integrated kernel code in pers_representation branch

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/kernels@3249 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 58e77263a0da3674e4699cef832b6d357dcf12e2

4 files changed, 158 insertions, 12 deletions

diff --git a/src/Persistence_representations/example/CMakeLists.txt b/src/Persistence_representations/example/CMakeLists.txt
index 7788b603..54d719ac 100644
--- a/src/Persistence_representations/example/CMakeLists.txt
+++ b/src/Persistence_representations/example/CMakeLists.txt
@@ -1,34 +1,29 @@
 cmake_minimum_required(VERSION 2.6)
 project(Persistence_representations_example)
 
-file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/")
-
 add_executable ( Persistence_representations_example_landscape_on_grid persistence_landscape_on_grid.cpp )
-target_link_libraries(Persistence_representations_example_landscape_on_grid ${Boost_SYSTEM_LIBRARY})
 add_test(NAME Persistence_representations_example_landscape_on_grid
     COMMAND $<TARGET_FILE:Persistence_representations_example_landscape_on_grid>)
+install(TARGETS Persistence_representations_example_landscape_on_grid DESTINATION bin)
 
 add_executable ( Persistence_representations_example_landscape persistence_landscape.cpp )
-target_link_libraries(Persistence_representations_example_landscape ${Boost_SYSTEM_LIBRARY})
 add_test(NAME Persistence_representations_example_landscape
     COMMAND $<TARGET_FILE:Persistence_representations_example_landscape>)
+install(TARGETS Persistence_representations_example_landscape DESTINATION bin)
 
 add_executable ( Persistence_representations_example_intervals persistence_intervals.cpp )
-target_link_libraries(Persistence_representations_example_intervals ${Boost_SYSTEM_LIBRARY})
 add_test(NAME Persistence_representations_example_intervals
     COMMAND $<TARGET_FILE:Persistence_representations_example_intervals>
-    "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt")
+    "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers")
+install(TARGETS Persistence_representations_example_intervals DESTINATION bin)
 
 add_executable ( Persistence_representations_example_vectors persistence_vectors.cpp )
-target_link_libraries(Persistence_representations_example_vectors ${Boost_SYSTEM_LIBRARY})
 add_test(NAME Persistence_representations_example_vectors
     COMMAND $<TARGET_FILE:Persistence_representations_example_vectors>)
+install(TARGETS Persistence_representations_example_vectors DESTINATION bin)
 
 add_executable ( Persistence_representations_example_heat_maps persistence_heat_maps.cpp )
-target_link_libraries(Persistence_representations_example_heat_maps ${Boost_SYSTEM_LIBRARY})
 add_test(NAME Persistence_representations_example_heat_maps
     COMMAND $<TARGET_FILE:Persistence_representations_example_heat_maps>)
-
-
-
+install(TARGETS Persistence_representations_example_heat_maps DESTINATION bin)
 
diff --git a/src/Persistence_representations/example/persistence_vectors.cpp b/src/Persistence_representations/example/persistence_vectors.cpp
index 59eca152..834ae644 100644
--- a/src/Persistence_representations/example/persistence_vectors.cpp
+++ b/src/Persistence_representations/example/persistence_vectors.cpp
@@ -30,7 +30,7 @@
 #include <utility>
 
 using Vector_distances_in_diagram =
-  Gudhi::Persistence_representations::Vector_distances_in_diagram<Gudhi::Euclidean_distance>;
+    Gudhi::Persistence_representations::Vector_distances_in_diagram<Gudhi::Euclidean_distance>;
 
 int main(int argc, char** argv) {
   // create two simple vectors with birth--death pairs:
diff --git a/src/Persistence_representations/example/persistence_weighted_gaussian.cpp b/src/Persistence_representations/example/persistence_weighted_gaussian.cpp
new file mode 100644
index 00000000..e95b9445
--- /dev/null
+++ b/src/Persistence_representations/example/persistence_weighted_gaussian.cpp
@@ -0,0 +1,96 @@
+/*    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 PD = std::vector<std::pair<double,double> >;
+using PWG = Gudhi::Persistence_representations::Persistence_weighted_gaussian;
+
+int main(int argc, char** argv) {
+
+  std::vector<std::pair<double, double> > persistence1;
+  std::vector<std::pair<double, double> > 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));
+
+  PWG PWG1(persistence1);
+  PWG PWG2(persistence2);
+  double sigma = 1;
+  double tau = 1;
+  int m = 1000;
+
+
+
+  // Linear PWG
+
+  std::cout << PWG1.compute_scalar_product  (PWG2, sigma, PWG::arctan_weight, m) << std::endl;
+  std::cout << PWG1.compute_scalar_product  (PWG2, sigma, PWG::arctan_weight, -1) << std::endl;
+
+  std::cout << PWG1.distance  (PWG2, sigma, PWG::arctan_weight, m) << std::endl;
+  std::cout << PWG1.distance  (PWG2, sigma, PWG::arctan_weight, -1) << std::endl;
+
+
+
+
+
+
+
+  // Gaussian PWG
+
+  std::cout << std::exp( -PWG1.distance (PWG2, sigma, PWG::arctan_weight, m, 2) ) / (2*tau*tau) << std::endl;
+  std::cout << std::exp( -PWG1.distance (PWG2, sigma, PWG::arctan_weight, -1, 2) ) / (2*tau*tau) << std::endl;
+
+
+
+
+
+
+
+  // PSS
+
+  PD pd1 = persistence1; int numpts = persistence1.size();    for(int i = 0; i < numpts; i++)  pd1.emplace_back(persistence1[i].second,persistence1[i].first);
+  PD pd2 = persistence2;     numpts = persistence2.size();    for(int i = 0; i < numpts; i++)  pd2.emplace_back(persistence2[i].second,persistence2[i].first);
+
+  PWG pwg1(pd1);
+  PWG pwg2(pd2);
+
+  std::cout << pwg1.compute_scalar_product  (pwg2, 2*std::sqrt(sigma), PWG::pss_weight, m) / (16*pi*sigma) << std::endl;
+  std::cout << pwg1.compute_scalar_product  (pwg2, 2*std::sqrt(sigma), PWG::pss_weight, -1) / (16*pi*sigma) << std::endl;
+
+  std::cout << pwg1.distance  (pwg2, 2*std::sqrt(sigma), PWG::pss_weight, m) / (16*pi*sigma) << std::endl;
+  std::cout << pwg1.distance  (pwg2, 2*std::sqrt(sigma), PWG::pss_weight, -1) / (16*pi*sigma) << std::endl;
+
+
+  return 0;
+}
diff --git a/src/Persistence_representations/example/sliced_wasserstein.cpp b/src/Persistence_representations/example/sliced_wasserstein.cpp
new file mode 100644
index 00000000..673d8474
--- /dev/null
+++ b/src/Persistence_representations/example/sliced_wasserstein.cpp
@@ -0,0 +1,55 @@
+/*    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/Sliced_Wasserstein.h>
+
+#include <iostream>
+#include <vector>
+#include <utility>
+
+using SW = Gudhi::Persistence_representations::Sliced_Wasserstein;
+
+int main(int argc, char** argv) {
+
+  std::vector<std::pair<double, double> > persistence1;
+  std::vector<std::pair<double, double> > 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));
+
+  SW SW1(persistence1);
+  SW SW2(persistence2);
+
+  std::cout << SW1.compute_sliced_wasserstein_distance(SW2,100) << std::endl;
+  std::cout << SW1.compute_sliced_wasserstein_distance(SW2,-1) << std::endl;
+  std::cout << SW1.compute_scalar_product(SW2,1,100) << std::endl;
+  std::cout << SW1.distance(SW2,1,100,1) << std::endl;
+
+  return 0;
+}