distclassipy 0.1.6a0__py3-none-any.whl → 0.2.0__py3-none-any.whl

distclassipy/distances.py

@@ -48,6 +48,52 @@ import numpy as np
 
 import scipy
 
+_ALL_METRICS = [
+    "euclidean",
+    "braycurtis",
+    "canberra",
+    "cityblock",
+    "chebyshev",
+    "clark",
+    "correlation",
+    "cosine",
+    "hellinger",
+    "jaccard",
+    "lorentzian",
+    "marylandbridge",
+    "meehl",
+    "motyka",
+    "soergel",
+    "wave_hedges",
+    "kulczynski",
+    "add_chisq",
+    "acc",
+    "chebyshev_min",
+    "czekanowski",
+    "dice",
+    "divergence",
+    "google",
+    "gower",
+    "jeffreys",
+    "jensenshannon_divergence",
+    "jensen_difference",
+    "kumarjohnson",
+    "matusita",
+    "minkowski",
+    "penroseshape",
+    "prob_chisq",
+    "ruzicka",
+    "sorensen",
+    "squared_chisq",
+    "squaredchord",
+    "squared_euclidean",
+    "taneja",
+    "tanimoto",
+    "topsoe",
+    "vicis_symmetric_chisq",
+    "vicis_wave_hedges",
+]
+
 
 class Distance:
     """A class to calculate various distance metrics between vectors.
@@ -352,7 +398,11 @@ class Distance:
               1(4), 300-307.
         """
         u, v = np.asarray(u), np.asarray(v)
-        return np.sqrt(2 * np.sum((np.sqrt(u) - np.sqrt(v)) ** 2))
+        # Clip negative values to zero for valid sqrt
+        with np.errstate(divide="ignore", invalid="ignore"):
+            u = np.clip(u, a_min=0, a_max=None)
+            v = np.clip(v, a_min=0, a_max=None)
+            return np.sqrt(2 * np.sum((np.sqrt(u) - np.sqrt(v)) ** 2))
 
     def jaccard(self, u, v):
         """Calculate the Jaccard distance between two vectors.
@@ -402,7 +452,8 @@ class Distance:
             eschew the log of zero.
         """
         u, v = np.asarray(u), np.asarray(v)
-        return np.sum(np.log(np.abs(u - v) + 1))
+        with np.errstate(divide="ignore", invalid="ignore"):
+            return np.sum(np.log(np.abs(u - v) + 1))
 
     def marylandbridge(self, u, v):
         """Calculate the Maryland Bridge distance between two vectors.
@@ -578,907 +629,932 @@ class Distance:
         with np.errstate(divide="ignore", invalid="ignore"):
             return np.sum(np.where(uvmult != 0, ((u - v) ** 2 * (u + v)) / uvmult, 0))
 
+    # NOTE: THE FOLLOWING DISTANCES HAVE NOT BEEN TESTED EXTENSIVELY AND ARE
+    # CURRENTLY IN ALPHA AND SO HAVE BEEN COMMENTED
+
+    def acc(self, u, v):
+        """Calculate the average of Cityblock and Chebyshev distance.
+
+        This function computes the ACC distance, also known as the
+        Average distance, between two vectors u and v. It is the average of the
+        Cityblock (or Manhattan) and Chebyshev distances.
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the distance is to be calculated.
+
+        Returns
+        -------
+        - The ACC distance between the two vectors.
+
+        References
+        ----------
+            1. Krause EF (2012) Taxicab Geometry An Adventure in Non-Euclidean
+               Geometry. Dover Publications.
+            2. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity
+               Measures between Probability Density Functions. International
+               Journal of Mathematical Models and Methods in Applied Sciences.
+               vol. 1(4), pp. 300-307.
+        """
+        return (self.cityblock(u, v) + self.chebyshev(u, v)) / 2
+
+    # def bhattacharyya(self, u, v):
+    #     """
+    #     Calculate the Bhattacharyya distance between two vectors.
+
+    #     Returns a distance value between 0 and 1.
+
+    #     Parameters
+    #     ----------
+    #     - u, v: Input vectors between which the distance is to be calculated.
+
+    #     Returns
+    #     -------
+    #     - The Bhattacharyya distance between the two vectors.
+
+    #     References
+    #     ----------
+    #         1. Bhattacharyya A (1947) On a measure of divergence between two
+    #            statistical populations defined by probability distributions,
+    #            Bull. Calcutta Math. Soc., 35, 99–109.
+    #         2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+    #            Measures between Probability Density Functions. International
+    #            Journal of Mathematical Models and Methods in Applied Sciences.
+    #            1(4), 300-307.
+    #         3. https://en.wikipedia.org/wiki/Bhattacharyya_distance
+    #     """
+    #     u, v = np.asarray(u), np.asarray(v)
+    #     with np.errstate(divide="ignore", invalid="ignore"):
+    #         return -np.log(np.sum(np.sqrt(u * v)))
+
+    def chebyshev_min(self, u, v):
+        """Calculate the minimum value distance between two vectors.
+
+        This measure represents a custom approach by Zielezinski to distance
+        measurement, focusing on the minimum absolute difference.
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the distance is to be calculated.
+
+        Returns
+        -------
+        - The minimum value distance between the two vectors.
+        """
+        u, v = np.asarray(u), np.asarray(v)
+        return np.amin(np.abs(u - v))
+
+    def czekanowski(self, u, v):
+        """Calculate the Czekanowski distance between two vectors.
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the distance is to be calculated.
+
+        Returns
+        -------
+        - The Czekanowski distance between the two vectors.
+
+        References
+        ----------
+            1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+               Measures between Probability Density Functions. International
+               Journal of Mathematical Models and Methods in Applied Sciences.
+               1(4), 300-307.
+        """
+        u, v = np.asarray(u), np.asarray(v)
+        return np.sum(np.abs(u - v)) / np.sum(u + v)
+
+    def dice(self, u, v):
+        """Calculate the Dice dissimilarity between two vectors.
+
+        Synonyms:
+            Sorensen distance
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the distance is to be calculated.
+
+        Returns
+        -------
+        - The Dice dissimilarity between the two vectors.
+
+        References
+        ----------
+            1. Dice LR (1945) Measures of the amount of ecologic association
+               between species. Ecology. 26, 297-302.
+            2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+               Measures between Probability Density Functions. International
+               Journal of Mathematical Models and Methods in Applied Sciences.
+               1(4), 300-307.
+        """
+        u, v = np.asarray(u), np.asarray(v)
+        u_v = u - v
+        return np.dot(u_v, u_v) / (np.dot(u, u) + np.dot(v, v))
+
+    def divergence(self, u, v):
+        """Calculate the divergence between two vectors.
 
-# NOTE: THE FOLLOWING DISTANCES HAVE NOT BEEN TESTED EXTENSIVELY AND ARE
-# CURRENTLY IN ALPHA AND SO HAVE BEEN COMMENTED
-
-#     def acc(self, u, v):
-#         """Calculate the average of Cityblock and Chebyshev distance.
-
-#         This function computes the ACC distance, also known as the
-#         Average distance, between two vectors u and v. It is the average of the
-#         Cityblock (or Manhattan) and Chebyshev distances.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The ACC distance between the two vectors.
-
-#         References
-#         ----------
-#             1. Krause EF (2012) Taxicab Geometry An Adventure in Non-Euclidean
-#                Geometry. Dover Publications.
-#             2. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity
-#                Measures between Probability Density Functions. International
-#                Journal of Mathematical Models and Methods in Applied Sciences.
-#                vol. 1(4), pp. 300-307.
-#         """
-#         return (self.cityblock(u, v) + self.chebyshev(u, v)) / 2
-
-#     # def bhattacharyya(self, u, v):
-#     #     """
-#     #     Calculate the Bhattacharyya distance between two vectors.
-
-#     #     Returns a distance value between 0 and 1.
-
-#     #     Parameters
-#     #     ----------
-#     #     - u, v: Input vectors between which the distance is to be calculated.
-
-#     #     Returns
-#     #     -------
-#     #     - The Bhattacharyya distance between the two vectors.
-
-#     #     References
-#     #     ----------
-#     #         1. Bhattacharyya A (1947) On a measure of divergence between two
-#     #            statistical populations defined by probability distributions,
-#     #            Bull. Calcutta Math. Soc., 35, 99–109.
-#     #         2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-#     #            Measures between Probability Density Functions. International
-#     #            Journal of Mathematical Models and Methods in Applied Sciences.
-#     #            1(4), 300-307.
-#     #         3. https://en.wikipedia.org/wiki/Bhattacharyya_distance
-#     #     """
-#     #     u, v = np.asarray(u), np.asarray(v)
-#     #     return -np.log(np.sum(np.sqrt(u * v)))
-
-#     def chebyshev_min(self, u, v):
-#         """Calculate the minimum value distance between two vectors.
-
-#         This measure represents a custom approach by Zielezinski to distance
-#         measurement, focusing on the minimum absolute difference.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The minimum value distance between the two vectors.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         return np.amin(np.abs(u - v))
-
-#     def czekanowski(self, u, v):
-#         """Calculate the Czekanowski distance between two vectors.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The Czekanowski distance between the two vectors.
-
-#         References
-#         ----------
-#             1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-#                Measures between Probability Density Functions. International
-#                Journal of Mathematical Models and Methods in Applied Sciences.
-#                1(4), 300-307.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         return np.sum(np.abs(u - v)) / np.sum(u + v)
-
-#     def dice(self, u, v):
-#         """Calculate the Dice dissimilarity between two vectors.
-
-#         Synonyms:
-#             Sorensen distance
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The Dice dissimilarity between the two vectors.
-
-#         References
-#         ----------
-#             1. Dice LR (1945) Measures of the amount of ecologic association
-#                between species. Ecology. 26, 297-302.
-#             2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-#                Measures between Probability Density Functions. International
-#                Journal of Mathematical Models and Methods in Applied Sciences.
-#                1(4), 300-307.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         u_v = u - v
-#         return np.dot(u_v, u_v) / (np.dot(u, u) + np.dot(v, v))
-
-#     def divergence(self, u, v):
-#         """Calculate the divergence between two vectors.
-
-#         Divergence equals squared Clark distance multiplied by 2.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The divergence between the two vectors.
-
-#         References
-#         ----------
-#             1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-#                Measures between Probability Density Functions. International
-#                Journal of Mathematical Models and Methods in Applied Sciences.
-#                1(4), 300-307.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         with np.errstate(invalid="ignore"):
-#             return 2 * np.nansum(np.power(u - v, 2) / np.power(u + v, 2))
-
-#     # def fidelity(self, u, v):
-#     #     """
-#     #     Calculate the fidelity distance between two vectors.
-
-#     #     The fidelity distance measures the similarity between two probability
-#     #     distributions.
-
-#     #     Parameters
-#     #     ----------
-#     #     - u, v: Input vectors between which the distance is to be calculated.
-
-#     #     Returns
-#     #     -------
-#     #     - The fidelity distance between the two vectors.
-
-#     #     Notes
-#     #     -----
-#     #         Added by SC.
-#     #     """
-#     #     u, v = np.asarray(u), np.asarray(v)
-#     #     return 1 - (np.sum(np.sqrt(u * v)))
-
-#     def google(self, u, v):
-#         """Calculate the Normalized Google Distance (NGD) between two vectors.
-
-#         NGD is a measure of similarity derived from the number of hits returned by the
-#         Google search engine for a given set of keywords.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The Normalized Google Distance between the two vectors.
-
-#         Notes
-#         -----
-#             When used for comparing two probability density functions (pdfs),
-#             Google distance equals half of Cityblock distance.
-
-#         References
-#         ----------
-#             1. Lee & Rashid (2008) Information Technology, ITSim 2008.
-#                doi:10.1109/ITSIM.2008.4631601.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         x = float(np.sum(u))
-#         y = float(np.sum(v))
-#         summin = float(np.sum(np.minimum(u, v)))
-#         return (max([x, y]) - summin) / ((x + y) - min([x, y]))
-
-#     def gower(self, u, v):
-#         """Calculate the Gower distance between two vectors.
-
-#         The Gower distance equals the Cityblock distance divided by the vector length.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The Gower distance between the two vectors.
-
-#         References
-#         ----------
-#             1. Gower JC. (1971) General Coefficient of Similarity
-#                and Some of Its Properties, Biometrics 27, 857-874.
-#             2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-#                Measures between Probability Density Functions. International
-#                Journal of Mathematical Models and Methods in Applied Sciences.
-#                1(4), 300-307.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         return np.sum(np.abs(u - v)) / u.size
-
-#     # NEEDS CHECKING
-#     # def harmonicmean(self, u, v):
-#     #     """
-#     #     Harmonic mean distance.
-#     #     Notes:
-#     #         Added by SC.
-#     #     """
-#     #     u,v = np.asarray(u), np.asarray(v)
-#     #     return 1 - 2.*np.sum(u*v/(u+v))
-
-#     # def inner(self, u, v):
-#     #     """
-#     #     Calculate the inner product distance between two vectors.
-
-#     #     The inner product distance is a measure of similarity between two vectors,
-#     #     based on their inner product.
-
-#     #     Parameters
-#     #     ----------
-#     #     - u, v: Input vectors between which the distance is to be calculated.
-
-#     #     Returns
-#     #     -------
-#     #     - The inner product distance between the two vectors.
-
-#     #     Notes
-#     #     -----
-#     #         Added by SC.
-#     #     """
-#     #     u, v = np.asarray(u), np.asarray(v)
-#     #     return 1 - np.dot(u, v)
-
-#     def jeffreys(self, u, v):
-#         """Calculate the Jeffreys divergence between two vectors.
-
-#         The Jeffreys divergence is a symmetric version of the Kullback-Leibler
-#         divergence.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the divergence is to be calculated.
-
-#         Returns
-#         -------
-#         - The Jeffreys divergence between the two vectors.
-
-#         References
-#         ----------
-#             1. Jeffreys H (1946) An Invariant Form for the Prior Probability
-#                in Estimation Problems. Proc.Roy.Soc.Lon., Ser. A 186, 453-461.
-#             2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-#                Measures between Probability Density Functions. International
-#                Journal of Mathematical Models and Methods in Applied Sciences.
-#                1(4), 300-307.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         # Add epsilon to zeros in vectors to avoid division
-#         # by 0 and/or log of 0. Alternatively, zeros in the
-#         # vectors could be ignored or masked (see below).
-#         # u = ma.masked_where(u == 0, u)
-#         # v = ma.masked_where(v == 0, u)
-#         u = np.where(u == 0, self.epsilon, u)
-#         v = np.where(v == 0, self.epsilon, v)
-#         return np.sum((u - v) * np.log(u / v))
-
-#     def jensenshannon_divergence(self, u, v):
-#         """Calculate the Jensen-Shannon divergence between two vectors.
-
-#         The Jensen-Shannon divergence is a symmetric and finite measure of similarity
-#         between two probability distributions.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the divergence is to be calculated.
-
-#         Returns
-#         -------
-#         - The Jensen-Shannon divergence between the two vectors.
-
-#         References
-#         ----------
-#             1. Lin J. (1991) Divergence measures based on the Shannon entropy.
-#                IEEE Transactions on Information Theory, 37(1):145–151.
-#             2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-#                Measures between Probability Density Functions. International
-#                Journal of Mathematical Models and Methods in Applied Sciences.
-#                1(4), 300-307.
-#         Comments:
-#             Equals Jensen difference in Sung-Hyuk (2007):
-#             u = np.where(u==0, self.epsilon, u)
-#             v = np.where(v==0, self.epsilon, v)
-#             el1 = (u * np.log(u) + v * np.log(v)) / 2
-#             el2 = (u + v)/2
-#             el3 = np.log(el2)
-#             return np.sum(el1 - el2 * el3)
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         u = np.where(u == 0, self.epsilon, u)
-#         v = np.where(v == 0, self.epsilon, v)
-#         dl = u * np.log(2 * u / (u + v))
-#         dr = v * np.log(2 * v / (u + v))
-#         return (np.sum(dl) + np.sum(dr)) / 2
-
-#     def jensen_difference(self, u, v):
-#         """Calculate the Jensen difference between two vectors.
-
-#         The Jensen difference is considered similar to the Jensen-Shannon divergence.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The Jensen difference between the two vectors.
-
-#         Notes
-#         -----
-#             1. Equals half of Topsøe distance
-#             2. Equals squared jensenshannon_distance.
-
-
-#         References
-#         ----------
-#             1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-#                Measures between Probability Density Functions. International
-#                Journal of Mathematical Models and Methods in Applied Sciences.
-#                1(4), 300-307.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         u = np.where(u == 0, self.epsilon, u)
-#         v = np.where(v == 0, self.epsilon, v)
-#         el1 = (u * np.log(u) + v * np.log(v)) / 2
-#         el2 = (u + v) / 2
-#         return np.sum(el1 - el2 * np.log(el2))
-
-#     def k_divergence(self, u, v):
-#         """Calculate the K divergence between two vectors.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the divergence is to be calculated.
-
-#         Returns
-#         -------
-#         - The K divergence between the two vectors.
-
-#         References
-#         ----------
-#             1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-#                Measures between Probability Density Functions. International
-#                Journal of Mathematical Models and Methods in Applied Sciences.
-#                1(4), 300-307.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         u = np.where(u == 0, self.epsilon, u)
-#         v = np.where(v == 0, self.epsilon, v)
-#         return np.sum(u * np.log(2 * u / (u + v)))
-
-#     def kl_divergence(self, u, v):
-#         """Calculate the Kullback-Leibler divergence between two vectors.
-
-#         The Kullback-Leibler divergence measures the difference between two
-#         probability distributions.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the divergence is to be calculated.
-
-#         Returns
-#         -------
-#         - The Kullback-Leibler divergence between the two vectors.
-
-#         References
-#         ----------
-#             1. Kullback S, Leibler RA (1951) On information and sufficiency.
-#                Ann. Math. Statist. 22:79–86
-#             2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-#                Measures between Probability Density Functions. International
-#                Journal of Mathematical Models and Methods in Applied Sciences.
-#                1(4):300-307.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         u = np.where(u == 0, self.epsilon, u)
-#         v = np.where(v == 0, self.epsilon, v)
-#         return np.sum(u * np.log(u / v))
-
-#     def kumarjohnson(self, u, v):
-#         """Calculate the Kumar-Johnson distance between two vectors.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The Kumar-Johnson distance between the two vectors.
-
-#         References
-#         ----------
-#             1. Kumar P, Johnson A. (2005) On a symmetric divergence measure
-#                and information inequalities, Journal of Inequalities in pure
-#                and applied Mathematics. 6(3).
-#             2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-#                Measures between Probability Density Functions. International
-#                Journal of Mathematical Models and Methods in Applied Sciences.
-#                1(4):300-307.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         uvmult = u * v
-#         with np.errstate(divide="ignore", invalid="ignore"):
-#             numer = np.power(u**2 - v**2, 2)
-#             denom = 2 * np.power(uvmult, 3 / 2)
-#             return np.sum(np.where(uvmult != 0, numer / denom, 0))
-
-#     def matusita(self, u, v):
-#         """Calculate the Matusita distance between two vectors.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The Matusita distance between the two vectors.
-
-#         References
-#         ----------
-#             1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-#                Measures between Probability Density Functions. International
-#                Journal of Mathematical Models and Methods in Applied Sciences.
-#                1(4):300-307.
-
-#         Notes
-#         -----
-#             Equals square root of Squared-chord distance.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         return np.sqrt(np.sum((np.sqrt(u) - np.sqrt(v)) ** 2))
-
-#     def max_symmetric_chisq(self, u, v):
-#         """Calculate the maximum symmetric chi-square distance.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The maximum symmetric chi-square distance between the two vectors.
-
-#         References
-#         ----------
-#             1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-#                Measures between Probability Density Functions. International
-#                Journal of Mathematical Models and Methods in Applied Sciences.
-#                1(4):300-307.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         return max(self.neyman_chisq(u, v), self.pearson_chisq(u, v))
-
-#     def min_symmetric_chisq(self, u, v):
-#         """Calculate the minimum symmetric chi-square distance.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The minimum symmetric chi-square distance between the two vectors.
-
-#         Notes
-#         -----
-#             Added by SC.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         return min(self.neyman_chisq(u, v), self.pearson_chisq(u, v))
-
-#     def minkowski(self, u, v, p=2):
-#         """Calculate the Minkowski distance between two vectors.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-#         - p: The order of the norm of the difference.
-
-#         Returns
-#         -------
-#         - The Minkowski distance between the two vectors.
-
-#         Notes
-#         -----
-#             When p goes to infinite, the Chebyshev distance is derived.
-
-#         References
-#         ----------
-#             1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-#                Measures between Probability Density Functions. International
-#                Journal of Mathematical Models and Methods in Applied Sciences.
-#                1(4):300-307.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         return np.linalg.norm(u - v, ord=p)
-
-#     def neyman_chisq(self, u, v):
-#         """Calculate the Neyman chi-square distance between two vectors.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The Neyman chi-square distance between the two vectors.
-
-#         References
-#         ----------
-#             1. Neyman J (1949) Contributions to the theory of the chi^2 test.
-#                In Proceedings of the First Berkley Symposium on Mathematical
-#                Statistics and Probability.
-#             2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-#                Measures between Probability Density Functions. International
-#                Journal of Mathematical Models and Methods in Applied Sciences.
-#                1(4), 300-307.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         with np.errstate(divide="ignore", invalid="ignore"):
-#             return np.sum(np.where(u != 0, (u - v) ** 2 / u, 0))
-
-#     # def nonintersection(self, u, v):
-#     #     """
-#     #     Calculate the Nonintersection distance between two vectors.
-
-#     #     Parameters
-#     #     ----------
-#     #     - u, v: Input vectors between which the distance is to be calculated.
-
-#     #     Returns
-#     #     -------
-#     #     - The Nonintersection distance between the two vectors.
-
-#     #     References
-#     #     ----------
-#     #         1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-#     #            Measures between Probability Density Functions. International
-#     #            Journal of Mathematical Models and Methods in Applied Sciences.
-#     #            1(4), 300-307.
-
-#     #     Notes
-#     #     -----
-#     #         When used for comparing two probability density functions (pdfs),
-#     #         Nonintersection distance equals half of Cityblock distance.
-#     #     """
-#     #     u, v = np.asarray(u), np.asarray(v)
-#     #     return 1 - np.sum(np.minimum(u, v))
-
-#     def pearson_chisq(self, u, v):
-#         """Calculate the Pearson chi-square divergence between two vectors.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the divergence is to be calculated.
-
-#         Returns
-#         -------
-#         - The Pearson chi-square divergence between the two vectors.
-
-#         References
-#         ----------
-#             1. Pearson K. (1900) On the Criterion that a given system of
-#                deviations from the probable in the case of correlated system
-#                of variables is such that it can be reasonable supposed to have
-#                arisen from random sampling, Phil. Mag. 50, 157-172.
-#             2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-#                Measures between Probability Density Functions. International
-#                Journal of Mathematical Models and Methods in Applied Sciences.
-#                1(4), 300-307.
-
-#         Notes
-#         -----
-#             Pearson chi-square divergence is asymmetric.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         with np.errstate(divide="ignore", invalid="ignore"):
-#             return np.sum(np.where(v != 0, (u - v) ** 2 / v, 0))
-
-#     def penroseshape(self, u, v):
-#         """Calculate the Penrose shape distance between two vectors.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The Penrose shape distance between the two vectors.
-
-#         References
-#         ----------
-#             1. Deza M, Deza E (2009) Encyclopedia of Distances.
-#                Springer-Verlag Berlin Heidelberg. 1-590.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         umu = np.mean(u)
-#         vmu = np.mean(v)
-#         return np.sqrt(np.sum(((u - umu) - (v - vmu)) ** 2))
-
-#     def prob_chisq(self, u, v):
-#         """Calculate the Probabilistic chi-square distance between two vectors.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The Probabilistic chi-square distance between the two vectors.
-
-#         Notes
-#         -----
-#             Added by SC.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         uvsum = u + v
-#         with np.errstate(divide="ignore", invalid="ignore"):
-#             return 2 * np.sum(np.where(uvsum != 0, (u - v) ** 2 / uvsum, 0))
-
-#     def ruzicka(self, u, v):
-#         """Calculate the Ruzicka distance between two vectors.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The Ruzicka distance between the two vectors.
-
-#         Notes
-#         -----
-#             Added by SC.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         den = np.sum(np.maximum(u, v))
-
-#         return 1 - np.sum(np.minimum(u, v)) / den
-
-#     def sorensen(self, u, v):
-#         """Calculate the Sorensen distance between two vectors.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The Sorensen distance between the two vectors.
-
-#         Notes
-#         -----
-#             The Sorensen distance equals the Manhattan distance divided by the sum of
-#             the two vectors.
-
-#             Added by SC.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         return np.sum(np.abs(u - v)) / np.sum(u + v)
-
-#     def squared_chisq(self, u, v):
-#         """Calculate the Squared chi-square distance between two vectors.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The Squared chi-square distance between the two vectors.
-
-#         References
-#         ----------
-#             1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-#                Measures between Probability Density Functions. International
-#                Journal of Mathematical Models and Methods in Applied Sciences.
-#                1(4), 300-307.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         uvsum = u + v
-#         with np.errstate(divide="ignore", invalid="ignore"):
-#             return np.sum(np.where(uvsum != 0, (u - v) ** 2 / uvsum, 0))
-
-#     def squaredchord(self, u, v):
-#         """Calculate the Squared-chord distance between two vectors.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The Squared-chord distance between the two vectors.
-
-#         References
-#         ----------
-#             1. Gavin DG et al. (2003) A statistical approach to evaluating
-#                distance metrics and analog assignments for pollen records.
-#                Quaternary Research 60:356–367.
-#             2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-#                Measures between Probability Density Functions. International
-#                Journal of Mathematical Models and Methods in Applied Sciences.
-#                1(4), 300-307.
-
-#         Notes
-#         -----
-#             Equals to squared Matusita distance.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         return np.sum((np.sqrt(u) - np.sqrt(v)) ** 2)
-
-#     def squared_euclidean(self, u, v):
-#         """Calculate the Squared Euclidean distance between two vectors.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The Squared Euclidean distance between the two vectors.
-
-#         References
-#         ----------
-#             1. Gavin DG et al. (2003) A statistical approach to evaluating
-#                distance metrics and analog assignments for pollen records.
-#                Quaternary Research 60:356–367.
-#             2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-#                Measures between Probability Density Functions. International
-#                Journal of Mathematical Models and Methods in Applied Sciences.
-#                1(4), 300-307.
-
-#         Notes
-#         -----
-#             Equals to squared Euclidean distance.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         return np.dot((u - v), (u - v))
-
-#     def taneja(self, u, v):
-#         """Calculate the Taneja distance between two vectors.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The Taneja distance between the two vectors.
-
-#         References
-#         ----------
-#             1. Taneja IJ. (1995), New Developments in Generalized Information
-#                Measures, Chapter in: Advances in Imaging and Electron Physics,
-#                Ed. P.W. Hawkes, 91, 37-135.
-#             2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-#                Measures between Probability Density Functions. International
-#                Journal of Mathematical Models and Methods in Applied Sciences.
-#                1(4), 300-307.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         u = np.where(u == 0, self.epsilon, u)
-#         v = np.where(v == 0, self.epsilon, v)
-#         uvsum = u + v
-#         return np.sum((uvsum / 2) * np.log(uvsum / (2 * np.sqrt(u * v))))
-
-#     def tanimoto(self, u, v):
-#         """Calculate the Tanimoto distance between two vectors.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The Tanimoto distance between the two vectors.
-
-#         References
-#         ----------
-#             1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-#                Measures between Probability Density Functions. International
-#                Journal of Mathematical Models and Methods in Applied Sciences.
-#                1(4), 300-307.
-
-#         Notes
-#         -----
-#             Equals Soergel distance.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         # return np.sum(abs(u-v)) / np.sum(np.maximum(u, v))
-#         usum = np.sum(u)
-#         vsum = np.sum(v)
-#         minsum = np.sum(np.minimum(u, v))
-#         return (usum + vsum - 2 * minsum) / (usum + vsum - minsum)
-
-#     def topsoe(self, u, v):
-#         """Calculate the Topsøe distance between two vectors.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The Topsøe distance between the two vectors.
-
-#         References
-#         ----------
-#             1. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity
-#                Measures between Probability Density Functions. International
-#                Journal of Mathematical Models and Methods in Applied Sciences.
-#                1(4), 300-307.
-
-#         Notes
-#         -----
-#             Equals two times Jensen-Shannon divergence.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         u = np.where(u == 0, self.epsilon, u)
-#         v = np.where(v == 0, self.epsilon, v)
-#         dl = u * np.log(2 * u / (u + v))
-#         dr = v * np.log(2 * v / (u + v))
-#         return np.sum(dl + dr)
-
-#     def vicis_symmetric_chisq(self, u, v):
-#         """Calculate the Vicis Symmetric chi-square distance.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The Vicis Symmetric chi-square distance between the two vectors.
-
-#         References
-#         ----------
-#             1. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity
-#                Measures between Probability Density Functions. International
-#                Journal of Mathematical Models and Methods in Applied Sciences.
-#                1(4), 300-307
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         with np.errstate(divide="ignore", invalid="ignore"):
-#             u_v = (u - v) ** 2
-#             uvmin = np.minimum(u, v) ** 2
-#             return np.sum(np.where(uvmin != 0, u_v / uvmin, 0))
-
-#     def vicis_wave_hedges(self, u, v):
-#         """Calculate the Vicis-Wave Hedges distance between two vectors.
-
-#         Parameters
-#         ----------
-#         - u, v: Input vectors between which the distance is to be calculated.
-
-#         Returns
-#         -------
-#         - The Vicis-Wave Hedges distance between the two vectors.
-
-#         References
-#         ----------
-#             1. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity
-#                Measures between Probability Density Functions. International
-#                Journal of Mathematical Models and Methods in Applied Sciences.
-#                1(4), 300-307.
-#         """
-#         u, v = np.asarray(u), np.asarray(v)
-#         with np.errstate(divide="ignore", invalid="ignore"):
-#             u_v = abs(u - v)
-#             uvmin = np.minimum(u, v)
-#             return np.sum(np.where(uvmin != 0, u_v / uvmin, 0))
+        Divergence equals squared Clark distance multiplied by 2.
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the distance is to be calculated.
+
+        Returns
+        -------
+        - The divergence between the two vectors.
+
+        References
+        ----------
+            1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+               Measures between Probability Density Functions. International
+               Journal of Mathematical Models and Methods in Applied Sciences.
+               1(4), 300-307.
+        """
+        u, v = np.asarray(u), np.asarray(v)
+        with np.errstate(invalid="ignore"):
+            return 2 * np.nansum(np.power(u - v, 2) / np.power(u + v, 2))
+
+    def google(self, u, v):
+        """Calculate the Normalized Google Distance (NGD) between two vectors.
+
+        NGD is a measure of similarity derived from the number of hits returned by the
+        Google search engine for a given set of keywords.
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the distance is to be calculated.
+
+        Returns
+        -------
+        - The Normalized Google Distance between the two vectors.
+
+        Notes
+        -----
+            When used for comparing two probability density functions (pdfs),
+            Google distance equals half of Cityblock distance.
+
+        References
+        ----------
+            1. Lee & Rashid (2008) Information Technology, ITSim 2008.
+               doi:10.1109/ITSIM.2008.4631601.
+        """
+        u, v = np.asarray(u), np.asarray(v)
+        x = float(np.sum(u))
+        y = float(np.sum(v))
+        summin = float(np.sum(np.minimum(u, v)))
+        return (max([x, y]) - summin) / ((x + y) - min([x, y]))
+
+    def gower(self, u, v):
+        """Calculate the Gower distance between two vectors.
+
+        The Gower distance equals the Cityblock distance divided by the vector length.
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the distance is to be calculated.
+
+        Returns
+        -------
+        - The Gower distance between the two vectors.
+
+        References
+        ----------
+            1. Gower JC. (1971) General Coefficient of Similarity
+               and Some of Its Properties, Biometrics 27, 857-874.
+            2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+               Measures between Probability Density Functions. International
+               Journal of Mathematical Models and Methods in Applied Sciences.
+               1(4), 300-307.
+        """
+        u, v = np.asarray(u), np.asarray(v)
+        return np.sum(np.abs(u - v)) / u.size
+
+    def jeffreys(self, u, v):
+        """Calculate the Jeffreys divergence between two vectors.
+
+        The Jeffreys divergence is a symmetric version of the Kullback-Leibler
+        divergence.
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the divergence is to be calculated.
+
+        Returns
+        -------
+        - The Jeffreys divergence between the two vectors.
+
+        References
+        ----------
+            1. Jeffreys H (1946) An Invariant Form for the Prior Probability
+               in Estimation Problems. Proc.Roy.Soc.Lon., Ser. A 186, 453-461.
+            2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+               Measures between Probability Density Functions. International
+               Journal of Mathematical Models and Methods in Applied Sciences.
+               1(4), 300-307.
+        """
+        u, v = np.asarray(u), np.asarray(v)
+        # Add epsilon to zeros in vectors to avoid division
+        # by 0 and/or log of 0. Alternatively, zeros in the
+        # vectors could be ignored or masked (see below).
+        # u = ma.masked_where(u == 0, u)
+        # v = ma.masked_where(v == 0, u)
+        with np.errstate(divide="ignore", invalid="ignore"):
+            u[u == 0] = self.epsilon
+            v[v == 0] = self.epsilon
+            # Clip negative values to zero for valid log
+            udivv = np.clip(u / v, a_min=self.epsilon, a_max=None)
+            return np.sum((u - v) * np.log(udivv))
+
+    def jensenshannon_divergence(self, u, v):
+        """Calculate the Jensen-Shannon divergence between two vectors.
+
+        The Jensen-Shannon divergence is a symmetric and finite measure of similarity
+        between two probability distributions.
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the divergence is to be calculated.
+
+        Returns
+        -------
+        - The Jensen-Shannon divergence between the two vectors.
+
+        References
+        ----------
+            1. Lin J. (1991) Divergence measures based on the Shannon entropy.
+               IEEE Transactions on Information Theory, 37(1):145–151.
+            2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+               Measures between Probability Density Functions. International
+               Journal of Mathematical Models and Methods in Applied Sciences.
+               1(4), 300-307.
+        Comments:
+            Equals Jensen difference in Sung-Hyuk (2007):
+            u = np.where(u==0, self.epsilon, u)
+            v = np.where(v==0, self.epsilon, v)
+            el1 = (u * np.log(u) + v * np.log(v)) / 2
+            el2 = (u + v)/2
+            el3 = np.log(el2)
+            return np.sum(el1 - el2 * el3)
+        """
+        u, v = np.asarray(u), np.asarray(v)
+        with np.errstate(divide="ignore", invalid="ignore"):
+            # Clip negative values to zero for valid log
+            u[u == 0] = self.epsilon
+            v[v == 0] = self.epsilon
+
+            term1 = np.clip(2 * u / (u + v), a_min=self.epsilon, a_max=None)
+            term2 = np.clip(2 * v / (u + v), a_min=self.epsilon, a_max=None)
+
+            dl = u * np.log(term1)
+            dr = v * np.log(term2)
+            return (np.sum(dl) + np.sum(dr)) / 2
+
+    def jensen_difference(self, u, v):
+        """Calculate the Jensen difference between two vectors.
+
+        The Jensen difference is considered similar to the Jensen-Shannon divergence.
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the distance is to be calculated.
+
+        Returns
+        -------
+        - The Jensen difference between the two vectors.
+
+        Notes
+        -----
+            1. Equals half of Topsøe distance
+            2. Equals squared jensenshannon_distance.
+
+
+        References
+        ----------
+            1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+               Measures between Probability Density Functions. International
+               Journal of Mathematical Models and Methods in Applied Sciences.
+               1(4), 300-307.
+        """
+        u, v = np.asarray(u), np.asarray(v)
+
+        with np.errstate(divide="ignore", invalid="ignore"):
+            # Clip negative values to eps for valid log
+            u = np.clip(u, self.epsilon, None)
+            v = np.clip(v, self.epsilon, None)
+            el1 = (u * np.log(u) + v * np.log(v)) / 2
+            el2 = np.clip((u + v) / 2, a_min=self.epsilon, a_max=None)
+            return np.sum(el1 - el2 * np.log(el2))
+
+    def kumarjohnson(self, u, v):
+        """Calculate the Kumar-Johnson distance between two vectors.
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the distance is to be calculated.
+
+        Returns
+        -------
+        - The Kumar-Johnson distance between the two vectors.
+
+        References
+        ----------
+            1. Kumar P, Johnson A. (2005) On a symmetric divergence measure
+               and information inequalities, Journal of Inequalities in pure
+               and applied Mathematics. 6(3).
+            2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+               Measures between Probability Density Functions. International
+               Journal of Mathematical Models and Methods in Applied Sciences.
+               1(4):300-307.
+        """
+        u, v = np.asarray(u), np.asarray(v)
+        uvmult = u * v
+        with np.errstate(divide="ignore", invalid="ignore"):
+            numer = np.power(u**2 - v**2, 2)
+            denom = 2 * np.power(uvmult, 3 / 2)
+            return np.sum(np.where(uvmult != 0, numer / denom, 0))
+
+    def matusita(self, u, v):
+        """Calculate the Matusita distance between two vectors.
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the distance is to be calculated.
+
+        Returns
+        -------
+        - The Matusita distance between the two vectors.
+
+        References
+        ----------
+            1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+               Measures between Probability Density Functions. International
+               Journal of Mathematical Models and Methods in Applied Sciences.
+               1(4):300-307.
+
+        Notes
+        -----
+            Equals square root of Squared-chord distance.
+        """
+        u, v = np.asarray(u), np.asarray(v)
+        with np.errstate(divide="ignore", invalid="ignore"):
+            return np.sqrt(np.sum((np.sqrt(u) - np.sqrt(v)) ** 2))
+
+    def minkowski(self, u, v, p=2):
+        """Calculate the Minkowski distance between two vectors.
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the distance is to be calculated.
+        - p: The order of the norm of the difference.
+
+        Returns
+        -------
+        - The Minkowski distance between the two vectors.
+
+        Notes
+        -----
+            When p goes to infinite, the Chebyshev distance is derived.
+
+        References
+        ----------
+            1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+                Measures between Probability Density Functions. International
+                Journal of Mathematical Models and Methods in Applied Sciences.
+                1(4):300-307.
+        """
+        u, v = np.asarray(u), np.asarray(v)
+        return np.linalg.norm(u - v, ord=p)
+
+    def penroseshape(self, u, v):
+        """Calculate the Penrose shape distance between two vectors.
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the distance is to be calculated.
+
+        Returns
+        -------
+        - The Penrose shape distance between the two vectors.
+
+        References
+        ----------
+            1. Deza M, Deza E (2009) Encyclopedia of Distances.
+               Springer-Verlag Berlin Heidelberg. 1-590.
+        """
+        u, v = np.asarray(u), np.asarray(v)
+        umu = np.mean(u)
+        vmu = np.mean(v)
+        with np.errstate(divide="ignore", invalid="ignore"):
+            return np.sqrt(np.sum(((u - umu) - (v - vmu)) ** 2))
+
+    def prob_chisq(self, u, v):
+        """Calculate the Probabilistic chi-square distance between two vectors.
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the distance is to be calculated.
+
+        Returns
+        -------
+        - The Probabilistic chi-square distance between the two vectors.
+
+        Notes
+        -----
+            Added by SC.
+        """
+        u, v = np.asarray(u), np.asarray(v)
+        uvsum = u + v
+        with np.errstate(divide="ignore", invalid="ignore"):
+            return 2 * np.sum(np.where(uvsum != 0, (u - v) ** 2 / uvsum, 0))
+
+    def ruzicka(self, u, v):
+        """Calculate the Ruzicka distance between two vectors.
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the distance is to be calculated.
+
+        Returns
+        -------
+        - The Ruzicka distance between the two vectors.
+
+        Notes
+        -----
+            Added by SC.
+        """
+        u, v = np.asarray(u), np.asarray(v)
+        den = np.sum(np.maximum(u, v))
+
+        return 1 - np.sum(np.minimum(u, v)) / den
+
+    def sorensen(self, u, v):
+        """Calculate the Sorensen distance between two vectors.
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the distance is to be calculated.
+
+        Returns
+        -------
+        - The Sorensen distance between the two vectors.
+
+        Notes
+        -----
+            The Sorensen distance equals the Manhattan distance divided by the sum of
+            the two vectors.
+
+            Added by SC.
+        """
+        u, v = np.asarray(u), np.asarray(v)
+        return np.sum(np.abs(u - v)) / np.sum(u + v)
+
+    def squared_chisq(self, u, v):
+        """Calculate the Squared chi-square distance between two vectors.
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the distance is to be calculated.
+
+        Returns
+        -------
+        - The Squared chi-square distance between the two vectors.
+
+        References
+        ----------
+            1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+               Measures between Probability Density Functions. International
+               Journal of Mathematical Models and Methods in Applied Sciences.
+               1(4), 300-307.
+        """
+        u, v = np.asarray(u), np.asarray(v)
+        uvsum = u + v
+        with np.errstate(divide="ignore", invalid="ignore"):
+            return np.sum(np.where(uvsum != 0, (u - v) ** 2 / uvsum, 0))
+
+    def squaredchord(self, u, v):
+        """Calculate the Squared-chord distance between two vectors.
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the distance is to be calculated.
+
+        Returns
+        -------
+        - The Squared-chord distance between the two vectors.
+
+        References
+        ----------
+            1. Gavin DG et al. (2003) A statistical approach to evaluating
+               distance metrics and analog assignments for pollen records.
+               Quaternary Research 60:356–367.
+            2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+               Measures between Probability Density Functions. International
+               Journal of Mathematical Models and Methods in Applied Sciences.
+               1(4), 300-307.
+
+        Notes
+        -----
+            Equals to squared Matusita distance.
+        """
+        u, v = np.asarray(u), np.asarray(v)
+        with np.errstate(divide="ignore", invalid="ignore"):
+            return np.sum((np.sqrt(u) - np.sqrt(v)) ** 2)
+
+    def squared_euclidean(self, u, v):
+        """Calculate the Squared Euclidean distance between two vectors.
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the distance is to be calculated.
+
+        Returns
+        -------
+        - The Squared Euclidean distance between the two vectors.
+
+        References
+        ----------
+            1. Gavin DG et al. (2003) A statistical approach to evaluating
+               distance metrics and analog assignments for pollen records.
+               Quaternary Research 60:356–367.
+            2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+               Measures between Probability Density Functions. International
+               Journal of Mathematical Models and Methods in Applied Sciences.
+               1(4), 300-307.
+
+        Notes
+        -----
+            Equals to squared Euclidean distance.
+        """
+        u, v = np.asarray(u), np.asarray(v)
+        return np.dot((u - v), (u - v))
+
+    def taneja(self, u, v):
+        """Calculate the Taneja distance between two vectors.
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the distance is to be calculated.
+
+        Returns
+        -------
+        - The Taneja distance between the two vectors.
+
+        References
+        ----------
+            1. Taneja IJ. (1995), New Developments in Generalized Information
+               Measures, Chapter in: Advances in Imaging and Electron Physics,
+               Ed. P.W. Hawkes, 91, 37-135.
+            2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+               Measures between Probability Density Functions. International
+               Journal of Mathematical Models and Methods in Applied Sciences.
+               1(4), 300-307.
+        """
+        u, v = np.asarray(u), np.asarray(v)
+        with np.errstate(divide="ignore", invalid="ignore"):
+            u[u == 0] = self.epsilon
+            v[v == 0] = self.epsilon
+            uvsum = u + v
+            logarg = np.clip(
+                uvsum / (2 * np.sqrt(u * v)), a_min=self.epsilon, a_max=None
+            )
+            return np.sum((uvsum / 2) * np.log(logarg))
+
+    def tanimoto(self, u, v):
+        """Calculate the Tanimoto distance between two vectors.
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the distance is to be calculated.
+
+        Returns
+        -------
+        - The Tanimoto distance between the two vectors.
+
+        References
+        ----------
+            1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+               Measures between Probability Density Functions. International
+               Journal of Mathematical Models and Methods in Applied Sciences.
+               1(4), 300-307.
+
+        Notes
+        -----
+            Equals Soergel distance.
+        """
+        u, v = np.asarray(u), np.asarray(v)
+        # return np.sum(abs(u-v)) / np.sum(np.maximum(u, v))
+        usum = np.sum(u)
+        vsum = np.sum(v)
+        minsum = np.sum(np.minimum(u, v))
+        return (usum + vsum - 2 * minsum) / (usum + vsum - minsum)
+
+    def topsoe(self, u, v):
+        """Calculate the Topsøe distance between two vectors.
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the distance is to be calculated.
+
+        Returns
+        -------
+        - The Topsøe distance between the two vectors.
+
+        References
+        ----------
+            1. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity
+               Measures between Probability Density Functions. International
+               Journal of Mathematical Models and Methods in Applied Sciences.
+               1(4), 300-307.
+
+        Notes
+        -----
+            Equals two times Jensen-Shannon divergence.
+        """
+        u, v = np.asarray(u), np.asarray(v)
+        with np.errstate(divide="ignore", invalid="ignore"):
+            u[u == 0] = self.epsilon
+            v[v == 0] = self.epsilon
+            logarg1 = np.clip(2 * u / (u + v), a_min=self.epsilon, a_max=None)
+            logarg2 = np.clip(2 * v / (u + v), a_min=self.epsilon, a_max=None)
+            dl = u * np.log(logarg1)
+            dr = v * np.log(logarg2)
+            return np.sum(dl + dr)
+
+    def vicis_symmetric_chisq(self, u, v):
+        """Calculate the Vicis Symmetric chi-square distance.
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the distance is to be calculated.
+
+        Returns
+        -------
+        - The Vicis Symmetric chi-square distance between the two vectors.
+
+        References
+        ----------
+            1. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity
+               Measures between Probability Density Functions. International
+               Journal of Mathematical Models and Methods in Applied Sciences.
+               1(4), 300-307
+        """
+        u, v = np.asarray(u), np.asarray(v)
+        with np.errstate(divide="ignore", invalid="ignore"):
+            u_v = (u - v) ** 2
+            uvmin = np.minimum(u, v) ** 2
+            return np.sum(np.where(uvmin != 0, u_v / uvmin, 0))
+
+    def vicis_wave_hedges(self, u, v):
+        """Calculate the Vicis-Wave Hedges distance between two vectors.
+
+        Parameters
+        ----------
+        - u, v: Input vectors between which the distance is to be calculated.
+
+        Returns
+        -------
+        - The Vicis-Wave Hedges distance between the two vectors.
+
+        References
+        ----------
+            1. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity
+               Measures between Probability Density Functions. International
+               Journal of Mathematical Models and Methods in Applied Sciences.
+               1(4), 300-307.
+        """
+        u, v = np.asarray(u), np.asarray(v)
+        with np.errstate(divide="ignore", invalid="ignore"):
+            u_v = abs(u - v)
+            uvmin = np.minimum(u, v)
+            return np.sum(np.where(uvmin != 0, u_v / uvmin, 0))
+
+    # def fidelity(self, u, v):
+    #     """
+    #     Calculate the fidelity distance between two vectors.
+
+    #     The fidelity distance measures the similarity between two probability
+    #     distributions.
+
+    #     Parameters
+    #     ----------
+    #     - u, v: Input vectors between which the distance is to be calculated.
+
+    #     Returns
+    #     -------
+    #     - The fidelity distance between the two vectors.
+
+    #     Notes
+    #     -----
+    #         Added by SC.
+    #     """
+    #     u, v = np.asarray(u), np.asarray(v)
+    #     return 1 - (np.sum(np.sqrt(u * v)))
+
+    # # NEEDS CHECKING
+    # # def harmonicmean(self, u, v):
+    # #     """
+    # #     Harmonic mean distance.
+    # #     Notes:
+    # #         Added by SC.
+    # #     """
+    # #     u, v = np.asarray(u), np.asarray(v)
+    # #     return 1 - 2.0 * np.sum(u * v / (u + v))
+
+    #     # def inner(self, u, v):
+    #     #     """
+    #     #     Calculate the inner product distance between two vectors.
+
+    #     #     The inner product distance is a measure of
+    #     #     similarity between two vectors,
+    #     #     based on their inner product.
+
+    #     #     Parameters
+    #     #     ----------
+    #     #     - u, v: Input vectors between which the distance is to be calculated.
+
+    #     #     Returns
+    #     #     -------
+    #     #     - The inner product distance between the two vectors.
+
+    #     #     Notes
+    #     #     -----
+    #     #         Added by SC.
+    #     #     """
+    #     #     u, v = np.asarray(u), np.asarray(v)
+    #     #     return 1 - np.dot(u, v)
+
+    # def k_divergence(self, u, v):
+    #     """Calculate the K divergence between two vectors.
+
+    #     Parameters
+    #     ----------
+    #     - u, v: Input vectors between which the divergence is to be calculated.
+
+    #     Returns
+    #     -------
+    #     - The K divergence between the two vectors.
+
+    #     References
+    #     ----------
+    #         1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+    #            Measures between Probability Density Functions. International
+    #            Journal of Mathematical Models and Methods in Applied Sciences.
+    #            1(4), 300-307.
+    #     """
+    #     u, v = np.asarray(u), np.asarray(v)
+    #     u[u == 0] = self.epsilon
+    #     v[v == 0] = self.epsilon
+    #     with np.errstate(divide="ignore", invalid="ignore"):
+    #         return np.sum(u * np.log(2 * u / (u + v)))
+
+    # def kl_divergence(self, u, v):
+    #     """Calculate the Kullback-Leibler divergence between two vectors.
+
+    #     The Kullback-Leibler divergence measures the difference between two
+    #     probability distributions.
+
+    #     Parameters
+    #     ----------
+    #     - u, v: Input vectors between which the divergence is to be calculated.
+
+    #     Returns
+    #     -------
+    #     - The Kullback-Leibler divergence between the two vectors.
+
+    #     References
+    #     ----------
+    #         1. Kullback S, Leibler RA (1951) On information and sufficiency.
+    #            Ann. Math. Statist. 22:79–86
+    #         2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+    #            Measures between Probability Density Functions. International
+    #            Journal of Mathematical Models and Methods in Applied Sciences.
+    #            1(4):300-307.
+    #     """
+    #     u, v = np.asarray(u), np.asarray(v)
+    #     u[u == 0] = self.epsilon
+    #     v[v == 0] = self.epsilon
+    #     with np.errstate(divide="ignore", invalid="ignore"):
+    #         return np.sum(u * np.log(u / v))
+
+    # def max_symmetric_chisq(self, u, v):
+    #     """Calculate the maximum symmetric chi-square distance.
+
+    #     Parameters
+    #     ----------
+    #     - u, v: Input vectors between which the distance is to be calculated.
+
+    #     Returns
+    #     -------
+    #     - The maximum symmetric chi-square distance between the two vectors.
+
+    #     References
+    #     ----------
+    #         1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+    #            Measures between Probability Density Functions. International
+    #            Journal of Mathematical Models and Methods in Applied Sciences.
+    #            1(4):300-307.
+    #     """
+    #     u, v = np.asarray(u), np.asarray(v)
+    #     return max(self.neyman_chisq(u, v), self.pearson_chisq(u, v))
+
+    # def min_symmetric_chisq(self, u, v):
+    #     """Calculate the minimum symmetric chi-square distance.
+
+    #     Parameters
+    #     ----------
+    #     - u, v: Input vectors between which the distance is to be calculated.
+
+    #     Returns
+    #     -------
+    #     - The minimum symmetric chi-square distance between the two vectors.
+
+    #     Notes
+    #     -----
+    #         Added by SC.
+    #     """
+    #     u, v = np.asarray(u), np.asarray(v)
+    #     return min(self.neyman_chisq(u, v), self.pearson_chisq(u, v))
+
+    # def neyman_chisq(self, u, v):
+    #     """Calculate the Neyman chi-square distance between two vectors.
+
+    #     Parameters
+    #     ----------
+    #     - u, v: Input vectors between which the distance is to be calculated.
+
+    #     Returns
+    #     -------
+    #     - The Neyman chi-square distance between the two vectors.
+
+    #     References
+    #     ----------
+    #         1. Neyman J (1949) Contributions to the theory of the chi^2 test.
+    #            In Proceedings of the First Berkley Symposium on Mathematical
+    #            Statistics and Probability.
+    #         2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+    #            Measures between Probability Density Functions. International
+    #            Journal of Mathematical Models and Methods in Applied Sciences.
+    #            1(4), 300-307.
+    #     """
+    #     u, v = np.asarray(u), np.asarray(v)
+    #     with np.errstate(divide="ignore", invalid="ignore"):
+    #         return np.sum(np.where(u != 0, (u - v) ** 2 / u, 0))
+
+    # def pearson_chisq(self, u, v):
+    #     """Calculate the Pearson chi-square divergence between two vectors.
+
+    #     Parameters
+    #     ----------
+    #     - u, v: Input vectors between which the divergence is to be calculated.
+
+    #     Returns
+    #     -------
+    #     - The Pearson chi-square divergence between the two vectors.
+
+    #     References
+    #     ----------
+    #         1. Pearson K. (1900) On the Criterion that a given system of
+    #            deviations from the probable in the case of correlated system
+    #            of variables is such that it can be reasonable supposed to have
+    #            arisen from random sampling, Phil. Mag. 50, 157-172.
+    #         2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+    #            Measures between Probability Density Functions. International
+    #            Journal of Mathematical Models and Methods in Applied Sciences.
+    #            1(4), 300-307.
+
+    #     Notes
+    #     -----
+    #         Pearson chi-square divergence is asymmetric.
+    #     """
+    #     u, v = np.asarray(u), np.asarray(v)
+    #     with np.errstate(divide="ignore", invalid="ignore"):
+    #         return np.sum(np.where(v != 0, (u - v) ** 2 / v, 0))
+
+    # def nonintersection(self, u, v):
+    #     """
+    #     Calculate the Nonintersection distance between two vectors.
+
+    #     Parameters
+    #     ----------
+    #     - u, v: Input vectors between which the distance is to be calculated.
+
+    #     Returns
+    #     -------
+    #     - The Nonintersection distance between the two vectors.
+
+    #     References
+    #     ----------
+    #         1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+    #             Measures between Probability Density Functions. International
+    #             Journal of Mathematical Models and Methods in Applied Sciences.
+    #             1(4), 300-307.
+
+    #     Notes
+    #     -----
+    #         When used for comparing two probability density functions (pdfs),
+    #         Nonintersection distance equals half of Cityblock distance.
+    #     """
+    #     u, v = np.asarray(u), np.asarray(v)
+    #     return 1 - np.sum(np.minimum(u, v))