git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/kernels@3628 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 12f32a1c8ca31e7e0a40e1c3502e2a3d810d5bc5

6 files changed, 12 insertions, 275 deletions

diff --git a/src/Persistence_representations/example/CMakeLists.txt b/src/Persistence_representations/example/CMakeLists.txt
index 9be22085..d236c3a6 100644
--- a/src/Persistence_representations/example/CMakeLists.txt
+++ b/src/Persistence_representations/example/CMakeLists.txt
@@ -31,23 +31,3 @@ add_executable ( Sliced_Wasserstein sliced_wasserstein.cpp )
 add_test(NAME Sliced_Wasserstein
     COMMAND $<TARGET_FILE:Sliced_Wasserstein>)
 install(TARGETS Sliced_Wasserstein DESTINATION bin)
-
-add_executable ( Persistence_weighted_gaussian persistence_weighted_gaussian.cpp )
-add_test(NAME Persistence_weighted_gaussian
-    COMMAND $<TARGET_FILE:Persistence_weighted_gaussian>)
-install(TARGETS Persistence_weighted_gaussian DESTINATION bin)
-
-add_executable ( Persistence_heat_maps_exact persistence_heat_maps_exact.cpp )
-add_test(NAME Persistence_heat_maps_exact
-    COMMAND $<TARGET_FILE:Persistence_heat_maps_exact>)
-install(TARGETS Persistence_heat_maps_exact DESTINATION bin)
-
-add_executable ( Persistence_landscape_on_grid_exact persistence_landscape_on_grid_exact.cpp )
-add_test(NAME Persistence_landscape_on_grid_exact
-    COMMAND $<TARGET_FILE:Persistence_landscape_on_grid_exact>)
-install(TARGETS Persistence_landscape_on_grid_exact DESTINATION bin)
-
-add_executable ( Betti_sequence betti_sequence.cpp )
-add_test(NAME Betti_sequence
-    COMMAND $<TARGET_FILE:Betti_sequence>)
-install(TARGETS Betti_sequence DESTINATION bin)
diff --git a/src/Persistence_representations/example/betti_sequence.cpp b/src/Persistence_representations/example/betti_sequence.cpp
deleted file mode 100644
index a422a822..00000000
--- a/src/Persistence_representations/example/betti_sequence.cpp
+++ /dev/null
@@ -1,49 +0,0 @@
-/*    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 (France)
- *
- *    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/>.
- */
-
-#include <gudhi/Betti_sequence.h>
-
-#include <iostream>
-#include <vector>
-#include <utility>
-
-using Persistence_diagram = Gudhi::Persistence_representations::Persistence_diagram;
-using BS = Gudhi::Persistence_representations::Betti_sequence;
-
-int main(int argc, char** argv) {
-
-  Persistence_diagram persistence;
-
-  persistence.push_back(std::make_pair(1, 2));
-  persistence.push_back(std::make_pair(6, 8));
-  persistence.push_back(std::make_pair(0, 4));
-  persistence.push_back(std::make_pair(3, 8));
-
-  double min_x = 0; double max_x = 8; int res_x = 1000;
-
-  BS bs(persistence, min_x, max_x, res_x);
-  std::vector<int> B = bs.vectorize();
-
-  for(int i = 0; i < res_x; i++)  std::cout << B[i] << ", ";
-
-  return 0;
-}
diff --git a/src/Persistence_representations/example/persistence_heat_maps.cpp b/src/Persistence_representations/example/persistence_heat_maps.cpp
index 323b57e9..f1791e97 100644
--- a/src/Persistence_representations/example/persistence_heat_maps.cpp
+++ b/src/Persistence_representations/example/persistence_heat_maps.cpp
@@ -21,6 +21,7 @@
  */
 
 #include <gudhi/Persistence_heat_maps.h>
+#include <gudhi/common_persistence_representations.h>
 
 #include <iostream>
 #include <vector>
@@ -76,5 +77,16 @@ int main(int argc, char** argv) {
   // to compute scalar product of hm1 and hm2:
   std::cout << "Scalar product is : " << hm1.compute_scalar_product(hm2) << std::endl;
 
+  Gudhi::Persistence_representations::Kernel k = Gudhi::Persistence_representations::Gaussian_kernel(1.0);
+
+  Persistence_heat_maps hm1k(persistence1, k);
+  Persistence_heat_maps hm2k(persistence2, k);
+
+  Persistence_heat_maps hm1i(persistence1, 20, 20, 0, 11, 0, 11, k);
+  Persistence_heat_maps hm2i(persistence2, 20, 20, 0, 11, 0, 11, k);
+
+  std::cout << "Scalar product computed with exact kernel is : " << hm1i.compute_scalar_product(hm2i) << std::endl;
+  std::cout << "Kernel value between PDs seen as functions is : " << hm1k.compute_scalar_product(hm2k) << std::endl;
+
   return 0;
 }
diff --git a/src/Persistence_representations/example/persistence_heat_maps_exact.cpp b/src/Persistence_representations/example/persistence_heat_maps_exact.cpp
deleted file mode 100644
index f15b710d..00000000
--- a/src/Persistence_representations/example/persistence_heat_maps_exact.cpp
+++ /dev/null
@@ -1,55 +0,0 @@
-/*    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 (France)
- *
- *    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/>.
- */
-
-#include <gudhi/Persistence_heat_maps_exact.h>
-#include <gudhi/Weight_functions.h>
-
-#include <iostream>
-#include <vector>
-#include <utility>
-#include <string>
-
-using Persistence_diagram = Gudhi::Persistence_representations::Persistence_diagram;
-using PI = Gudhi::Persistence_representations::Persistence_heat_maps_exact;
-using Weight = std::function<double (std::pair<double,double>) >;
-
-int main(int argc, char** argv) {
-
-  Persistence_diagram persistence;
-
-  persistence.push_back(std::make_pair(1, 2));
-  persistence.push_back(std::make_pair(6, 8));
-  persistence.push_back(std::make_pair(0, 4));
-  persistence.push_back(std::make_pair(3, 8));
-
-  double min_x = 0.0; double max_x = 10.0; int res_x = 100; double min_y = 0.0; double max_y = 10.0; int res_y = 100; double sigma = 1.0; Weight weight = Gudhi::Persistence_representations::linear_weight;
-
-  PI pim(persistence, min_x, max_x, res_x, min_y, max_y, res_y, weight, sigma);
-  std::vector<std::vector<double> > P = pim.vectorize();
-
-  for(int i = 0; i < res_y; i++){
-    for(int j = 0; j < res_x; j++) std::cout << P[i][j] << " ";
-    std::cout << std::endl;
-  }
-
-  return 0;
-}
diff --git a/src/Persistence_representations/example/persistence_landscape_on_grid_exact.cpp b/src/Persistence_representations/example/persistence_landscape_on_grid_exact.cpp
deleted file mode 100644
index 9ce42649..00000000
--- a/src/Persistence_representations/example/persistence_landscape_on_grid_exact.cpp
+++ /dev/null
@@ -1,52 +0,0 @@
-/*    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 (France)
- *
- *    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/>.
- */
-
-#include <gudhi/Persistence_landscape_on_grid_exact.h>
-
-#include <iostream>
-#include <vector>
-#include <utility>
-
-using Persistence_diagram = Gudhi::Persistence_representations::Persistence_diagram;
-using LS = Gudhi::Persistence_representations::Persistence_landscape_on_grid_exact;
-
-int main(int argc, char** argv) {
-
-  Persistence_diagram persistence;
-
-  persistence.push_back(std::make_pair(1, 2));
-  persistence.push_back(std::make_pair(6, 8));
-  persistence.push_back(std::make_pair(0, 4));
-  persistence.push_back(std::make_pair(3, 8));
-
-  int nb_ls = 2; double min_x = 0; double max_x = 8; int res_x = 1000;
-
-  LS ls(persistence, nb_ls, min_x, max_x, res_x);
-  std::vector<std::vector<double> > L = ls.vectorize();
-
-  for(int i = 0; i < nb_ls; i++){
-    for(int j = 0; j < res_x; j++) std::cout << L[i][j] << ", ";
-    std::cout << std::endl;
-  }
-
-  return 0;
-}
diff --git a/src/Persistence_representations/example/persistence_weighted_gaussian.cpp b/src/Persistence_representations/example/persistence_weighted_gaussian.cpp
deleted file mode 100644
index 7945e4f1..00000000
--- a/src/Persistence_representations/example/persistence_weighted_gaussian.cpp
+++ /dev/null
@@ -1,99 +0,0 @@
-/*    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 (France)
- *
- *    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/>.
- */
-
-#include <gudhi/Persistence_weighted_gaussian.h>
-
-#include <iostream>
-#include <vector>
-#include <utility>
-
-using Persistence_diagram = Gudhi::Persistence_representations::Persistence_diagram;
-using PWG = Gudhi::Persistence_representations::Persistence_weighted_gaussian;
-
-int main(int argc, char** argv) {
-
-  Persistence_diagram persistence1, persistence2;
-
-  persistence1.push_back(std::make_pair(1, 2));
-  persistence1.push_back(std::make_pair(6, 8));
-  persistence1.push_back(std::make_pair(0, 4));
-  persistence1.push_back(std::make_pair(3, 8));
-
-  persistence2.push_back(std::make_pair(2, 9));
-  persistence2.push_back(std::make_pair(1, 6));
-  persistence2.push_back(std::make_pair(3, 5));
-  persistence2.push_back(std::make_pair(6, 10));
-
-  double sigma = 1;
-  double tau = 1;
-  int m = 10000;
-
-  PWG PWG1(persistence1, sigma, m, Gudhi::Persistence_representations::arctan_weight(1,1));
-  PWG PWG2(persistence2, sigma, m, Gudhi::Persistence_representations::arctan_weight(1,1));
-
-  PWG PWGex1(persistence1, sigma, -1, Gudhi::Persistence_representations::arctan_weight(1,1));
-  PWG PWGex2(persistence2, sigma, -1, Gudhi::Persistence_representations::arctan_weight(1,1));
-
-
-  // Linear PWG
-
-  std::cout << "Approx PWG kernel: " << PWG1.compute_scalar_product  (PWG2) << std::endl;
-  std::cout << "Exact  PWG kernel: " << PWGex1.compute_scalar_product  (PWGex2) << std::endl;
-
-  std::cout << "Distance induced by approx PWG kernel: " << PWG1.distance  (PWG2) << std::endl;
-  std::cout << "Distance induced by exact  PWG kernel: " << PWGex1.distance  (PWGex2) << std::endl;
-
-
-
-
-
-
-
-  // Gaussian PWG
-
-  std::cout << "Approx Gaussian PWG kernel: " << std::exp( -PWG1.distance (PWG2) ) / (2*tau*tau) << std::endl;
-  std::cout << "Exact  Gaussian PWG kernel: " << std::exp( -PWGex1.distance (PWGex2) ) / (2*tau*tau) << std::endl;
-
-
-
-
-
-
-
-  // PSS
-
-  Persistence_diagram pd1 = persistence1; int numpts = persistence1.size();    for(int i = 0; i < numpts; i++)  pd1.emplace_back(persistence1[i].second,persistence1[i].first);
-  Persistence_diagram pd2 = persistence2;     numpts = persistence2.size();    for(int i = 0; i < numpts; i++)  pd2.emplace_back(persistence2[i].second,persistence2[i].first);
-
-  PWG pwg1(pd1, 2*std::sqrt(sigma), m, Gudhi::Persistence_representations::pss_weight);
-  PWG pwg2(pd2, 2*std::sqrt(sigma), m, Gudhi::Persistence_representations::pss_weight);
-
-  PWG pwgex1(pd1, 2*std::sqrt(sigma), -1, Gudhi::Persistence_representations::pss_weight);
-  PWG pwgex2(pd2, 2*std::sqrt(sigma), -1, Gudhi::Persistence_representations::pss_weight);
-
-  std::cout << "Approx PSS kernel: " << pwg1.compute_scalar_product  (pwg2) / (16*Gudhi::Persistence_representations::pi*sigma) << std::endl;
-  std::cout << "Exact  PSS kernel: " << pwgex1.compute_scalar_product  (pwgex2) / (16*Gudhi::Persistence_representations::pi*sigma) << std::endl;
-
-
-
-  return 0;
-}