbose level (see mne.verbose() and Logging documentation for more). Defaults to self.verbose.

Returns
epochsinstance of Epochs

The epochs with indices dropped. Operates in-place.

drop_bad(self, reject='existing', flat='existing', verbose=None)[source]

Drop bad epochs without retaining the epochs data.

Should be used before slicing operations.

Warning

This operation is slow since all epochs have to be read from disk. To avoid reading epochs from disk multiple times, use mne.Epochs.load_data().

Parameters
reject

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. If ‘existing’, then the rejection parameters set at instantiation are used.

flat

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. If ‘existing’, then the flat parameters set at instantiation are used.

verbose

If not None, override default verbose level (see mne.verbose() and Logging documentation for more). Defaults to self.verbose.

Returns
epochsinstance of Epochs

The epochs with bad epochs dropped. Operates in-place.

Notes

Dropping bad epochs can be done multiple times with different reject and flat parameters. However, once an epoch is dropped, it is dropped forever, so if more lenient thresholds may subsequently be applied, epochs.copy should be used.

drop_channels(self, ch_names)[source]

Drop channel(s).

Parameters
ch_names

List of channel name(s) or channel name to remove.

Returns
instinstance of Raw, Epochs, or Evoked

The modified instance.

Notes

New in version 0.9.0.

drop_log_stats(self, ignore=('IGNORED', ))[source]

Compute the channel stats based on a drop_log from Epochs.

Parameters
ignorelist

The drop reasons to ignore.

Returns
percfloat

Total percentage of epochs dropped.

equalize_event_counts(self, event_ids, method='mintime')[source]

Equalize the number of trials in each condition.

It tries to make the remaining epochs occurring as close as possible in time. This method works based on the idea that if there happened to be some time-varying (like on the scale of minutes) noise characteristics during a recording, they could be compensated for (to some extent) in the equalization process. This method thus seeks to reduce any of those effects by minimizing the differences in the times of the events in the two sets of epochs. For example, if one had event times [1, 2, 3, 4, 120, 121] and the other one had [3.5, 4.5, 120.5, 121.5], it would remove events at times [1, 2] in the first epochs and not [20, 21].

Parameters
event_idslist

The event types to equalize. Each entry in the list can either be a str (single event) or a list of str. In the case where one of the entries is a list of str, event_ids in that list will be grouped together before equalizing trial counts across conditions. In the case where partial matching is used (using ‘/’ in event_ids), event_ids will be matched according to the provided tags, that is, processing works as if the event_ids matched by the provided tags had been supplied instead. The event_ids must identify nonoverlapping subsets of the epochs.

methodstr

If ‘truncate’, events will be truncated from the end of each event list. If ‘mintime’, timing differences between each event list will be minimized.

Returns
epochsinstance of Epochs

The modified Epochs instance.

indices

Indices from the original events list that were dropped.

Notes

For example (if epochs.event_id was {‘Left’: 1, ‘Right’: 2, ‘Nonspatial’:3}:

epochs.equalize_event_counts([[‘Left’, ‘Right’], ‘Nonspatial’])

would equalize the number of trials in the ‘Nonspatial’ condition with the total number of trials in the ‘Left’ and ‘Right’ conditions.

If multiple indices are provided (e.g. ‘Left’ and ‘Right’ in the example above), it is not guaranteed that after equalization, the conditions will contribute evenly. E.g., it is possible to end up with 70 ‘Nonspatial’ trials, 69 ‘Left’ and 1 ‘Right’.

property filename

The filename.

filter(self, l_freq, h_freq, picks=None, filter_length='auto', l_trans_bandwidth='auto', h_trans_bandwidth='auto', n_jobs=1, method='fir', iir_params=None, phase='zero', fir_window='hamming', fir_design='firwin', pad='edge', verbose=None)[source]

Filter a subset of channels.

Parameters
l_freq

For FIR filters, the lower pass-band edge; for IIR filters, the upper cutoff frequency. If None the data are only low-passed.

h_freq

For FIR filters, the upper pass-band edge; for IIR filters, the upper cutoff frequency. If None the data are only low-passed.

picks

Channels to include. Slices and lists of integers will be interpreted as channel indices. In lists, channel type strings (e.g., ['meg', 'eeg']) will pick channels of those types, channel name strings (e.g., ['MEG0111', 'MEG2623'] will pick the given channels. Can also be the string values “all” to pick all channels, or “data” to pick data channels. None (default) will pick all data channels.

filter_length

Length of the FIR filter to use (if applicable):

• ‘auto’ (default): The filter length is chosen based on the size of the transition regions (6.6 times the reciprocal of the shortest transition band for fir_window=’hamming’ and fir_design=”firwin2”, and half that for “firwin”).

• str: A human-readable time in units of “s” or “ms” (e.g., “10s” or “5500ms”) will be converted to that number of samples if phase="zero", or the shortest power-of-two length at least that duration for phase="zero-double".

• int: Specified length in samples. For fir_design=”firwin”, this should not be used.

l_trans_bandwidth

Width of the transition band at the low cut-off frequency in Hz (high pass or cutoff 1 in bandpass). Can be “auto” (default) to use a multiple of l_freq:

min(max(l_freq * 0.25, 2), l_freq)


Only used for method='fir'.

h_trans_bandwidth

Width of the transition band at the high cut-off frequency in Hz (low pass or cutoff 2 in bandpass). Can be “auto” (default in 0.14) to use a multiple of h_freq:

min(max(h_freq * 0.25, 2.), info['sfreq'] / 2. - h_freq)


Only used for method='fir'.

n_jobs

Number of jobs to run in parallel. Can be ‘cuda’ if cupy is installed properly and method=’fir’.

methodstr

‘fir’ will use overlap-add FIR filtering, ‘iir’ will use IIR forward-backward filtering (via filtfilt).

iir_params

Dictionary of parameters to use for IIR filtering. If iir_params is None and method=”iir”, 4th order Butterworth will be used. For more information, see mne.filter.construct_iir_filter().

phasestr

Phase of the filter, only used if method='fir'. Symmetric linear-phase FIR filters are constructed, and if phase='zero' (default), the delay of this filter is compensated for, making it non-causal. If phase=='zero-double', then this filter is applied twice, once forward, and once backward (also making it non-causal). If ‘minimum’, then a minimum-phase filter will be constricted and applied, which is causal but has weaker stop-band suppression.

New in version 0.13.

fir_windowstr

The window to use in FIR design, can be “hamming” (default), “hann” (default in 0.13), or “blackman”.

New in version 0.15.

fir_designstr

Can be “firwin” (default) to use scipy.signal.firwin(), or “firwin2” to use scipy.signal.firwin2(). “firwin” uses a time-domain design technique that generally gives improved attenuation using fewer samples than “firwin2”.

New in version 0.15.

padstr

The type of padding to use. Supports all numpy.pad() mode options. Can also be “reflect_limited”, which pads with a reflected version of each vector mirrored on the first and last values of the vector, followed by zeros. Only used for method='fir'. The default is 'edge', which pads with the edge values of each vector.

verbose

If not None, override default verbose level (see mne.verbose() and Logging documentation for more). Defaults to self.verbose.

Returns
instinstance of Epochs or Evoked

The filtered data.

Notes

Applies a zero-phase low-pass, high-pass, band-pass, or band-stop filter to the channels selected by picks. The data are modified inplace.

The object has to have the data loaded e.g. with preload=True or self.load_data().

l_freq and h_freq are the frequencies below which and above which, respectively, to filter out of the data. Thus the uses are:

• l_freq < h_freq: band-pass filter

• l_freq > h_freq: band-stop filter

• l_freq is not None and h_freq is None: high-pass filter

• l_freq is None and h_freq is not None: low-pass filter

self.info['lowpass'] and self.info['highpass'] are only updated with picks=None.

Note

If n_jobs > 1, more memory is required as len(picks) * n_times additional time points need to be temporaily stored in memory.

New in version 0.15.

get_data(self, picks=None)[source]

Get all epochs as a 3D array.

Parameters
picks

Channels to include. Slices and lists of integers will be interpreted as channel indices. In lists, channel type strings (e.g., ['meg', 'eeg']) will pick channels of those types, channel name strings (e.g., ['MEG0111', 'MEG2623'] will pick the given channels. Can also be the string values “all” to pick all channels, or “data” to pick data channels. None (default) will pick all channels.

Returns
dataarray of shape (n_epochs, n_channels, n_times)

A view on epochs data.

interpolate_bads(self, reset_bads=True, mode='accurate', origin=(0.0, 0.0, 0.04), verbose=None)[source]

Interpolate bad MEG and EEG channels.

Operates in place.

Parameters

If True, remove the bads from info.

modestr

Either 'accurate' or 'fast', determines the quality of the Legendre polynomial expansion used for interpolation of MEG channels.

originarray_like, shape (3,) | str

Origin of the sphere in the head coordinate frame and in meters. Can be 'auto', which means a head-digitization-based origin fit. Default is (0., 0., 0.04).

New in version 0.17.

verbose

If not None, override default verbose level (see mne.verbose() and Logging documentation for more). Defaults to self.verbose.

Returns
instinstance of Raw, Epochs, or Evoked

The modified instance.

Notes

New in version 0.9.0.

iter_evoked(self)[source]

Iterate over epochs as a sequence of Evoked objects.

The Evoked objects yielded will each contain a single epoch (i.e., no averaging is performed).

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

load_data(self)[source]

Returns
epochsinstance of Epochs

The epochs object.

Notes

This function operates in-place.

New in version 0.10.0.

property metadata

next(self, return_event_id=False)[source]

Iterate over epoch data.

Parameters
return_event_idbool

If True, return both the epoch data and an event_id.

Returns
epocharray of shape (n_channels, n_times)

The epoch data.

event_idint

The event id. Only returned if return_event_id is True.

pick(self, picks, exclude=())[source]

Pick a subset of channels.

Parameters
picks

Channels to include. Slices and lists of integers will be interpreted as channel indices. In lists, channel type strings (e.g., ['meg', 'eeg']) will pick channels of those types, channel name strings (e.g., ['MEG0111', 'MEG2623'] will pick the given channels. Can also be the string values “all” to pick all channels, or “data” to pick data channels. None (default) will pick all channels.

exclude

Set of channels to exclude, only used when picking based on types (e.g., exclude=”bads” when picks=”meg”).

Returns
instinstance of Raw, Epochs, or Evoked

The modified instance.

pick_channels(self, ch_names)[source]

Pick some channels.

Parameters
ch_nameslist

The list of channels to select.

Returns
instinstance of Raw, Epochs, or Evoked

The modified instance.

Notes

The channel names given are assumed to be a set, i.e. the order does not matter. The original order of the channels is preserved. You can use reorder_channels to set channel order if necessary.

New in version 0.9.0.

pick_types(self, meg=True, eeg=False, stim=False, eog=False, ecg=False, emg=False, ref_meg='auto', misc=False, resp=False, chpi=False, exci=False, ias=False, syst=False, seeg=False, dipole=False, gof=False, bio=False, ecog=False, fnirs=False, include=(), exclude='bads', selection=None, verbose=None)[source]

Pick some channels by type and names.

Parameters
meg

If True include all MEG channels. If False include None If string it can be ‘mag’, ‘grad’, ‘planar1’ or ‘planar2’ to select only magnetometers, all gradiometers, or a specific type of gradiometer.

eegbool

If True include EEG channels.

stimbool

If True include stimulus channels.

eogbool

If True include EOG channels.

ecgbool

If True include ECG channels.

emgbool

If True include EMG channels.

ref_meg: bool | str

If True include CTF / 4D reference channels. If ‘auto’, the reference channels are only included if compensations are present.

miscbool

If True include miscellaneous analog channels.

respbool

If True include response-trigger channel. For some MEG systems this is separate from the stim channel.

chpibool

If True include continuous HPI coil channels.

excibool

Flux excitation channel used to be a stimulus channel.

iasbool

Internal Active Shielding data (maybe on Triux only).

systbool

System status channel information (on Triux systems only).

seegbool

Stereotactic EEG channels.

dipolebool

Dipole time course channels.

gofbool

Dipole goodness of fit channels.

biobool

Bio channels.

ecogbool

Electrocorticography channels.

fnirs

Functional near-infrared spectroscopy channels. If True include all fNIRS channels. If False (default) include none. If string it can be ‘hbo’ (to include channels measuring oxyhemoglobin) or ‘hbr’ (to include channels measuring deoxyhemoglobin).

include

List of additional channels to include. If empty do not include any.

exclude

List of channels to exclude. If ‘bads’ (default), exclude channels in info['bads'].

selection

Restrict sensor channels (MEG, EEG) to this list of channel names.

verbose

If not None, override default verbose level (see mne.verbose() and Logging documentation for more). Defaults to self.verbose.

Returns
instinstance of Raw, Epochs, or Evoked

The modified instance.

Notes

New in version 0.9.0.

plot(self, picks=None, scalings=None, n_epochs=20, n_channels=20, title=None, events=None, event_colors=None, order=None, show=True, block=False, decim='auto', noise_cov=None, butterfly=False)[source]

Visualize epochs.

Bad epochs can be marked with a left click on top of the epoch. Bad channels can be selected by clicking the channel name on the left side of the main axes. Calling this function drops all the selected bad epochs as well as bad epochs marked beforehand with rejection parameters.

Parameters
picks

Channels to include. Slices and lists of integers will be interpreted as channel indices. In lists, channel type strings (e.g., ['meg', 'eeg']) will pick channels of those types, channel name strings (e.g., ['MEG0111', 'MEG2623'] will pick the given channels. Can also be the string values “all” to pick all channels, or “data” to pick data channels. None (default) will pick good data channels.

scalingsdict | ‘auto’ | None

Scaling factors for the traces. If any fields in scalings are ‘auto’, the scaling factor is set to match the 99.5th percentile of a subset of the corresponding data. If scalings == ‘auto’, all scalings fields are set to ‘auto’. If any fields are ‘auto’ and data is not preloaded, a subset of epochs up to 100mb will be loaded. If None, defaults to:

dict(mag=1e-12, grad=4e-11, eeg=20e-6, eog=150e-6, ecg=5e-4,
emg=1e-3, ref_meg=1e-12, misc=1e-3, stim=1, resp=1, chpi=1e-4,
whitened=10.)

n_epochsint

The number of epochs per view. Defaults to 20.

n_channelsint

The number of channels per view. Defaults to 20.

title

The title of the window. If None, epochs name will be displayed. Defaults to None.

eventsNone, array, shape (n_events, 3)

Events to show with vertical bars. If events are provided, the epoch numbers are not shown to prevent overlap. You can toggle epoch numbering through options (press ‘o’ key). You can use mne.viz.plot_events() as a legend for the colors. By default, the coloring scheme is the same.

Warning

If the epochs have been resampled, the events no longer align with the data.

New in version 0.14.0.

event_colors

Dictionary of event_id value and its associated color. If None, colors are automatically drawn from a default list (cycled through if number of events longer than list of default colors). Uses the same coloring scheme as mne.viz.plot_events().

New in version 0.14.0.

order

Order in which to plot channel types.

New in version 0.18.0.

showbool

Show figure if True. Defaults to True

blockbool

Whether to halt program execution until the figure is closed. Useful for rejecting bad trials on the fly by clicking on an epoch. Defaults to False.

decimint | ‘auto’

Amount to decimate the data during display for speed purposes. You should only decimate if the data are sufficiently low-passed, otherwise aliasing can occur. The ‘auto’ mode (default) uses the decimation that results in a sampling rate at least three times larger than info['lowpass'] (e.g., a 40 Hz lowpass will result in at least a 120 Hz displayed sample rate).

New in version 0.15.0.

noise_covinstance of Covariance | str | None

Noise covariance used to whiten the data while plotting. Whitened data channels are scaled by scalings['whitened'], and their channel names are shown in italic. Can be a string to load a covariance from disk. See also mne.Evoked.plot_white() for additional inspection of noise covariance properties when whitening evoked data. For data processed with SSS, the effective dependence between magnetometers and gradiometers may introduce differences in scaling, consider using mne.Evoked.plot_white().

New in version 0.16.0.

butterflybool

Whether to directly call the butterfly view.

New in version 0.18.0.

Returns
figinstance of matplotlib.figure.Figure

The figure.

Notes

The arrow keys (up/down/left/right) can be used to navigate between channels and epochs and the scaling can be adjusted with - and + (or =) keys, but this depends on the backend matplotlib is configured to use (e.g., mpl.use(TkAgg) should work). Full screen mode can be toggled with f11 key. The amount of epochs and channels per view can be adjusted with home/end and page down/page up keys. These can also be set through options dialog by pressing o key. h key plots a histogram of peak-to-peak values along with the used rejection thresholds. Butterfly plot can be toggled with b key. Right mouse click adds a vertical line to the plot. Click ‘help’ button at bottom left corner of the plotter to view all the options.

New in version 0.10.0.

plot_drop_log(self, threshold=0, n_max_plot=20, subject='Unknown', color=(0.9, 0.9, 0.9), width=0.8, ignore=('IGNORED', ), show=True)[source]

Show the channel stats based on a drop_log from Epochs.

Parameters
thresholdfloat

The percentage threshold to use to decide whether or not to plot. Default is zero (always plot).

n_max_plotint

Maximum number of channels to show stats for.

subjectstr

The subject name to use in the title of the plot.

color

Color to use for the bars.

widthfloat

Width of the bars.

ignorelist

The drop reasons to ignore.

showbool

Show figure if True.

Returns
figinstance of matplotlib.figure.Figure

The figure.

plot_image(self, picks=None, sigma=0.0, vmin=None, vmax=None, colorbar=True, order=None, show=True, units=None, scalings=None, cmap=None, fig=None, axes=None, overlay_times=None, combine=None, group_by=None, evoked=True, ts_args={'show_sensors': False}, title=None)[source]

Plot Event Related Potential / Fields image.

Parameters
picks

Channels to include. Slices and lists of integers will be interpreted as channel indices. In lists, channel type strings (e.g., ['meg', 'eeg']) will pick channels of those types, channel name strings (e.g., ['MEG0111', 'MEG2623'] will pick the given channels. Can also be the string values “all” to pick all channels, or “data” to pick data channels. None (default) will pick good data channels. If None and group_by is also None, only the first five good channels are plotted.

sigmafloat

The standard deviation of the Gaussian smoothing to apply along the epoch axis to apply in the image. If 0., no smoothing is applied. Defaults to 0.

vmin

The min value in the image (and the ER[P/F]). The unit is uV for EEG channels, fT for magnetometers and fT/cm for gradiometers. If vmin is None and multiple plots are returned, the limit is equalized within channel types. Hint: to specify the lower limit of the data, use vmin=lambda data: data.min().

vmax

The max value in the image (and the ER[P/F]). The unit is uV for EEG channels, fT for magnetometers and fT/cm for gradiometers. If vmin is None and multiple plots are returned, the limit is equalized within channel types.

colorbarbool

Display or not a colorbar.

order

If not None, order is used to reorder the epochs on the y-axis of the image. If it’s an array of int it should be of length the number of good epochs. If it’s a callable the arguments passed are the times vector and the data as 2d array (data.shape[1] == len(times).

showbool

Show figure if True.

units

The units of the channel types used for axes labels. If None, defaults to units=dict(eeg=’uV’, grad=’fT/cm’, mag=’fT’).

scalings

The scalings of the channel types to be applied for plotting. If None, defaults to scalings=dict(eeg=1e6, grad=1e13, mag=1e15, eog=1e6).

cmapNone | colormap | (colormap, bool) | ‘interactive’

Colormap. If tuple, the first value indicates the colormap to use and the second value is a boolean defining interactivity. In interactive mode the colors are adjustable by clicking and dragging the colorbar with left and right mouse button. Left mouse button moves the scale up and down and right mouse button adjusts the range. Hitting space bar resets the scale. Up and down arrows can be used to change the colormap. If ‘interactive’, translates to (‘RdBu_r’, True). If None, “RdBu_r” is used, unless the data is all positive, in which case “Reds” is used.

fig

Figure instance to draw the image to. Figure must contain two axes for drawing the single trials and evoked responses. If None a new figure is created. Defaults to None.

axes

List of axes instances to draw the image, erp and colorbar to. Must be of length three if colorbar is True (with the last list element being the colorbar axes) or two if colorbar is False. If both fig and axes are passed, an error is raised. If group_by is a dict, this cannot be a list, but it can be a dict of lists of axes, with the keys matching those of group_by. In that case, the provided axes will be used for the corresponding groups. Defaults to None.

overlay_timesarray_like, shape (n_epochs,) | None

If not None the parameter is interpreted as time instants in seconds and is added to the image. It is typically useful to display reaction times. Note that it is defined with respect to the order of epochs such that overlay_times[0] corresponds to epochs[0].

combine

If None, return one figure per pick. If not None, aggregate over channels via the indicated method. If str, must be one of “mean”, “median”, “std” or “gfp”, in which case the mean, the median, the standard deviation or the GFP over channels are plotted. array (n_epochs, n_times). If callable, it must accept one positional input, the data in the format (n_epochs, n_channels, n_times). It must return an array (n_epochs, n_times). For example:

combine = lambda data: np.median(data, axis=1)


Defaults to None if picks are provided, otherwise ‘gfp’.

group_by

If not None, combining happens over channel groups defined by this parameter. If str, must be “type”, in which case one figure per channel type is returned (combining within channel types). If a dict, the values must be picks and one figure will be returned for each entry, aggregating over the corresponding pick groups; keys will become plot titles. This is useful for e.g. ROIs. Each entry must contain only one channel type. For example:

group_by=dict(Left_ROI=[1, 2, 3, 4], Right_ROI=[5, 6, 7, 8])


If not None, combine must not be None. Defaults to None if picks are provided, otherwise ‘type’.

evokedbool

Draw the ER[P/F] below the image or not.

ts_argsdict

Arguments passed to a call to mne.viz.plot_compare_evoked to style the evoked plot below the image. Defaults to an empty dictionary, meaning plot_compare_evokeds will be called with default parameters (yaxis truncation will be turned off, and inversion of the y axis via invert_y=True will raise an error).

title

If str, will be plotted as figure title. Else, the channels will be indicated.

Returns
figs

One figure per channel displayed.

plot_projs_topomap(self, ch_type=None, layout=None, axes=None)[source]

Plot SSP vector.

Parameters
ch_type‘mag’ | ‘grad’ | ‘planar1’ | ‘planar2’ | ‘eeg’ | None | list

The channel type to plot. For ‘grad’, the gradiometers are collec- ted in pairs and the RMS for each pair is plotted. If None (default), it will return all channel types present. If a list of ch_types is provided, it will return multiple figures.

layout

Layout instance specifying sensor positions (does not need to be specified for Neuromag data). If possible, the correct layout file is inferred from the data; if no appropriate layout file was found, the layout is automatically generated from the sensor locations. Or a list of Layout if projections are from different sensor types.

axesinstance of Axes | list | None

The axes to plot to. If list, the list must be a list of Axes of the same length as the number of projectors. If instance of Axes, there must be only one projector. Defaults to None.

Returns
figinstance of Figure

Figure distributing one image per channel across sensor topography.

plot_psd(self, fmin=0, fmax=inf, tmin=None, tmax=None, proj=False, bandwidth=None, adaptive=False, low_bias=True, normalization='length', picks=None, ax=None, color='black', area_mode='std', area_alpha=0.33, dB=True, n_jobs=1, show=True, verbose=None)[source]

Plot the power spectral density across epochs.

Parameters
fminfloat

Start frequency to consider.

fmaxfloat

End frequency to consider.

tmin

Start time to consider.

tmax

End time to consider.

projbool

Apply projection.

bandwidthfloat

The bandwidth of the multi taper windowing function in Hz. The default value is a window half-bandwidth of 4.

Use adaptive weights to combine the tapered spectra into PSD (slow, use n_jobs >> 1 to speed up computation).

low_biasbool

Only use tapers with more than 90% spectral concentration within bandwidth.

normalizationstr

Either “full” or “length” (default). If “full”, the PSD will be normalized by the sampling rate as well as the length of the signal (as in nitime).

picks

Channels to include. Slices and lists of integers will be interpreted as channel indices. In lists, channel type strings (e.g., ['meg', 'eeg']) will pick channels of those types, channel name strings (e.g., ['MEG0111', 'MEG2623'] will pick the given channels. Can also be the string values “all” to pick all channels, or “data” to pick data channels. None (default) will pick good data channels.

axinstance of Axes | None

Axes to plot into. If None, axes will be created.

color

A matplotlib-compatible color to use.

area_mode

Mode for plotting area. If ‘std’, the mean +/- 1 STD (across channels) will be plotted. If ‘range’, the min and max (across channels) will be plotted. Bad channels will be excluded from these calculations. If None, no area will be plotted.

area_alphafloat

Alpha for the area.

dBbool

If True, transform data to decibels.

n_jobsint

The number of jobs to run in parallel (default 1). Requires the joblib package.

showbool

Show figure if True.

verbose

If not None, override default verbose level (see mne.verbose() and Logging documentation for more).

Returns
figinstance of Figure

Figure distributing one image per channel across sensor topography.

plot_psd_topomap(self, bands=None, vmin=None, vmax=None, tmin=None, tmax=None, proj=False, bandwidth=None, adaptive=False, low_bias=True, normalization='length', ch_type=None, layout=None, cmap='RdBu_r', agg_fun=None, dB=True, n_jobs=1, normalize=False, cbar_fmt='%0.3f', outlines='head', axes=None, show=True, verbose=None)[source]

Plot the topomap of the power spectral density across epochs.

Parameters
bands

The lower and upper frequency and the name for that band. If None, (default) expands to:

bands = [(0, 4, ‘Delta’), (4, 8, ‘Theta’), (8, 12, ‘Alpha’),

(12, 30, ‘Beta’), (30, 45, ‘Gamma’)]

vmin

The value specifying the lower bound of the color range. If None np.min(data) is used. If callable, the output equals vmin(data).

vmax

The value specifying the upper bound of the color range. If None, the maximum absolute value is used. If callable, the output equals vmax(data). Defaults to None.

tmin

Start time to consider.

tmax

End time to consider.

projbool

Apply projection.

bandwidthfloat

The bandwidth of the multi taper windowing function in Hz. The default value is a window half-bandwidth of 4 Hz.

Use adaptive weights to combine the tapered spectra into PSD (slow, use n_jobs >> 1 to speed up computation).

low_biasbool

Only use tapers with more than 90% spectral concentration within bandwidth.

normalizationstr

Either “full” or “length” (default). If “full”, the PSD will be normalized by the sampling rate as well as the length of the signal (as in nitime).

ch_type‘mag’ | ‘grad’ | ‘planar1’ | ‘planar2’ | ‘eeg’ | None

The channel type to plot. For ‘grad’, the gradiometers are collected in pairs and the RMS for each pair is plotted. If None, then first available channel type from order given above is used. Defaults to None.

layout

Layout instance specifying sensor positions (does not need to be specified for Neuromag data). If possible, the correct layout file is inferred from the data; if no appropriate layout file was found, the layout is automatically generated from the sensor locations.

cmapmatplotlib colormap | (colormap, bool) | ‘interactive’ | None

Colormap to use. If tuple, the first value indicates the colormap to use and the second value is a boolean defining interactivity. In interactive mode the colors are adjustable by clicking and dragging the colorbar with left and right mouse button. Left mouse button moves the scale up and down and right mouse button adjusts the range. Hitting space bar resets the range. Up and down arrows can be used to change the colormap. If None (default), ‘Reds’ is used for all positive data, otherwise defaults to ‘RdBu_r’. If ‘interactive’, translates to (None, True).

agg_funcallable()

The function used to aggregate over frequencies. Defaults to np.sum. if normalize is True, else np.mean.

dBbool

If True, transform data to decibels (with 10 * np.log10(data)) following the application of agg_fun. Only valid if normalize is False.

n_jobsint

The number of jobs to run in parallel (default 1). Requires the joblib package.

normalizebool

If True, each band will be divided by the total power. Defaults to False.

cbar_fmtstr

The colorbar format. Defaults to ‘%0.3f’.

outlines‘head’ | ‘skirt’ | dict | None

The outlines to be drawn. If ‘head’, the default head scheme will be drawn. If ‘skirt’ the head scheme will be drawn, but sensors are allowed to be plotted outside of the head circle. If dict, each key refers to a tuple of x and y positions, the values in ‘mask_pos’ will serve as image mask, and the ‘autoshrink’ (bool) field will trigger automated shrinking of the positions due to points outside the outline. Alternatively, a matplotlib patch object can be passed for advanced masking options, either directly or as a function that returns patches (required for multi-axis plots). If None, nothing will be drawn. Defaults to ‘head’.

axes

List of axes to plot consecutive topographies to. If None the axes will be created automatically. Defaults to None.

showbool

Show figure if True.

verbose

If not None, override default verbose level (see mne.verbose() and Logging documentation for more).

Returns
figinstance of Figure

Figure distributing one image per channel across sensor topography.

plot_sensors(self, kind='topomap', ch_type=None, title=None, show_names=False, ch_groups=None, to_sphere=True, axes=None, block=False, show=True)[source]

Plot sensor positions.

Parameters
kindstr

Whether to plot the sensors as 3d, topomap or as an interactive sensor selection dialog. Available options ‘topomap’, ‘3d’, ‘select’. If ‘select’, a set of channels can be selected interactively by using lasso selector or clicking while holding control key. The selected channels are returned along with the figure instance. Defaults to ‘topomap’.

ch_type

The channel type to plot. Available options ‘mag’, ‘grad’, ‘eeg’, ‘seeg’, ‘ecog’, ‘all’. If 'all', all the available mag, grad, eeg, seeg and ecog channels are plotted. If None (default), then channels are chosen in the order given above.

title

Title for the figure. If None (default), equals to 'Sensor positions (%s)' % ch_type.

show_names

Whether to display all channel names. If an array, only the channel names in the array are shown. Defaults to False.

ch_groups‘position’ | array of shape (n_ch_groups, n_picks) | None

Channel groups for coloring the sensors. If None (default), default coloring scheme is used. If ‘position’, the sensors are divided into 8 regions. See order kwarg of mne.viz.plot_raw(). If array, the channels are divided by picks given in the array.

New in version 0.13.0.

to_spherebool

Whether to project the 3d locations to a sphere. When False, the sensor array appears similar as to looking downwards straight above the subject’s head. Has no effect when kind=‘3d’. Defaults to True.

New in version 0.14.0.

axesinstance of Axes | instance of Axes3D | None

Axes to draw the sensors to. If kind='3d', axes must be an instance of Axes3D. If None (default), a new axes will be created.

New in version 0.13.0.

blockbool

Whether to halt program execution until the figure is closed. Defaults to False.

New in version 0.13.0.

showbool

Show figure if True. Defaults to True.

Returns
figinstance of Figure

Figure containing the sensor topography.

selectionlist

A list of selected channels. Only returned if kind=='select'.

Notes

This function plots the sensor locations from the info structure using matplotlib. For drawing the sensors using mayavi see mne.viz.plot_alignment().

New in version 0.12.0.

plot_topo_image(self, layout=None, sigma=0.0, vmin=None, vmax=None, colorbar=None, order=None, cmap='RdBu_r', layout_scale=0.95, title=None, scalings=None, border='none', fig_facecolor='k', fig_background=None, font_color='w', show=True)[source]

Plot Event Related Potential / Fields image on topographies.

Parameters
layout: instance of Layout

System specific sensor positions.

sigmafloat

The standard deviation of the Gaussian smoothing to apply along the epoch axis to apply in the image. If 0., no smoothing is applied.

vminfloat

The min value in the image. The unit is uV for EEG channels, fT for magnetometers and fT/cm for gradiometers.

vmaxfloat

The max value in the image. The unit is uV for EEG channels, fT for magnetometers and fT/cm for gradiometers.

colorbar

Whether to display a colorbar or not. If None a colorbar will be shown only if all channels are of the same type. Defaults to None.

order

If not None, order is used to reorder the epochs on the y-axis of the image. If it’s an array of int it should be of length the number of good epochs. If it’s a callable the arguments passed are the times vector and the data as 2d array (data.shape[1] == len(times)).

cmapcolormap

Colors to be mapped to the values.

layout_scale: float

scaling factor for adjusting the relative size of the layout on the canvas.

titlestr

Title of the figure.

scalings

The scalings of the channel types to be applied for plotting. If None, defaults to dict(eeg=1e6, grad=1e13, mag=1e15).

borderstr

matplotlib borders style to be used for each sensor plot.

fig_facecolorcolor

The figure face color. Defaults to black.

fig_background

A background image for the figure. This must be a valid input to matplotlib.pyplot.imshow(). Defaults to None.

font_colorcolor

The color of tick labels in the colorbar. Defaults to white.

showbool

Whether to show the figure. Defaults to True.

Returns
figinstance of matplotlib.figure.Figure

Figure distributing one image per channel across sensor topography.

Notes

In an interactive Python session, this plot will be interactive; clicking on a channel image will pop open a larger view of the image; this image will always have a colorbar even when the topo plot does not (because it shows multiple sensor types).

property proj

Whether or not projections are active.

rename_channels(self, mapping)[source]

Rename channels.

Parameters
mapping

a dictionary mapping the old channel to a new channel name e.g. {‘EEG061’ : ‘EEG161’}. Can also be a callable function that takes and returns a string (new in version 0.10.0).

Notes

New in version 0.9.0.

reorder_channels(self, ch_names)[source]

Reorder channels.

Parameters
ch_nameslist

The desired channel order.

Returns
instinstance of Raw, Epochs, or Evoked

The modified instance.

Notes

Channel names must be unique. Channels that are not in ch_names are dropped.

New in version 0.16.0.

resample(self, sfreq, npad='auto', window='boxcar', n_jobs=1, pad='edge', verbose=None)[source]

Resample data.

Note

Parameters
sfreqfloat

New sample rate to use.

Amount to pad the start and end of the data. Can also be “auto” to use a padding that will result in a power-of-two size (can be much faster).

window

Frequency-domain window to use in resampling. See scipy.signal.resample().

n_jobs

Number of jobs to run in parallel. Can be ‘cuda’ if cupy is installed properly.

padstr

The type of padding to use. Supports all numpy.pad() mode options. Can also be “reflect_limited”, which pads with a reflected version of each vector mirrored on the first and last values of the vector, followed by zeros. Only used for method='fir'. The default is 'edge', which pads with the edge values of each vector.

New in version 0.15.

verbose

If not None, override default verbose level (see mne.verbose() and Logging documentation for more). Defaults to self.verbose.

Returns
instinstance of Epochs or Evoked

The resampled object.

Notes

For some data, it may be more accurate to use npad=0 to reduce artifacts. This is dataset dependent – check your data!

save(self, fname, split_size='2GB', fmt='single', overwrite=None, verbose=True)[source]

Save epochs in a fif file.

Parameters
fnamestr

The name of the file, which should end with -epo.fif or -epo.fif.gz.

split_size

Large raw files are automatically split into multiple pieces. This parameter specifies the maximum size of each piece. If the parameter is an integer, it specifies the size in Bytes. It is also possible to pass a human-readable string, e.g., 100MB. Note: Due to FIFF file limitations, the maximum split size is 2GB.

New in version 0.10.0.

fmtstr

Format to save data. Valid options are ‘double’ or ‘single’ for 64- or 32-bit float, or for 128- or 64-bit complex numbers respectively. Note: Data are processed with double precision. Choosing single-precision, the saved data will slightly differ due to the reduction in precision.

New in version 0.17.

overwritebool

If True, the destination file (if it exists) will be overwritten. If False (default), an error will be raised if the file exists. To overwrite original file (the same one that was loaded), data must be preloaded upon reading. This defaults to True in 0.18 but will change to False in 0.19.

New in version 0.18.

verbose

If not None, override default verbose level (see mne.verbose() and Logging documentation for more). Defaults to self.verbose.

Notes

Bad epochs will be dropped before saving the epochs to disk.

savgol_filter(self, h_freq, verbose=None)[source]

Filter the data using Savitzky-Golay polynomial method.

Parameters
h_freqfloat

Approximate high cut-off frequency in Hz. Note that this is not an exact cutoff, since Savitzky-Golay filtering [1] is done using polynomial fits instead of FIR/IIR filtering. This parameter is thus used to determine the length of the window over which a 5th-order polynomial smoothing is used.

verbose

If not None, override default verbose level (see mne.verbose() and Logging documentation for more). Defaults to self.verbose.

Returns
instinstance of Epochs or Evoked

The object with the filtering applied.

Notes

For Savitzky-Golay low-pass approximation, see:

New in version 0.9.0.

References

1

Savitzky, A., Golay, M.J.E. (1964). “Smoothing and Differentiation of Data by Simplified Least Squares Procedures”. Analytical Chemistry 36 (8): 1627-39.

Examples

>>> import mne
>>> from os import path as op
>>> evoked_fname = op.join(mne.datasets.sample.data_path(), 'MEG', 'sample', 'sample_audvis-ave.fif')  # doctest:+SKIP
>>> evoked = mne.read_evokeds(evoked_fname, baseline=(None, 0))[0]  # doctest:+SKIP
>>> evoked.savgol_filter(10.)  # low-pass at around 10 Hz # doctest:+SKIP
>>> evoked.plot()  # doctest:+SKIP

set_channel_types(self, mapping)[source]

Define the sensor type of channels.

Note: The following sensor types are accepted:

ecg, eeg, emg, eog, exci, ias, misc, resp, seeg, stim, syst, ecog, hbo, hbr

Parameters
mappingdict

a dictionary mapping a channel to a sensor type (str) {‘EEG061’: ‘eog’}.

Notes

New in version 0.9.0.

set_eeg_reference(self, ref_channels='average', projection=False, verbose=None)[source]

Specify which reference to use for EEG data.

By default, MNE-Python will automatically re-reference the EEG signal to use an average reference (see below). Use this function to explicitly specify the desired reference for EEG. This can be either an existing electrode or a new virtual channel. This function will re-reference the data according to the desired reference and prevent MNE-Python from automatically adding an average reference projection.

Some common referencing schemes and the corresponding value for the ref_channels parameter:

No re-referencing:

If the EEG data is already using the proper reference, set ref_channels=[]. This will prevent MNE-Python from automatically adding an average reference projection.

Average reference:

A new virtual reference electrode is created by averaging the current EEG signal by setting ref_channels='average'. Bad EEG channels are automatically excluded if they are properly set in info['bads'].

A single electrode:

Set ref_channels to a list containing the name of the channel that will act as the new reference, for example ref_channels=['Cz'].

The mean of multiple electrodes:

A new virtual reference electrode is created by computing the average of the current EEG signal recorded from two or more selected channels. Set ref_channels to a list of channel names, indicating which channels to use. For example, to apply an average mastoid reference, when using the 10-20 naming scheme, set ref_channels=['M1', 'M2'].

Parameters
ref_channels

The name(s) of the channel(s) used to construct the reference. To apply an average reference, specify 'average' here (default). If an empty list is specified, the data is assumed to already have a proper reference and MNE will not attempt any re-referencing of the data. Defaults to an average reference.

projectionbool

If ref_channels='average' this argument specifies if the average reference should be computed as a projection (True) or not (False; default). If projection=True, the average reference is added as a projection and is not applied to the data (it can be applied afterwards with the apply_proj method). If projection=False, the average reference is directly applied to the data. If ref_channels is not 'average', projection must be set to False (the default in this case).

verbose

If not None, override default verbose level (see mne.verbose() and Logging documentation for more). Defaults to self.verbose.

Returns
instinstance of Raw | Epochs | Evoked

Data with EEG channels re-referenced. If ref_channels='average' and projection=True a projection will be added instead of directly re-referencing the data.

mne.set_bipolar_reference

Convenience function for creating bipolar references.

Notes

1. If a reference is requested that is not the average reference, this function removes any pre-existing average reference projections.

2. During source localization, the EEG signal should have an average reference.

3. In order to apply a reference, the data must be preloaded. This is not necessary if ref_channels='average' and projection=True.

4. For an average reference, bad EEG channels are automatically excluded if they are properly set in info['bads'].

New in version 0.9.0.

set_montage(self, montage, set_dig=True, verbose=None)[source]

Set EEG sensor configuration and head digitization.

Parameters
montageinstance of Montage | instance of DigMontage | str | None

The montage to use (None removes any location information).

set_digbool

If True, update the digitization information (info['dig']) in addition to the channel positions (info['chs'][idx]['loc']).

verbose

If not None, override default verbose level (see mne.verbose() and Logging documentation for more). Defaults to self.verbose.

Notes

Operates in place.

New in version 0.9.0.

shift_time(self, tshift, relative=True)[source]

Shift time scale in epoched data.

Parameters
tshiftfloat

The amount of time shift to be applied if relative is True else the first time point. When relative is True, positive value of tshift moves the data forward while negative tshift moves it backward.

relativebool

If true, move the time backwards or forwards by specified amount. Else, set the starting time point to the value of tshift.

Notes

Maximum accuracy of time shift is 1 / epochs.info[‘sfreq’]

standard_error(self, picks=None)[source]

Compute standard error over epochs.

Parameters
picks

Channels to include. Slices and lists of integers will be interpreted as channel indices. In lists, channel type strings (e.g., ['meg', 'eeg']) will pick channels of those types, channel name strings (e.g., ['MEG0111', 'MEG2623'] will pick the given channels. Can also be the string values “all” to pick all channels, or “data” to pick data channels. None (default) will pick all data channels.

Returns
evokedinstance of Evoked

The standard error over epochs.

subtract_evoked(self, evoked=None)[source]

Subtract an evoked response from each epoch.

Can be used to exclude the evoked response when analyzing induced activity, see e.g. [1].

Parameters
evokedinstance of Evoked | None

The evoked response to subtract. If None, the evoked response is computed from Epochs itself.

Returns
selfinstance of Epochs

The modified instance (instance is also modified inplace).

References

[1] David et al. “Mechanisms of evoked and induced responses in MEG/EEG”, NeuroImage, vol. 31, no. 4, pp. 1580-1591, July 2006.

time_as_index(self, times, use_rounding=False)[source]

Convert time to indices.

Parameters
timeslist-like | float | int

List of numbers or a number representing points in time.

use_roundingbool

If True, use rounding (instead of truncation) when converting times to indices. This can help avoid non-unique indices.

Returns
indexndarray

Indices corresponding to the times supplied.

property times

Time vector in seconds.

property tmax

Last time point.

property tmin

First time point.

to_data_frame(self, picks=None, index=None, scaling_time=1000.0, scalings=None, copy=True, start=None, stop=None, long_format=False)[source]

Export data in tabular structure as a pandas DataFrame.

Columns and indices will depend on the object being converted. Generally this will include as much relevant information as possible for the data type being converted. This makes it easy to convert data for use in packages that utilize dataframes, such as statsmodels or seaborn.

Parameters
picks

Channels to include. Slices and lists of integers will be interpreted as channel indices. In lists, channel type strings (e.g., ['meg', 'eeg']) will pick channels of those types, channel name strings (e.g., ['MEG0111', 'MEG2623'] will pick the given channels. Can also be the string values “all” to pick all channels, or “data” to pick data channels. None (default) will pick all channels.

index

Column to be used as index for the data. Valid string options are ‘epoch’, ‘time’ and ‘condition’. If None, all three info columns will be included in the table as categorial data.

scaling_timefloat

Scaling to be applied to time units.

scalings

Scaling to be applied to the channels picked. If None, defaults to scalings=dict(eeg=1e6, grad=1e13, mag=1e15, misc=1.0).

copybool

If true, data will be copied. Else data may be modified in place.

start

If it is a Raw object, this defines a starting index for creating the dataframe from a slice. The times will be interpolated from the index and the sampling rate of the signal.

stop

If it is a Raw object, this defines a stop index for creating the dataframe from a slice. The times will be interpolated from the index and the sampling rate of the signal.

long_formatbool

If True, the dataframe is returned in long format where each row is one observation of the signal at a unique coordinate of channels, time points, epochs and conditions. The number of factors depends on the data container. For convenience, a ch_type column is added when using this option that will facilitate subsetting the resulting dataframe. Defaults to False.

Returns
dfinstance of pandas.DataFrame

A dataframe suitable for usage with other statistical/plotting/analysis packages. Column/Index values will depend on the object type being converted, but should be human-readable.