1 files changed, 125 insertions, 0 deletions
diff --git a/src/cython/include/Kernels_interface.h b/src/cython/include/Kernels_interface.h
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+++ b/src/cython/include/Kernels_interface.h
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+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Mathieu Carriere
+ *
+ *    Copyright (C) 2018 INRIA
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef INCLUDE_KERNELS_INTERFACE_H_
+#define INCLUDE_KERNELS_INTERFACE_H_
+
+#include <gudhi/Sliced_Wasserstein.h>
+#include <gudhi/Persistence_weighted_gaussian.h>
+#include <gudhi/Weight_functions.h>
+
+#include <iostream>
+#include <vector>
+#include <utility>  // for std::pair
+
+namespace Gudhi {
+
+namespace persistence_diagram {
+
+
+  // *******************
+  // Kernel evaluations.
+  // *******************
+
+  double sw(const std::vector<std::pair<double, double>>& diag1, const std::vector<std::pair<double, double>>& diag2, double sigma, int N) {
+    Gudhi::Persistence_representations::Sliced_Wasserstein sw1(diag1, sigma, N);
+    Gudhi::Persistence_representations::Sliced_Wasserstein sw2(diag2, sigma, N);
+    return sw1.compute_scalar_product(sw2);
+  }
+
+  double pwg(const std::vector<std::pair<double, double>>& diag1, const std::vector<std::pair<double, double>>& diag2, double sigma, int N, double C, double p) {
+    Gudhi::Persistence_representations::Persistence_weighted_gaussian pwg1(diag1, sigma, N, Gudhi::Persistence_representations::arctan_weight(C,p));
+    Gudhi::Persistence_representations::Persistence_weighted_gaussian pwg2(diag2, sigma, N, Gudhi::Persistence_representations::arctan_weight(C,p));
+    return pwg1.compute_scalar_product(pwg2);
+  }
+
+  double pss(const std::vector<std::pair<double, double>>& diag1, const std::vector<std::pair<double, double>>& diag2, double sigma, int N) {
+    std::vector<std::pair<double, double>> pd1 = diag1; int numpts = diag1.size();    for(int i = 0; i < numpts; i++)  pd1.emplace_back(diag1[i].second,diag1[i].first);
+    std::vector<std::pair<double, double>> pd2 = diag2;     numpts = diag2.size();    for(int i = 0; i < numpts; i++)  pd2.emplace_back(diag2[i].second,diag2[i].first);
+
+    Gudhi::Persistence_representations::Persistence_weighted_gaussian pwg1(pd1, 2*std::sqrt(sigma), N, Gudhi::Persistence_representations::pss_weight);
+    Gudhi::Persistence_representations::Persistence_weighted_gaussian pwg2(pd2, 2*std::sqrt(sigma), N, Gudhi::Persistence_representations::pss_weight);
+
+    return pwg1.compute_scalar_product  (pwg2) / (16*Gudhi::Persistence_representations::pi*sigma);
+  }
+
+  double pss_sym(const std::vector<std::pair<double, double>>& diag1, const std::vector<std::pair<double, double>>& diag2, double sigma, int N) {
+    Gudhi::Persistence_representations::Persistence_weighted_gaussian pwg1(diag1, 2*std::sqrt(sigma), N, Gudhi::Persistence_representations::pss_weight);
+    Gudhi::Persistence_representations::Persistence_weighted_gaussian pwg2(diag2, 2*std::sqrt(sigma), N, Gudhi::Persistence_representations::pss_weight);
+
+    return pwg1.compute_scalar_product  (pwg2) / (16*Gudhi::Persistence_representations::pi*sigma);
+  }
+
+
+  // ****************
+  // Kernel matrices.
+  // ****************
+
+  std::vector<std::vector<double> > sw_matrix(const std::vector<std::vector<std::pair<double, double> > >& s1, const std::vector<std::vector<std::pair<double, double> > >& s2, double sigma, int N){
+    std::vector<std::vector<double> > matrix;
+    std::vector<Gudhi::Persistence_representations::Sliced_Wasserstein> ss1;
+    int num_diag_1 = s1.size(); for(int i = 0; i < num_diag_1; i++){Gudhi::Persistence_representations::Sliced_Wasserstein sw1(s1[i], sigma, N); ss1.push_back(sw1);}
+    std::vector<Gudhi::Persistence_representations::Sliced_Wasserstein> ss2;
+    int num_diag_2 = s2.size(); for(int i = 0; i < num_diag_2; i++){Gudhi::Persistence_representations::Sliced_Wasserstein sw2(s2[i], sigma, N); ss2.push_back(sw2);}
+    for(int i = 0; i < num_diag_1; i++){
+      std::cout << 100.0*i/num_diag_1 << " %" << std::endl;
+      std::vector<double> ps; for(int j = 0; j < num_diag_2; j++) ps.push_back(ss1[i].compute_scalar_product(ss2[j])); matrix.push_back(ps);
+    }
+    return matrix;
+  }
+
+  std::vector<std::vector<double> > pwg_matrix(const std::vector<std::vector<std::pair<double, double> > >& s1, const std::vector<std::vector<std::pair<double, double> > >& s2, double sigma, int N, double C, double p){
+    std::vector<std::vector<double> > matrix; int num_diag_1 = s1.size(); int num_diag_2 = s2.size();
+    for(int i = 0; i < num_diag_1; i++){
+      std::cout << 100.0*i/num_diag_1 << " %" << std::endl;
+      std::vector<double> ps; for(int j = 0; j < num_diag_2; j++) ps.push_back(pwg(s1[i], s2[j], sigma, N, C, p)); matrix.push_back(ps);
+    }
+    return matrix;
+  }
+
+  std::vector<std::vector<double> > pss_matrix(const std::vector<std::vector<std::pair<double, double> > >& s1, const std::vector<std::vector<std::pair<double, double> > >& s2, double sigma, int N){
+    std::vector<std::vector<std::pair<double, double> > > ss1, ss2; std::vector<std::vector<double> > matrix; int num_diag_1 = s1.size(); int num_diag_2 = s2.size();
+    for(int i = 0; i < num_diag_1; i++){
+      std::vector<std::pair<double, double>> pd1 = s1[i]; int numpts = s1[i].size();    
+      for(int j = 0; j < numpts; j++)  pd1.emplace_back(s1[i][j].second,s1[i][j].first);
+      ss1.push_back(pd1);
+    }
+    
+    for(int i = 0; i < num_diag_2; i++){
+      std::vector<std::pair<double, double>> pd2 = s2[i]; int numpts = s2[i].size();    
+      for(int j = 0; j < numpts; j++)  pd2.emplace_back(s2[i][j].second,s2[i][j].first);
+      ss2.push_back(pd2);
+    }
+
+    for(int i = 0; i < num_diag_1; i++){
+      std::cout << 100.0*i/num_diag_1 << " %" << std::endl;
+      std::vector<double> ps; for(int j = 0; j < num_diag_2; j++) ps.push_back(pss_sym(ss1[i], ss2[j], sigma, N)); matrix.push_back(ps);
+    }
+    return matrix;
+  }
+
+}  // namespace persistence_diagram
+
+}  // namespace Gudhi
+
+
+#endif  // INCLUDE_KERNELS_INTERFACE_H_