pyriemann.clustering.PotatoField¶
- class pyriemann.clustering.PotatoField(n_potatoes=1, p_threshold=0.01, z_threshold=3, metric='riemann', n_iter_max=10, pos_label=1, neg_label=0)¶
Artefact detection with the Riemannian Potato Field.
The Riemannian Potato Field [1] is a clustering method used to detect artifact in EEG signals. The algorithm combines several potatoes of low dimension, each one being designed to capture specific artifact typically affecting specific subsets of channels and/or specific frequency bands.
- Parameters
- n_potatoesint, default=1
Number of potatoes in the field.
- p_thresholdfloat, default=0.01
Threshold on probability to being clean, in (0, 1), combining probabilities of potatoes using Fisher’s method.
- z_thresholdfloat, default=3
Threshold on z-score of distance to reject artifacts. It is the number of standard deviations from the mean of distances to the centroid.
- metricstring, default=’riemann’
The type of metric used for centroid and distance estimation.
- n_iter_maxint, default=10
The maximum number of iteration to reach convergence.
- pos_label: int, default=1
The positive label corresponding to clean data.
- neg_label: int, default=0
The negative label corresponding to artifact data.
See also
Notes
New in version 0.3.
References
- 1
The Riemannian Potato Field: A Tool for Online Signal Quality Index of EEG Q. Barthélemy, L. Mayaud, D. Ojeda, and M. Congedo. IEEE Transactions on Neural Systems and Rehabilitation Engineering, IEEE Institute of Electrical and Electronics Engineers, 2019, 27 (2), pp.244-255
- __init__(n_potatoes=1, p_threshold=0.01, z_threshold=3, metric='riemann', n_iter_max=10, pos_label=1, neg_label=0)¶
Init.
- fit(X, y=None)¶
Fit the potato field from covariance matrices.
Fit the potato field from covariance matrices, with iterative outlier removal to obtain reliable potatoes.
- Parameters
- Xlist of n_potatoes ndarrays of shape (n_matrices, n_channels, n_channels) with same n_matrices but potentially different n_channels
List of sets of SPD matrices, each corresponding to a different subset of EEG channels and/or filtering with a specific frequency band.
- yNone | ndarray, shape (n_matrices,), default=None
Labels corresponding to each matrix: positive (resp. negative) label corresponds to a clean (resp. artifact) matrix. If None, all matrices are considered as clean.
- Returns
- selfPotatoField instance
The PotatoField instance.
- fit_transform(X, y=None, **fit_params)¶
Fit to data, then transform it.
Fits transformer to X and y with optional parameters fit_params and returns a transformed version of X.
- Parameters
- Xarray-like of shape (n_samples, n_features)
Input samples.
- yarray-like of shape (n_samples,) or (n_samples, n_outputs), default=None
Target values (None for unsupervised transformations).
- **fit_paramsdict
Additional fit parameters.
- Returns
- X_newndarray array of shape (n_samples, n_features_new)
Transformed array.
- get_params(deep=True)¶
Get parameters for this estimator.
- Parameters
- deepbool, default=True
If True, will return the parameters for this estimator and contained subobjects that are estimators.
- Returns
- paramsdict
Parameter names mapped to their values.
- partial_fit(X, y=None, alpha=0.1)¶
Partially fit the potato field from covariance matrices.
This partial fit can be used to update dynamic or semi-dymanic online potatoes with clean EEG.
- Parameters
- Xlist of n_potatoes ndarrays of shape (n_matrices, n_channels, n_channels) with same n_matrices but potentially different n_channels
List of sets of SPD matrices, each corresponding to a different subset of EEG channels and/or filtering with a specific frequency band.
- yNone | ndarray, shape (n_matrices,), default=None
Labels corresponding to each matrix: positive (resp. negative) label corresponds to a clean (resp. artifact) matrix. If None, all matrices are considered as clean.
- alphafloat, default=0.1
Update rate in [0, 1] for the centroid, and mean and standard deviation of log-distances: 0 for no update, 1 for full update.
- Returns
- selfPotatoField instance
The PotatoField instance.
- predict(X)¶
Predict artefact from data.
- Parameters
- Xlist of n_potatoes ndarrays of shape (n_matrices, n_channels, n_channels) with same n_matrices but potentially different n_channels
List of sets of SPD matrices, each corresponding to a different subset of EEG channels and/or filtering with a specific frequency band.
- Returns
- predndarray of bool, shape (n_matrices,)
The artefact detection: True if the matrix is clean, and False if the matrix contain an artefact.
- predict_proba(X)¶
Predict probability obtained combining probabilities of potatoes.
Predict probability obtained combining probabilities of potatoes using Fisher’s method. A threshold of 0.01 can be used.
- Parameters
- Xlist of n_potatoes ndarrays of shape (n_matrices, n_channels, n_channels) with same n_matrices but potentially different n_channels
List of sets of SPD matrices, each corresponding to a different subset of EEG channels and/or filtering with a specific frequency band.
- Returns
- probandarray, shape (n_matrices,)
Matrix is considered as normal/clean for high value of proba. It is considered as abnormal/artifacted for low value of proba.
- score(X, y, sample_weight=None)¶
Return the mean accuracy on the given test data and labels.
In multi-label classification, this is the subset accuracy which is a harsh metric since you require for each sample that each label set be correctly predicted.
- Parameters
- Xarray-like of shape (n_samples, n_features)
Test samples.
- yarray-like of shape (n_samples,) or (n_samples, n_outputs)
True labels for X.
- sample_weightarray-like of shape (n_samples,), default=None
Sample weights.
- Returns
- scorefloat
Mean accuracy of
self.predict(X)
wrt. y.
- set_params(**params)¶
Set the parameters of this estimator.
The method works on simple estimators as well as on nested objects (such as
Pipeline
). The latter have parameters of the form<component>__<parameter>
so that it’s possible to update each component of a nested object.- Parameters
- **paramsdict
Estimator parameters.
- Returns
- selfestimator instance
Estimator instance.
- transform(X)¶
Return the normalized log-distances to the centroids.
Return the normalized log-distances to the centroids, ie geometric z-scores of distances.
- Parameters
- Xlist of n_potatoes ndarrays of shape (n_matrices, n_channels, n_channels) with same n_matrices but potentially different n_channels
List of sets of SPD matrices, each corresponding to a different subset of EEG channels and/or filtering with a specific frequency band.
- Returns
- zndarray, shape (n_matrices, n_potatoes)
The normalized log-distances to the centroids.