/* 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 */ #include #include #include #include #include // Hera #include namespace py = pybind11; typedef py::array_t Dgm; // Get m[i,0] and m[i,1] as a pair static auto pairify(void* p, ssize_t h, ssize_t w) { return [=](ssize_t i){ char* birth = (char*)p + i * h; char* death = birth + w; return std::make_pair(*(double*)birth, *(double*)death); }; } inline auto numpy_to_range_of_pairs(py::array_t dgm) { py::buffer_info buf = dgm.request(); // shape (n,2) or (0) for empty if((buf.ndim!=2 || buf.shape[1]!=2) && (buf.ndim!=1 || buf.shape[0]!=0)) throw std::runtime_error("Diagram must be an array of size n x 2"); // In the case of shape (0), avoid reading non-existing strides[1] even if we won't use it. ssize_t stride1 = buf.ndim == 2 ? buf.strides[1] : 0; auto cnt = boost::counting_range(0, buf.shape[0]); return boost::adaptors::transform(cnt, pairify(buf.ptr, buf.strides[0], stride1)); // Be careful that the returned range cannot contain references to dead temporaries. } double wasserstein_distance( Dgm d1, Dgm d2, double wasserstein_power, double internal_p, double delta) { // I *think* the call to request() has to be before releasing the GIL. auto diag1 = numpy_to_range_of_pairs(d1); auto diag2 = numpy_to_range_of_pairs(d2); py::gil_scoped_release release; hera::AuctionParams params; params.wasserstein_power = wasserstein_power; // hera encodes infinity as -1... if(std::isinf(internal_p)) internal_p = hera::get_infinity(); params.internal_p = internal_p; params.delta = delta; // The extra parameters are purposedly not exposed for now. return hera::wasserstein_dist(diag1, diag2, params); } PYBIND11_MODULE(hera, m) { m.def("wasserstein_distance", &wasserstein_distance, py::arg("X"), py::arg("Y"), py::arg("order") = 1, py::arg("internal_p") = std::numeric_limits::infinity(), py::arg("delta") = .01, R"pbdoc( Compute the Wasserstein distance between two diagrams. Points at infinity are supported. Parameters: X (n x 2 numpy array): First diagram Y (n x 2 numpy array): Second diagram order (float): Wasserstein exponent W_q internal_p (float): Internal Minkowski norm L^p in R^2 delta (float): Relative error 1+delta Returns: float: Approximate Wasserstein distance W_q(X,Y) )pbdoc"); }