tacco.utils.dense_distance_matrix

dense_distance_matrix(A, B=None, parallel=True)

Calclulate a dense pairwise euclidean distance matrix of dense inputs. Compared to tacco.tools.cdist() this has a few extra optimizations for 1D-3D data - and only works for dense inputs.

For a sparse version, see sparse_distance_matrix().

Parameters:

• A – A 2d ndarray.

• B – A 2d ndarray with the same second dimension as A. If None, use A.

• parallel – Whether to run the operation in parallel.

Returns:

A ndarray containing the distances.