SpectralPipe

class sleepeegpy.pipeline.SpectralPipe(*, prec_pipe=None, path_to_eeg=_Nothing.NOTHING, output_dir=_Nothing.NOTHING, path_to_hypno=None, hypno_freq=_Nothing.NOTHING, hypno=_Nothing.NOTHING)

Bases: BaseHypnoPipe, SpectrumPlots

The spectral analyses pipeline element.

Contains methods for computing and plotting PSD, spectrogram and topomaps per sleep stage.

Methods:

compute_psd	For each sleep stage creates a mne.time_frequency.SpectrumArray object.
interpolate_bads	A wrapper for mne.io.Raw.interpolate_bads()
parametrize	Spectral parametrization by FOOOF - fitting oscillations & one over f.
plot	A wrapper for mne.io.Raw.plot().
plot_hypnospectrogram	Plots hypnogram and spectrogram.
plot_psds	Plot PSD per sleep stage.
plot_sensors	A wrapper for mne.viz.plot_sensors() with a legend.
plot_topomap	Plots topomap for a sleep stage and a frequency band.
plot_topomap_collage	Plots topomap collage for multiple sleep stages and bands.
predict_hypno	Runs YASA's automatic sleep staging.
read_spectra	Loads spectra stored in hdf5 files.
save_psds	Saves SleepSpectrum objects to h5 files.
save_raw	A wrapper for mne.io.Raw.save().
set_eeg_reference	A wrapper for mne.io.Raw.set_eeg_reference().
sleep_stats	A wrapper for yasa.sleep_statistics().

Attributes:

mne_raw	An instanse of mne.io.Raw or mne.Epochs.
fooofs	Instances of fooof.FOOOF per sleep stage.
bad_data_percent	Calculates percent of data segments annotated as BAD.
sf	A wrapper for raw.info["sfreq"].
path_to_hypno	Path to hypnogram.
hypno_freq	Sampling rate of the hypnogram in Hz.
hypno	Hypnogram with sampling frequency hypno_freq with int representing sleep stage.
hypno_up	Hypnogram upsampled to the sampling frequency of the raw data.
prec_pipe	Preceding pipe that hands over mne_raw object and output_dir.
path_to_eeg	Can be any eeg file type supported by mne.io.read_raw().
output_dir	Path to the directory where the output will be saved.
psds	Instances of SleepSpectrum per sleep stage.

mne_raw: Raw | Epochs

An instanse of mne.io.Raw or mne.Epochs.

fooofs: dict

Instances of fooof.FOOOF per sleep stage.

compute_psd(sleep_stages={'N1': 1, 'N2': 2, 'N3': 3, 'REM': 4, 'Wake': 0}, reference=None, fmin=0, fmax=60, picks='eeg', reject_by_annotation=True, save=False, overwrite=False, **psd_kwargs)

For each sleep stage creates a mne.time_frequency.SpectrumArray object.

Parameters:

• sleep_stages (dict) – Sleep stages mapping in hypnogram. Defaults to {“Wake”: 0, “N1”: 1, “N2”: 2, “N3”: 3, “REM”: 4}.

• reference (UnionType[Iterable[str], str, None]) – Which eeg reference to compute PSD with. If None, the reference isn’t changed. Defaults to None.

• fmin (float) – Lower frequency bound. Defaults to 0.

• fmax (float) – Upper frequency bound. Defaults to 60.

• picks (str | Iterable[str]) – Channels to compute spectra for. Refer to mne.io.Raw.pick(). Defaults to “eeg”.

• reject_by_annotation (bool) – Whether to not use the annotations for the spectra computation. Defaults to True.

• save (bool) – Whether to save the spectra in .h5 files. Defaults to False.

• overwrite (bool) – Whether to overwrite psd files. Defaults to False.

• **psd_kwargs – Additional arguments passed to mne.time_frequency.psd_array_welch().

parametrize(picks, freq_range=None, average_ch=False, **kwargs)

Spectral parametrization by FOOOF - fitting oscillations & one over f.

Parameters:

• picks – Channels to use in parametrization.

• freq_range – Range of frequencies to parametrize. If None, set to bandpass filter boundaries. Defaults to None.

• average_ch – Whether to average psds over channels. If False or multiple channels are provided, the FOOOFGroup will be used. Defaults to False.

• **kwargs – Arguments passed to fooof.FOOOF.

read_spectra(dirpath=None)

Loads spectra stored in hdf5 files.

Filenames should end with {sleep_stage}-psd.h5

Parameters:

dirpath (Optional[str]) – Path to the directory containing hdf5 files. Defaults to None.

plot_hypnospectrogram(picks=('E101',), win_sec=10, trimperc=2.5, freq_range=(0, 40), cmap='Spectral_r', overlap=False, reject_by_annotation='NaN', save=False, axis=None)

Plots hypnogram and spectrogram.

Adapted from YASA.

Parameters:

• picks (str | Iterable[str]) – Channels to compute the spectrogram on. Defaults to (“E101”,).

• win_sec (float) – The length of the sliding window, in seconds, used for multitaper PSD calculation. Defaults to 30.

• trimperc (float) – The amount of data to trim on both ends of the distribution when normalizing the colormap. Defaults to 2.5.

• freq_range (tuple) – Range of x axis on spectrogram plot. Defaults to (0, 40).

• cmap (str) – Matplotlib colormap. Choosing Colormaps. Defaults to “Spectral_r”.

• overlap (bool) – Whether to plot hypnogram over the spectrogram or on top of it. Defaults to False.

• reject_by_annotation (Optional[str]) – Whether to reject the annotations for the spectrogram computation. Can be ‘NaN’, ‘omit’ or None. Defaults to ‘NaN’.

• save (bool) – Whether to save the figure. Defaults to False.

• axis (Axes) – Instance of matplotlib.axes.Axes. Defaults to None.

property bad_data_percent

Calculates percent of data segments annotated as BAD.

Returns:

percent of bad data spans in raw data

Return type:

float

interpolate_bads(**interp_kwargs)

A wrapper for mne.io.Raw.interpolate_bads()

Parameters:

**interp_kwargs – Arguments passed to mne.io.Raw.interpolate_bads().

plot(save_annotations=False, save_bad_channels=False, overwrite=False, **kwargs)

A wrapper for mne.io.Raw.plot().

Parameters:

• save_annotations (bool) – Whether to save annotations as txt. Defaults to False.

• save_bad_channels (bool) – Whether to save bad channels as txt. Defaults to False.

• overwrite (bool) – Whether to overwrite annotations and bad_channels files if exist. Defaults to False.

• **kwargs – Arguments passed to mne.io.Raw.plot().

plot_psds(picks, psd_range=(-40, 60), freq_range=(0, 60), dB=True, xscale='linear', axis=None, plot_sensors=False, save=False, legend_args=None, **plot_kwargs)

Plot PSD per sleep stage.

Parameters:

• picks (Iterable[str] | str) – Channels to plot PSDs for. Refer to mne.io.Raw.pick().

• psd_range (tuple) – Range of y axis on PSD plot. Defaults to (-40, 60).

• freq_range (tuple) – Range of x axis on PSD plot. Defaults to (0, 40).

• dB – Whether transform PSD to dB. Defaults to True.

• xscale (str) – Scale of the X axis, check available values at matplotlib.axes.Axes.set_xscale(). Defaults to “linear”.

• axis (axis) – Instance of matplotlib.axes.Axes. Defaults to None.

• plot_sensors (bool) – Whether to plot sensor map showing which channels were used for computing PSD. Defaults to False.

• save (bool) – Whether to save the figure. Defaults to False.

• **plot_kwargs – Arguments passed to the matplotlib.pyplot.plot(). Have no effect if axis is provided.Defaults to None.

plot_sensors(legend=None, legend_args=None, **kwargs)

A wrapper for mne.viz.plot_sensors() with a legend.

Parameters:

• legend (Iterable[str]) – ch_groups names to connect to colors. Defaults to None.

• legend_args (dict) – Arguments passed to matplotlib.axes.Axes.legend(). Defaults to None.

• **kwargs – Arguments passed to mne.viz.plot_sensors().

plot_topomap(stage='REM', band={'Delta': (0, 4)}, dB=False, axis=None, save=False, topomap_args=None, cbar_args=None)

Plots topomap for a sleep stage and a frequency band.

Parameters:

• stage (str) – One of the sleep_stages keys. Defaults to “REM”.

• band (dict) – Name-value pair - with name=arbitrary name and value=(l_freq, h_freq). Defaults to {“Delta”: (0, 4)}.

• dB (bool) – Whether transform PSD to dB. Defaults to False.

• axis (axis) – Instance of matplotlib.axes.Axes. Defaults to None.

• save (bool) – Whether to save the figure. Defaults to False.

• topomap_args (dict) – Arguments passed to mne.viz.plot_topomap().Defaults to None.

• cbar_args (dict) – Arguments passed to matplotlib.pyplot.colorbar().Defaults to None.

plot_topomap_collage(stages_to_plot='all', bands={'Alpha': (8, 12.49), 'Beta': (12.5, 29.99), 'Delta': (0, 3.99), 'Gamma': (30, 60), 'Sigma': (12.5, 15), 'Theta': (4, 7.99)}, dB=False, low_percentile=5, high_percentile=95, fig=None, save=False, topomap_args=None, cbar_args=None)

Plots topomap collage for multiple sleep stages and bands.

Parameters:

• stages_to_plot (tuple) – Tuple of strings representing names from sleep_stages, e.g., (“REM”, “N1”). If set to “all” plots every stage provided in sleep_stages. Defaults to “all”.

• bands (dict) – Dict of name-value pairs - with name=arbitrary name and value=(l_freq, h_freq). Defaults to { “Delta”: (0, 3.99), “Theta”: (4, 7.99), “Alpha”: (8, 12.49), “Sigma”: (12.5, 15), “Beta”: (12.5, 29.99), “Gamma”: (30, 60), }.

• dB (bool) – Whether transform PSD to dB. Defaults to False.

• sleep_stages – Mapping between sleep stages names and their integer representations. Defaults to {“Wake”: 0, “N1”: 1, “N2”: 2, “N3”: 3, “REM”: 4}.

• low_percentile (float) – Set min color value by percentile of the band data. Defaults to 5.

• high_percentile (float) – Set max color value by percentile of the band data. Defaults to 95.

• fig (figure) – Instance of mpl:matplotlib.pyplot.figure. Defaults to None.

• save (bool) – Whether to save the figure. Defaults to False.

• topomap_args (dict) – Arguments passed to mne.viz.plot_topomap(). Defaults to None.

• cbar_args (dict) – Arguments passed to matplotlib.pyplot.colorbar(). Defaults to None.

predict_hypno(eeg_name='E183', eog_name='E252', emg_name='E247', ref_name='E26', save=True)

Runs YASA’s automatic sleep staging.

Parameters:

• eeg_name (str) – Preferentially a central electrode. Defaults to “E183”.

• eog_name (str) – Preferentially, the left LOC channel. Defaults to “E252”.

• emg_name (str) – Preferentially a chin electrode. Defaults to “E247”.

• ref_name (str) – Reference channel, preferentially a mastoid. Defaults to “E26”.

• save (bool) – Whether to save the hypnogram to file. Defaults to True.

save_psds(overwrite)

Saves SleepSpectrum objects to h5 files.

Parameters:

overwrite – Whether to overwrite existing spectrum files.

save_raw(fname, **kwargs)

A wrapper for mne.io.Raw.save().

Parameters:

• fname (str) – Filename for the fif file being saved.

• **kwargs – Arguments passed to mne.io.Raw.save().

set_eeg_reference(ref_channels='average', projection=False, **kwargs)

A wrapper for mne.io.Raw.set_eeg_reference().

Parameters:

• ref_channels – ref_channels. Defaults to ‘average’.

• projection – projection. Defaults to False.

• **kwargs – Additional arguments passed to mne.io.Raw.set_eeg_reference().

property sf

A wrapper for raw.info["sfreq"].

Returns:

sampling frequency

Return type:

float

sleep_stats(save=False)

A wrapper for yasa.sleep_statistics().

Parameters:

save (bool) – Whether to save the stats to csv. Defaults to False.

path_to_hypno: Path

Path to hypnogram. Must be text file with every row being int representing sleep stage for the epoch.

hypno_freq: float

Sampling rate of the hypnogram in Hz.

E.g., 1/30 means 1 sample per 30 secs epoch, 250 means 1 sample per 1/250 sec epoch.

hypno: np.ndarray

Hypnogram with sampling frequency hypno_freq with int representing sleep stage.

hypno_up: np.array

Hypnogram upsampled to the sampling frequency of the raw data.

prec_pipe: Type[BasePipeType]

Preceding pipe that hands over mne_raw object and output_dir.

path_to_eeg: Path

Can be any eeg file type supported by mne.io.read_raw().

output_dir: Path

Path to the directory where the output will be saved.

psds: dict

Instances of SleepSpectrum per sleep stage.