tropea_clustering.OnionUniSmooth¶

class tropea_clustering.OnionUniSmooth(delta_t, bins='auto', number_of_sigmas=3.0, max_area_overlap=0.8)[source]¶

Performs onion clustering on a data array.

Returns an array of integer labels, one for each frame. Unclassified frames are labelled “-1”.

Note

This class is currently in beta testing. Its operations could change in the future. Use with caution.

Parameters:

delta_t (int) – The minimum lifetime required for the clusters. Also referred to as the “time resolution” of the clustering analysis.
bins (int, default="auto") – The number of bins used for the construction of the histograms. Can be an integer value, or “auto”. If “auto”, the default of numpy.histogram_bin_edges is used (see https://numpy.org/doc/stable/reference/generated/numpy.histogram_bin_edges.html#numpy.histogram_bin_edges).
number_of_sigmas (float, default=3.0) – Sets the thresholds for classifing a signal sequence inside a state: the sequence is contained in the state if it is entirely contained inside number_of_sigmas * state.sigmas times from state.mean.
max_area_overlap (float, default=0.8) – Thresold to consider two Gaussian states overlapping, and thus merge them together.

states_list_¶

The list of the identified states. Refer to the documentation of StateUni for accessing the information on the states.

Type:: List[StateUni]

labels_¶

Cluster labels for each frame. Unclassified points are given the label “-1”.

Type:: ndarray of shape (n_particles, n_frames)

Example

import numpy as np
from tropea_clustering import OnionUniSmooth

# Create random input data
np.random.seed(1234)
n_particles = 5
n_steps = 1000

delta_t = 5
input_data = np.random.rand(n_particles, n_steps)

# Run Onion Clustering
clusterer = OnionUniSmooth(delta_t)
clust_params = {"bins": 100, "number_of_sigmas": 3.0}
clusterer.set_params(**clust_params)
clusterer.fit(input_data)

Methods

`fit`	Performs onion clustering on the data array 'X'.
`fit_predict`	Computes clusters on the data array 'X' and returns labels.
`get_params`
`set_params`

fit(X, y=None)[source]¶

Performs onion clustering on the data array ‘X’.

Parameters:: X (ndarray of shape (n_particles, n_frames)) – The time-series data to cluster.
Returns:: self – A fitted instance of self.
Return type:: object

fit_predict(X, y=None)[source]¶

Computes clusters on the data array ‘X’ and returns labels.

Parameters:: X (ndarray of shape (n_particles, n_frames)) – The time-series data to cluster.
Returns:: labels – Cluster labels for each frame. Unclassified points are given the label “-1”.
Return type:: ndarray of shape (n_particles, n_frames)