onion_clustering.onion_multi.onion_inner

onion_clustering.onion_multi.onion_inner(matrix, ndims, bins, number_of_sigmas)

Returns the clustering object with the analysis.

Parameters:
  • matrix (ndarray of shape (dims, n_particles, n_frames)) – The values of the signal for each particle at each frame.

  • n_dims (int) – Number of components. Must be 2 or 3.

  • bins (Union[str, int] = "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_sigma (float = 2.0) – Sets the thresholds for classifing a signal window inside a state: the window is contained in the state if it is entirely contained inside number_of_sigma * state.sigms times from state.mean.

  • ndims (int)

  • number_of_sigmas (float)

Returns:

clustering_object – The final clustering object.

Return type:

ClusteringObject2D

Notes

  • Reads the data and the parameters

  • Performs the quick analysis for all the values in tau_window_list

  • Performs a detailed analysis with the selected parameters