visbrain.gui.Sleep¶
-
class
visbrain.gui.
Sleep
(data=None, hypno=None, config_file=None, annotations=None, channels=None, sf=None, downsample=100.0, axis=True, href=['art', 'wake', 'rem', 'n1', 'n2', 'n3'], preload=True, use_mne=False, kwargs_mne={}, verbose=None)[source][source]¶ Visualize and edit sleep data.
Use this module to :
Load and visualize polysomnographic data and spectrogram.
Load, edit and save hypnogram from the interface
Perform automatic events detection
Further signal processing tools (de-mean, de-trend and filtering)
Topographic data visualization
Sleep has been developped in collaboration with Raphael Vallat.
- Parameters
- datastring, array_like | None
Polysomnographic data. Must either be a path to a supported file (see notes) or an array of raw data of shape (n_channels, n_pts). If None, a dialog window to load the file should appear.
- hypnoarray_like | None
Hypnogram data. Should be a raw vector of shape (n_pts,)
- config_filestring | None
Path to the configuration file (.txt)
- annotationsstring | None
Path to the annotation file (.txt, .csv). Alternatively, you can pass an annotation instance of MNE or simply an (N,) array describing the onset.
- channelslist | None
List of channel names. The length of this list must be n_channels.
- sffloat | None
The sampling frequency of raw data.
- downsamplefloat | 100.
The downsampling frequency for the data and hypnogram raw data.
- axisbool | False
Specify if each axis have to contains its own axis. Be carefull with this option, the rendering can be much slower.
- hreflist | [‘art’, ‘wake’, ‘rem’, ‘n1’, ‘n2’, ‘n3’]
List of sleep stages. This list can be used to changed the display order into the GUI.
- preloadbool | True
Preload data into memory. For large datasets, turn this parameter to True.
- use_mnebool | False
Force to load the file using mne.io functions.
- kwargs_mnedict | {}
Dictionary to pass to the mne.io loading function.
Notes
Note
Supported polysomnographic files : by default, Sleep support .vhdr (BrainVision), .eeg (Elan), .trc (Micromed) and .edf (European Data Format). If mne-python is installed, this default list of supported files is extended to .cnt, .egi, .mff, .edf, .bdf, .gdf, .set, .vhdr.
Supported hypnogram files : by default, Sleep support .txt, .csv and .hyp hypnogram files.
Deprecated since version 0.3.4: Input arguments file and hypno_file has been deprecated in 0.3.4 release. Use instead the data and hypno inputs.
-
replace_detections
(self, dtype, method)[source][source]¶ Replace the default detection methods.
- Parameters
- dtypestring
Name of the method to replace. Should be ‘spindle’, ‘sw’ (slow waves), ‘kc’ (k-complexes), ‘rem’ (rapid eye movements), ‘mt’ (muscle twitches) or ‘peak’.
- methodfunction
Function to replace the detection. The function should take as an input :
A vector array of data of shape (n_time_points,)
The sampling frequency (float)
The time vector of shape (n_time_points,)
A vector array for the hypnogram of shape (n_time_points,)
Then, the function should return indices of relevant events. Returned indices should either be :
An array of shape (n_events, 2) where n_events describe the number of detected events. The first and second columns of the array respectively describe where detected events start and finished.
A boolean vector of shape (n_time_points,) where True values refer to detected events.
An array which contains consecutive indices of detected events.
Examples
>>> def method(data, sf, hypno): >>> # Do stuff >>> indices = ... >>> return indices