Pipeline Functions¶

Classes and Functions for running the Lossless Pipeline.

pylossless.pipeline.chan_neighbour_r(epochs, nneigbr, method)¶

Compute nearest Neighbor R.

Parameters:

epochsmne.Epochs
nneigbrint: Number of neighbours to compare in open interval
methodstr: One of ‘max’, ‘mean’, or ‘trimmean’. This is the function which aggregates the neighbours into one value.

Returns:

pylossless.pipeline.coregister(raw_edf, fiducials='estimated', show_coreg=False, verbose=False)¶

Coregister Raw object to ‘fsaverage’.

Parameters:

raw_edfmne.Raw: an instance of mne.Raw to coregister.
fiducialsstr (default ‘estimated’): fiducials to use for coregistration. if ‘estimated’, gets fiducials from fsaverage.
show_coregbool (default False): If True, shows the coregistration result in a plot.
verbosebool | str (default False): sets the logging level for mne.Coregistration.

Returns:

coregistration | numpy.array: a numpy array containing the coregistration trans values.

pylossless.pipeline.epochs_to_xr(epochs, kind='ch', ica=None)¶

Create an Xarray DataArray from an instance of mne.Epochs.

Parameters:

epochsmne.Epochs: an instance of mne.Epochs
kindstr: The name to be passed into the coords argument of xr.DataArray corresponding to the channel dimension of the epochs object. Must be 'ch' or 'ic'.
icamne.preprocessing.ICA: If not None, should be an instance of mne.preprocessing.ICA from which to pull the names of the ICA components.

Returns:

xarray.DataArray: an instance of xarray.DataArray, with dimensions 'epochs', 'time' (samples), and either 'ch' (channels) or 'ic' (independent components).

pylossless.pipeline.get_operate_dim(array, flag_dim)¶

Get the xarray.DataArray dimension to flag for a pipeline method.

Parameters:

arrayxarray.DataArray: An instance of Xarray.DataArray that was constructed from an mne.Epochs object, using pylossless.pipeline.epochs_to_xr. The array must be 2D.
flag_dimstr: Name of the dimension to remove in xarray.DataArray.dims. Must be one of 'epoch', 'ch', or 'ic'.

Returns:

listlist: a list of the dimensions of the xarray.DataArray, excluding the dimension that the pipeline will conduct flagging operations on.

pylossless.pipeline.warp_locs(self, raw)¶

Warp locs.

Parameters:

Returns: