#### Previous topic

scipy.spatial.cKDTree.sparse_distance_matrix

#### Next topic

scipy.spatial.distance.pdist

# scipy.spatial.distance¶

## Distance computations (scipy.spatial.distance)¶

### Function Reference¶

Distance matrix computation from a collection of raw observation vectors stored in a rectangular array.

 pdist(X[, metric, p, w, V, VI]) Pairwise distances between observations in n-dimensional space. cdist(XA, XB[, metric, p, V, VI, w]) Computes distance between each pair of the two collections of inputs. squareform(X[, force, checks]) Converts a vector-form distance vector to a square-form distance matrix, and vice-versa. directed_hausdorff(u, v[, seed]) Computes the directed Hausdorff distance between two N-D arrays.

Predicates for checking the validity of distance matrices, both condensed and redundant. Also contained in this module are functions for computing the number of observations in a distance matrix.

 is_valid_dm(D[, tol, throw, name, warning]) Returns True if input array is a valid distance matrix. is_valid_y(y[, warning, throw, name]) Returns True if the input array is a valid condensed distance matrix. num_obs_dm(d) Returns the number of original observations that correspond to a square, redundant distance matrix. num_obs_y(Y) Returns the number of original observations that correspond to a condensed distance matrix.

Distance functions between two numeric vectors u and v. Computing distances over a large collection of vectors is inefficient for these functions. Use pdist for this purpose.

 braycurtis(u, v) Computes the Bray-Curtis distance between two 1-D arrays. canberra(u, v) Computes the Canberra distance between two 1-D arrays. chebyshev(u, v) Computes the Chebyshev distance. cityblock(u, v) Computes the City Block (Manhattan) distance. correlation(u, v) Computes the correlation distance between two 1-D arrays. cosine(u, v) Computes the Cosine distance between 1-D arrays. euclidean(u, v) Computes the Euclidean distance between two 1-D arrays. mahalanobis(u, v, VI) Computes the Mahalanobis distance between two 1-D arrays. minkowski(u, v, p) Computes the Minkowski distance between two 1-D arrays. seuclidean(u, v, V) Returns the standardized Euclidean distance between two 1-D arrays. sqeuclidean(u, v) Computes the squared Euclidean distance between two 1-D arrays. wminkowski(u, v, p, w) Computes the weighted Minkowski distance between two 1-D arrays.

Distance functions between two boolean vectors (representing sets) u and v. As in the case of numerical vectors, pdist is more efficient for computing the distances between all pairs.

 dice(u, v) Computes the Dice dissimilarity between two boolean 1-D arrays. hamming(u, v) Computes the Hamming distance between two 1-D arrays. jaccard(u, v) Computes the Jaccard-Needham dissimilarity between two boolean 1-D arrays. kulsinski(u, v) Computes the Kulsinski dissimilarity between two boolean 1-D arrays. matching(u, v) Computes the Hamming distance between two boolean 1-D arrays. rogerstanimoto(u, v) Computes the Rogers-Tanimoto dissimilarity between two boolean 1-D arrays. russellrao(u, v) Computes the Russell-Rao dissimilarity between two boolean 1-D arrays. sokalmichener(u, v) Computes the Sokal-Michener dissimilarity between two boolean 1-D arrays. sokalsneath(u, v) Computes the Sokal-Sneath dissimilarity between two boolean 1-D arrays. yule(u, v) Computes the Yule dissimilarity between two boolean 1-D arrays.

hamming also operates over discrete numerical vectors.

Functions

 braycurtis(u, v) Computes the Bray-Curtis distance between two 1-D arrays. callable(obj) canberra(u, v) Computes the Canberra distance between two 1-D arrays. cdist(XA, XB[, metric, p, V, VI, w]) Computes distance between each pair of the two collections of inputs. cdist_fn chebyshev(u, v) Computes the Chebyshev distance. cityblock(u, v) Computes the City Block (Manhattan) distance. converter(X) correlation(u, v) Computes the correlation distance between two 1-D arrays. cosine(u, v) Computes the Cosine distance between 1-D arrays. dice(u, v) Computes the Dice dissimilarity between two boolean 1-D arrays. directed_hausdorff(u, v[, seed]) Computes the directed Hausdorff distance between two N-D arrays. euclidean(u, v) Computes the Euclidean distance between two 1-D arrays. hamming(u, v) Computes the Hamming distance between two 1-D arrays. is_valid_dm(D[, tol, throw, name, warning]) Returns True if input array is a valid distance matrix. is_valid_y(y[, warning, throw, name]) Returns True if the input array is a valid condensed distance matrix. jaccard(u, v) Computes the Jaccard-Needham dissimilarity between two boolean 1-D arrays. kulsinski(u, v) Computes the Kulsinski dissimilarity between two boolean 1-D arrays. mahalanobis(u, v, VI) Computes the Mahalanobis distance between two 1-D arrays. matching(u, v) Computes the Hamming distance between two boolean 1-D arrays. minkowski(u, v, p) Computes the Minkowski distance between two 1-D arrays. norm(a[, ord, axis, keepdims]) Matrix or vector norm. num_obs_dm(d) Returns the number of original observations that correspond to a square, redundant distance matrix. num_obs_y(Y) Returns the number of original observations that correspond to a condensed distance matrix. pdist(X[, metric, p, w, V, VI]) Pairwise distances between observations in n-dimensional space. pdist_fn rogerstanimoto(u, v) Computes the Rogers-Tanimoto dissimilarity between two boolean 1-D arrays. russellrao(u, v) Computes the Russell-Rao dissimilarity between two boolean 1-D arrays. seuclidean(u, v, V) Returns the standardized Euclidean distance between two 1-D arrays. sokalmichener(u, v) Computes the Sokal-Michener dissimilarity between two boolean 1-D arrays. sokalsneath(u, v) Computes the Sokal-Sneath dissimilarity between two boolean 1-D arrays. sqeuclidean(u, v) Computes the squared Euclidean distance between two 1-D arrays. squareform(X[, force, checks]) Converts a vector-form distance vector to a square-form distance matrix, and vice-versa. wminkowski(u, v, p, w) Computes the weighted Minkowski distance between two 1-D arrays. yule(u, v) Computes the Yule dissimilarity between two boolean 1-D arrays.

Classes

 partial partial(func, *args, **keywords) - new function with partial application xrange alias of range