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+# 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): Theo Lacombe
+#
+# Copyright (C) 2019 Inria
+#
+# Modification(s):
+# - YYYY/MM Author: Description of the modification
+
+import numpy as np
+import scipy.spatial.distance as sc
+
+try:
+ import ot
+except ImportError:
+ print("POT (Python Optimal Transport) package is not installed. Try to run $ conda install -c conda-forge pot ; or $ pip install POT")
+
+
+# Currently unused, but Théo says it is likely to be used again.
+def _proj_on_diag(X):
+ '''
+ :param X: (n x 2) array encoding the points of a persistent diagram.
+ :returns: (n x 2) array encoding the (respective orthogonal) projections of the points onto the diagonal
+ '''
+ Z = (X[:,0] + X[:,1]) / 2.
+ return np.array([Z , Z]).T
+
+
+def _dist_to_diag(X, internal_p):
+ '''
+ :param X: (n x 2) array encoding the points of a persistent diagram.
+ :param internal_p: Ground metric (i.e. norm L^p).
+ :returns: (n) array encoding the (respective orthogonal) distances of the points to the diagonal
+
+ .. note::
+ Assumes that the points are above the diagonal.
+ '''
+ return (X[:, 1] - X[:, 0]) * 2 ** (1.0 / internal_p - 1)
+
+
+def _build_dist_matrix(X, Y, order, internal_p):
+ '''
+ :param X: (n x 2) numpy.array encoding the (points of the) first diagram.
+ :param Y: (m x 2) numpy.array encoding the second diagram.
+ :param order: exponent for the Wasserstein metric.
+ :param internal_p: Ground metric (i.e. norm L^p).
+ :returns: (n+1) x (m+1) np.array encoding the cost matrix C.
+ For 0 <= i < n, 0 <= j < m, C[i,j] encodes the distance between X[i] and Y[j],
+ while C[i, m] (resp. C[n, j]) encodes the distance (to the p) between X[i] (resp Y[j])
+ and its orthogonal projection onto the diagonal.
+ note also that C[n, m] = 0 (it costs nothing to move from the diagonal to the diagonal).
+ '''
+ Cxd = _dist_to_diag(X, internal_p)**order
+ Cdy = _dist_to_diag(Y, internal_p)**order
+ if np.isinf(internal_p):
+ C = sc.cdist(X,Y, metric='chebyshev')**order
+ else:
+ C = sc.cdist(X,Y, metric='minkowski', p=internal_p)**order
+ Cf = np.hstack((C, Cxd[:,None]))
+ Cdy = np.append(Cdy, 0)
+
+ Cf = np.vstack((Cf, Cdy[None,:]))
+
+ return Cf
+
+
+def _perstot(X, order, internal_p):
+ '''
+ :param X: (n x 2) numpy.array (points of a given diagram).
+ :param order: exponent for Wasserstein. Default value is 2.
+ :param internal_p: Ground metric on the (upper-half) plane (i.e. norm L^p in R^2); Default value is 2 (Euclidean norm).
+ :returns: float, the total persistence of the diagram (that is, its distance to the empty diagram).
+ '''
+ return np.linalg.norm(_dist_to_diag(X, internal_p), ord=order)
+
+
+def wasserstein_distance(X, Y, matching=False, order=2., internal_p=2.):
+ '''
+ :param X: (n x 2) numpy.array encoding the (finite points of the) first diagram. Must not contain essential points
+ (i.e. with infinite coordinate).
+ :param Y: (m x 2) numpy.array encoding the second diagram.
+ :param matching: if True, computes and returns the optimal matching between X and Y, encoded as
+ a (n x 2) np.array [...[i,j]...], meaning the i-th point in X is matched to
+ the j-th point in Y, with the convention (-1) represents the diagonal.
+ :param order: exponent for Wasserstein; Default value is 2.
+ :param internal_p: Ground metric on the (upper-half) plane (i.e. norm L^p in R^2);
+ Default value is 2 (Euclidean norm).
+ :returns: the Wasserstein distance of order q (1 <= q < infinity) between persistence diagrams with
+ respect to the internal_p-norm as ground metric.
+ If matching is set to True, also returns the optimal matching between X and Y.
+ '''
+ n = len(X)
+ m = len(Y)
+
+ # handle empty diagrams
+ if X.size == 0:
+ if Y.size == 0:
+ if not matching:
+ return 0.
+ else:
+ return 0., np.array([])
+ else:
+ if not matching:
+ return _perstot(Y, order, internal_p)
+ else:
+ return _perstot(Y, order, internal_p), np.array([[-1, j] for j in range(m)])
+ elif Y.size == 0:
+ if not matching:
+ return _perstot(X, order, internal_p)
+ else:
+ return _perstot(X, order, internal_p), np.array([[i, -1] for i in range(n)])
+
+ M = _build_dist_matrix(X, Y, order=order, internal_p=internal_p)
+ a = np.ones(n+1) # weight vector of the input diagram. Uniform here.
+ a[-1] = m
+ b = np.ones(m+1) # weight vector of the input diagram. Uniform here.
+ b[-1] = n
+
+ if matching:
+ P = ot.emd(a=a,b=b,M=M, numItermax=2000000)
+ ot_cost = np.sum(np.multiply(P,M))
+ P[-1, -1] = 0 # Remove matching corresponding to the diagonal
+ match = np.argwhere(P)
+ # Now we turn to -1 points encoding the diagonal
+ match[:,0][match[:,0] >= n] = -1
+ match[:,1][match[:,1] >= m] = -1
+ return ot_cost ** (1./order) , match
+
+ # Comptuation of the otcost using the ot.emd2 library.
+ # Note: it is the Wasserstein distance to the power q.
+ # The default numItermax=100000 is not sufficient for some examples with 5000 points, what is a good value?
+ ot_cost = ot.emd2(a, b, M, numItermax=2000000)
+
+ return ot_cost ** (1./order)