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python scipy numpy add points to existing distance matrix
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import numpy as np | |
from scipy.spatial import distance | |
def add_points_to_distance_matrix(points, original_array, distance_matrix, metric='euclidean'): | |
""" | |
There is an NxM array of points, a square matrix NxN with distances between points. | |
This function adds new points to the distance matrix. | |
We need to create a diagonal block holding distances between the new points | |
and two identical blocks holding distances to original array. | |
E.g. | |
original_array = ([[1,2,3],[1,2,4],[1,2,5]]) | |
distance_matrix = distance.squareform(distance.pdist(original_array)) | |
>>> distance_matrix | |
array([[0., 1., 2.], | |
[1., 0., 1.], | |
[2., 1., 0.]]) | |
>>> add_points_to_distance_matrix([[1,2,5],[1,2,5]], original_array,distance_matrix) | |
array([[0., 1., 2., 2., 2.], | |
[1., 0., 1., 1., 1.], | |
[2., 1., 0., 0., 0.], | |
[2., 1., 0., 0., 0.], | |
[2., 1., 0., 0., 0.]]) | |
""" | |
diagonal = distance.squareform(distance.pdist(points, metric=metric)) | |
twin_block = distance.cdist(original_array, points, metric=metric) | |
return (np.vstack([np.hstack([distance_matrix,twin_block]), np.hstack([twin_block.T, diagonal])])) |
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