Merge last trunk modifications

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2928 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c5b02e64769ac4af51badc9215a433c50f63299f

6 files changed, 96 insertions, 45 deletions

diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt
index cefc1ad6..79d9e7dd 100644
--- a/src/Alpha_complex/utilities/CMakeLists.txt
+++ b/src/Alpha_complex/utilities/CMakeLists.txt
@@ -46,4 +46,20 @@ if(CGAL_FOUND)
     install(TARGETS periodic_alpha_complex_3d_persistence DESTINATION bin)
 
   endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+
+  if (NOT CGAL_VERSION VERSION_LESS 4.11.0)
+    add_executable(weighted_periodic_alpha_complex_3d_persistence weighted_periodic_alpha_complex_3d_persistence.cpp)
+    target_link_libraries(weighted_periodic_alpha_complex_3d_persistence ${CGAL_LIBRARY})
+    if (TBB_FOUND)
+      target_link_libraries(weighted_periodic_alpha_complex_3d_persistence ${TBB_LIBRARIES})
+    endif(TBB_FOUND)
+
+    add_test(NAME Persistent_cohomology_example_weigted_periodic_alpha_complex_3d COMMAND $<TARGET_FILE:weighted_periodic_alpha_complex_3d_persistence>
+        "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.weights"
+        "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" "3" "1.0")
+
+    install(TARGETS weighted_periodic_alpha_complex_3d_persistence DESTINATION bin)
+
+  endif (NOT CGAL_VERSION VERSION_LESS 4.11.0)
+
 endif(CGAL_FOUND)
diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
index 28daca5e..0a021a0f 100644
--- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
@@ -30,8 +30,6 @@
 #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
 #include <CGAL/Delaunay_triangulation_3.h>
 #include <CGAL/Alpha_shape_3.h>
-#include <CGAL/Alpha_shape_vertex_base_3.h>
-#include <CGAL/Alpha_shape_cell_base_3.h>
 #include <CGAL/iterator.h>
 
 #include <fstream>
@@ -42,6 +40,7 @@
 #include <utility>
 #include <list>
 #include <vector>
+#include <cstdlib>
 
 #include "alpha_complex_3d_helper.h"
 
@@ -76,7 +75,8 @@ using Simplex_tree_vertex = ST::Vertex_handle;
 using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
 using Alpha_shape_simplex_tree_pair = std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
 using Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>;
-using PCOH = Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>;
+using Persistent_cohomology =
+    Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>;
 
 void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag,
                      int &coeff_field_characteristic, Filtration_value &min_persistence);
@@ -132,28 +132,28 @@ int main(int argc, char **argv) {
   Filtration_value filtration_max = 0.0;
   for (auto object_iterator : the_objects) {
     // Retrieve Alpha shape vertex list from object
-    if (const Cell_handle *cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
+    if (const Cell_handle* cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
       vertex_list = from_cell<Vertex_list, Cell_handle>(*cell);
       count_cells++;
       if (dim_max < 3) {
         // Cell is of dim 3
         dim_max = 3;
       }
-    } else if (const Facet *facet = CGAL::object_cast<Facet>(&object_iterator)) {
+    } else if (const Facet* facet = CGAL::object_cast<Facet>(&object_iterator)) {
       vertex_list = from_facet<Vertex_list, Facet>(*facet);
       count_facets++;
       if (dim_max < 2) {
         // Facet is of dim 2
         dim_max = 2;
       }
-    } else if (const Edge_3 *edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
+    } else if (const Edge_3* edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
       vertex_list = from_edge<Vertex_list, Edge_3>(*edge);
       count_edges++;
       if (dim_max < 1) {
         // Edge_3 is of dim 1
         dim_max = 1;
       }
-    } else if (const Vertex_handle *vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
+    } else if (const Vertex_handle* vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
       count_vertices++;
       vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
     }
@@ -179,7 +179,7 @@ int main(int argc, char **argv) {
       }
     }
     // Construction of the simplex_tree
-    Filtration_value filtr = /*std::sqrt*/ (*the_alpha_value_iterator);
+    Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator);
 #ifdef DEBUG_TRACES
     std::cout << "filtration = " << filtr << std::endl;
 #endif  // DEBUG_TRACES
@@ -192,7 +192,6 @@ int main(int argc, char **argv) {
     else
       std::cout << "This shall not happen" << std::endl;
   }
-  simplex_tree.set_dimension(dim_max);
 
 #ifdef DEBUG_TRACES
   std::cout << "vertices \t\t" << count_vertices << std::endl;
@@ -218,7 +217,7 @@ int main(int argc, char **argv) {
 
   std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl;
   // Compute the persistence diagram of the complex
-  PCOH pcoh(simplex_tree);
+  Persistent_cohomology pcoh(simplex_tree, true);
   // initializes the coefficient field for homology
   pcoh.init_coefficients(coeff_field_characteristic);
 
diff --git a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp
index c69482ab..9a266418 100644
--- a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2014  INRIA Saclay (France)
+ *    Copyright (C) 2014  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
@@ -30,8 +30,6 @@
 #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
 #include <CGAL/Delaunay_triangulation_3.h>
 #include <CGAL/Alpha_shape_3.h>
-#include <CGAL/Alpha_shape_vertex_base_3.h>
-#include <CGAL/Alpha_shape_cell_base_3.h>
 #include <CGAL/iterator.h>
 
 #include <fstream>
@@ -42,6 +40,7 @@
 #include <utility>
 #include <list>
 #include <vector>
+#include <cstdlib>
 
 #include "alpha_complex_3d_helper.h"
 
@@ -77,7 +76,8 @@ using Simplex_tree_vertex = ST::Vertex_handle;
 using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
 using Alpha_shape_simplex_tree_pair = std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
 using Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>;
-using PCOH = Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>;
+using Persistent_cohomology =
+    Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>;
 
 void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag,
                      int &coeff_field_characteristic, Filtration_value &min_persistence);
@@ -133,28 +133,28 @@ int main(int argc, char **argv) {
   Filtration_value filtration_max = 0.0;
   for (auto object_iterator : the_objects) {
     // Retrieve Alpha shape vertex list from object
-    if (const Cell_handle *cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
+    if (const Cell_handle* cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
       vertex_list = from_cell<Vertex_list, Cell_handle>(*cell);
       count_cells++;
       if (dim_max < 3) {
         // Cell is of dim 3
         dim_max = 3;
       }
-    } else if (const Facet *facet = CGAL::object_cast<Facet>(&object_iterator)) {
+    } else if (const Facet* facet = CGAL::object_cast<Facet>(&object_iterator)) {
       vertex_list = from_facet<Vertex_list, Facet>(*facet);
       count_facets++;
       if (dim_max < 2) {
         // Facet is of dim 2
         dim_max = 2;
       }
-    } else if (const Edge_3 *edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
+    } else if (const Edge_3* edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
       vertex_list = from_edge<Vertex_list, Edge_3>(*edge);
       count_edges++;
       if (dim_max < 1) {
         // Edge_3 is of dim 1
         dim_max = 1;
       }
-    } else if (const Vertex_handle *vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
+    } else if (const Vertex_handle* vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
       count_vertices++;
       vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
     }
@@ -181,7 +181,7 @@ int main(int argc, char **argv) {
     }
     // Construction of the simplex_tree
     // you can also use the_alpha_value_iterator->exact()
-    Filtration_value filtr = /*std::sqrt*/ CGAL::to_double(the_alpha_value_iterator->exact());
+    Filtration_value filtr = /*std::sqrt*/CGAL::to_double(the_alpha_value_iterator->exact());
 #ifdef DEBUG_TRACES
     std::cout << "filtration = " << filtr << std::endl;
 #endif  // DEBUG_TRACES
@@ -194,7 +194,6 @@ int main(int argc, char **argv) {
     else
       std::cout << "This shall not happen" << std::endl;
   }
-  simplex_tree.set_dimension(dim_max);
 
 #ifdef DEBUG_TRACES
   std::cout << "vertices \t\t" << count_vertices << std::endl;
@@ -220,13 +219,21 @@ int main(int argc, char **argv) {
 
   std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl;
   // Compute the persistence diagram of the complex
-  PCOH pcoh(simplex_tree);
+  Persistent_cohomology pcoh(simplex_tree, true);
   // initializes the coefficient field for homology
   pcoh.init_coefficients(coeff_field_characteristic);
 
   pcoh.compute_persistent_cohomology(min_persistence);
 
-  pcoh.output_diagram();
+  // Output the diagram in filediag
+  if (output_file_diag.empty()) {
+    pcoh.output_diagram();
+  } else {
+    std::cout << "Result in file: " << output_file_diag << std::endl;
+    std::ofstream out(output_file_diag);
+    pcoh.output_diagram(out);
+    out.close();
+  }
 
   return 0;
 }
diff --git a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp
index b480a9ec..186a58f8 100644
--- a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp
@@ -31,8 +31,6 @@
 #include <CGAL/Periodic_3_Delaunay_triangulation_traits_3.h>
 #include <CGAL/Periodic_3_Delaunay_triangulation_3.h>
 #include <CGAL/Alpha_shape_3.h>
-#include <CGAL/Alpha_shape_vertex_base_3.h>
-#include <CGAL/Alpha_shape_cell_base_3.h>
 #include <CGAL/iterator.h>
 
 #include <fstream>
@@ -158,29 +156,28 @@ int main(int argc, char **argv) {
   Filtration_value filtration_max = 0.0;
   for (auto object_iterator : the_objects) {
     // Retrieve Alpha shape vertex list from object
-    if (const Cell_handle *cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
+    if (const Cell_handle* cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
       vertex_list = from_cell<Vertex_list, Cell_handle>(*cell);
       count_cells++;
       if (dim_max < 3) {
         // Cell is of dim 3
         dim_max = 3;
       }
-    } else if (const Facet *facet = CGAL::object_cast<Facet>(&object_iterator)) {
+    } else if (const Facet* facet = CGAL::object_cast<Facet>(&object_iterator)) {
       vertex_list = from_facet<Vertex_list, Facet>(*facet);
       count_facets++;
       if (dim_max < 2) {
         // Facet is of dim 2
         dim_max = 2;
       }
-    } else if (const Edge_3 *edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
+    } else if (const Edge_3* edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
       vertex_list = from_edge<Vertex_list, Edge_3>(*edge);
       count_edges++;
       if (dim_max < 1) {
         // Edge_3 is of dim 1
         dim_max = 1;
       }
-    } else if (const Alpha_shape_3::Vertex_handle *vertex =
-                   CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&object_iterator)) {
+    } else if (const Vertex_handle* vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
       count_vertices++;
       vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
     }
@@ -219,7 +216,6 @@ int main(int argc, char **argv) {
     else
       std::cout << "This shall not happen" << std::endl;
   }
-  simplex_tree.set_dimension(dim_max);
 
 #ifdef DEBUG_TRACES
   std::cout << "vertices \t\t" << count_vertices << std::endl;
@@ -251,7 +247,15 @@ int main(int argc, char **argv) {
 
   pcoh.compute_persistent_cohomology(min_persistence);
 
-  pcoh.output_diagram();
+  // Output the diagram in filediag
+  if (output_file_diag.empty()) {
+    pcoh.output_diagram();
+  } else {
+    std::cout << "Result in file: " << output_file_diag << std::endl;
+    std::ofstream out(output_file_diag);
+    pcoh.output_diagram(out);
+    out.close();
+  }
 
   return 0;
 }
diff --git a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp
index 91747a8c..0e73a99b 100644
--- a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp
@@ -27,14 +27,17 @@
 #include <gudhi/Persistent_cohomology.h>
 #include <gudhi/Points_3D_off_io.h>
 
+#include <CGAL/config.h>
 #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
-#include <CGAL/Regular_triangulation_euclidean_traits_3.h>
 #include <CGAL/Regular_triangulation_3.h>
 #include <CGAL/Alpha_shape_3.h>
-#include <CGAL/Alpha_shape_vertex_base_3.h>
-#include <CGAL/Alpha_shape_cell_base_3.h>
 #include <CGAL/iterator.h>
 
+// For CGAL < 4.11
+#if CGAL_VERSION_NR < 1041100000
+#include <CGAL/Regular_triangulation_euclidean_traits_3.h>
+#endif  // CGAL_VERSION_NR < 1041100000
+
 #include <fstream>
 #include <cmath>
 #include <string>
@@ -47,19 +50,37 @@
 
 #include "alpha_complex_3d_helper.h"
 
-// Traits
+// Alpha_shape_3 templates type definitions
 using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel;
+
+// For CGAL < 4.11
+#if CGAL_VERSION_NR < 1041100000
 using Gt = CGAL::Regular_triangulation_euclidean_traits_3<Kernel>;
 using Vb = CGAL::Alpha_shape_vertex_base_3<Gt>;
 using Fb = CGAL::Alpha_shape_cell_base_3<Gt>;
 using Tds = CGAL::Triangulation_data_structure_3<Vb, Fb>;
 using Triangulation_3 = CGAL::Regular_triangulation_3<Gt, Tds>;
-using Alpha_shape_3 = CGAL::Alpha_shape_3<Triangulation_3>;
 
 // From file type definition
 using Point_3 = Gt::Bare_point;
 using Weighted_point_3 = Gt::Weighted_point;
 
+// For CGAL >= 4.11
+#else  // CGAL_VERSION_NR < 1041100000
+using Rvb = CGAL::Regular_triangulation_vertex_base_3<Kernel>;
+using Vb = CGAL::Alpha_shape_vertex_base_3<Kernel,Rvb>;
+using Rcb = CGAL::Regular_triangulation_cell_base_3<Kernel>;
+using Cb = CGAL::Alpha_shape_cell_base_3<Kernel,Rcb>;
+using Tds = CGAL::Triangulation_data_structure_3<Vb,Cb>;
+using Triangulation_3 = CGAL::Regular_triangulation_3<Kernel,Tds>;
+
+// From file type definition
+using Point_3 = Triangulation_3::Bare_point;
+using Weighted_point_3 = Triangulation_3::Weighted_point;
+#endif  // CGAL_VERSION_NR < 1041100000
+
+using Alpha_shape_3 = CGAL::Alpha_shape_3<Triangulation_3>;
+
 // filtration with alpha values needed type definition
 using Alpha_value_type = Alpha_shape_3::FT;
 using Object = CGAL::Object;
@@ -160,29 +181,28 @@ int main(int argc, char **argv) {
   Filtration_value filtration_max = 0.0;
   for (auto object_iterator : the_objects) {
     // Retrieve Alpha shape vertex list from object
-    if (const Cell_handle *cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
+    if (const Cell_handle* cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
       vertex_list = from_cell<Vertex_list, Cell_handle>(*cell);
       count_cells++;
       if (dim_max < 3) {
         // Cell is of dim 3
         dim_max = 3;
       }
-    } else if (const Facet *facet = CGAL::object_cast<Facet>(&object_iterator)) {
+    } else if (const Facet* facet = CGAL::object_cast<Facet>(&object_iterator)) {
       vertex_list = from_facet<Vertex_list, Facet>(*facet);
       count_facets++;
       if (dim_max < 2) {
         // Facet is of dim 2
         dim_max = 2;
       }
-    } else if (const Edge_3 *edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
+    } else if (const Edge_3* edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
       vertex_list = from_edge<Vertex_list, Edge_3>(*edge);
       count_edges++;
       if (dim_max < 1) {
         // Edge_3 is of dim 1
         dim_max = 1;
       }
-    } else if (const Alpha_shape_3::Vertex_handle *vertex =
-                   CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&object_iterator)) {
+    } else if (const Vertex_handle* vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
       count_vertices++;
       vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
     }
@@ -221,7 +241,6 @@ int main(int argc, char **argv) {
     else
       std::cout << "This shall not happen" << std::endl;
   }
-  simplex_tree.set_dimension(dim_max);
 
 #ifdef DEBUG_TRACES
   std::cout << "vertices \t\t" << count_vertices << std::endl;
@@ -253,7 +272,15 @@ int main(int argc, char **argv) {
 
   pcoh.compute_persistent_cohomology(min_persistence);
 
-  pcoh.output_diagram();
+  // Output the diagram in filediag
+  if (output_file_diag.empty()) {
+    pcoh.output_diagram();
+  } else {
+    std::cout << "Result in file: " << output_file_diag << std::endl;
+    std::ofstream out(output_file_diag);
+    pcoh.output_diagram(out);
+    out.close();
+  }
 
   return 0;
 }
diff --git a/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp
index 67d830dc..13634ff7 100644
--- a/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp
@@ -30,8 +30,6 @@
 #include <CGAL/Periodic_3_regular_triangulation_traits_3.h>
 #include <CGAL/Periodic_3_regular_triangulation_3.h>
 #include <CGAL/Alpha_shape_3.h>
-#include <CGAL/Alpha_shape_vertex_base_3.h>
-#include <CGAL/Alpha_shape_cell_base_3.h>
 #include <CGAL/iterator.h>
 
 #include <fstream>