# This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. # See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. # Author(s): Marc Glisse # # Copyright (C) 2020 Inria # # Modification(s): # - YYYY/MM Author: Description of the modification from .knn import KNN class DTM: """ Class to compute the distance to the empirical measure defined by a point set. """ def __init__(self, k, q=None, **kwargs): """ Args: k (int): number of neighbors (possibly including the point itself). q (float): order used to compute the distance to measure. Defaults to the dimension, or 2 if metric is "neighbors" or "distance_matrix". kwargs: Same parameters as :class:`~gudhi.point_cloud.knn.KNN`, except that metric="neighbors" means that :func:`transform` expects an array with the distances to the k nearest neighbors. """ self.k = k self.q = q self.params = kwargs def fit_transform(self, X, y=None): return self.fit(X).transform(X) def fit(self, X, y=None): """ Args: X (numpy.array): coordinates for mass points. """ if self.params.setdefault("metric", "euclidean") != "neighbors": # KNN gives sorted distances, which is unnecessary here. # Maybe add a parameter to say we don't need sorting? self.knn = KNN(self.k, return_index=False, return_distance=True, **self.params) self.knn.fit(X) return self def transform(self, X): """ Args: X (numpy.array): coordinates for query points, or distance matrix if metric is "precomputed", or distances to the k nearest neighbors if metric is "neighbors" (if the array has more than k columns, the remaining ones are ignored). """ q = self.q if q is None: if self.params["metric"] in {"neighbors", "precomputed"}: q = 2 else: q = len(X[0]) if self.params["metric"] == "neighbors": distances = X[:, : self.k] else: distances = self.knn.transform(X) distances = distances ** q dtm = distances.sum(-1) / self.k dtm = dtm ** (1.0 / q) return dtm