`scipy.spatial._ckdtree:cKDTree.sparse_distance_matrix`

Signature

def sparse_distance_matrix(other, max_distance, p = 2.0, output_type = dok_matrix)

Summary

Compute a sparse distance matrix

Extended Summary

Computes a distance matrix between two cKDTrees, leaving as zero any distance greater than max_distance.

Parameters

other : cKDTree: The other KDTree to compute distances against.
max_distance : positive float: Maximum distance within which neighbors are returned. Distances above this value are returned as zero.
p : float, 1<=p<=infinity: Which Minkowski p-norm to use. A finite large p may cause a ValueError if overflow can occur.
output_type : str, optional: Which container to use for output data. Options: 'dok_array', 'coo_array', 'dict', or 'ndarray'. Legacy options 'dok_matrix' and 'coo_matrix' are still available. Default: 'dok_matrix'.
warning
dok_matrix and coo_matrix are being replaced. All new code using scipy sparse should use sparse array types 'dok_array' or 'coo_array'. The default value of output_type will be deprecated at v1.19 and switch from 'dok_matrix' to 'dok_array' in v1.21. The values 'dok_matrix' and 'coo_matrix' continue to work, but will go away eventually.

Returns

result : dok_array, coo_array, dict or ndarray: Sparse matrix representing the results in "dictionary of keys" format. If a dict is returned the keys are (i,j) tuples of indices. If output_type is 'ndarray' a record array with fields 'i', 'j', and 'v' is returned,

Examples

You can compute a sparse distance matrix between two kd-trees:

import numpy as np
from scipy.spatial import cKDTree
rng = np.random.default_rng()
points1 = rng.random((5, 2))
points2 = rng.random((5, 2))
kdtree1 = cKDTree(points1)
kdtree2 = cKDTree(points2)
sdm = kdtree1.sparse_distance_matrix(kdtree2, 0.3, output_type="dok_array")

✓

sdm.toarray()

✗

array([[0.     , 0.     , 0.     , 0.     , 0.     ],
       [0.     , 0.     , 0.     , 0.     , 0.     ],
       [0.     , 0.     , 0.     , 0.     , 0.     ],
       [0.     , 0.     , 0.     , 0.     , 0.     ],
       [0.16705, 0.     , 0.     , 0.     , 0.     ]])

You can check distances above the `max_distance` are zeros:

from scipy.spatial.distance import cdist

✓

cdist(points1, points2)

✗

array([[0.38065, 0.78542, 0.44928, 0.39562, 0.5381 ],
       [0.38275, 0.40985, 0.44793, 0.67419, 0.46706],
       [0.78963, 0.99555, 0.57206, 0.30512, 0.64905],
       [0.60485, 0.9141 , 0.51235, 0.31829, 0.6001 ],
       [0.16705, 0.66419, 0.61616, 0.76776, 0.6628 ]])

Aliases

scipy.spatial.cKDTree.sparse_distance_matrix