Merge of branch misc-glisse

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3074 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: d0842416dbf4ee1ff25a7421841efe8f097e5379

7 files changed, 43 insertions, 140 deletions

diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h
index 5f7d7622..63c6675c 100644
--- a/src/Alpha_complex/include/gudhi/Alpha_complex.h
+++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h
@@ -175,7 +175,7 @@ class Alpha_complex {
    *
    * @return The number of vertices.
    */
-  const std::size_t number_of_vertices() const {
+  std::size_t number_of_vertices() const {
     return vertex_handle_to_iterator_.size();
   }
 
diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_helper.h b/src/Alpha_complex/utilities/alpha_complex_3d_helper.h
index 6b3b7d5d..3747923f 100644
--- a/src/Alpha_complex/utilities/alpha_complex_3d_helper.h
+++ b/src/Alpha_complex/utilities/alpha_complex_3d_helper.h
@@ -52,13 +52,11 @@ Vertex_list from_facet(const Facet& fct) {
 template <class Vertex_list, class Edge_3>
 Vertex_list from_edge(const Edge_3& edg) {
   Vertex_list the_list;
-  for (auto i = 0; i < 4; i++) {
-    if ((edg.second == i) || (edg.third == i)) {
+  for (auto i : { edg.second, edg.third }) {
 #ifdef DEBUG_TRACES
-      std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl;
+    std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl;
 #endif  // DEBUG_TRACES
-      the_list.push_back(edg.first->vertex(i));
-    }
+    the_list.push_back(edg.first->vertex(i));
   }
   return the_list;
 }
diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
index 0a021a0f..f4a14ae3 100644
--- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
@@ -22,6 +22,7 @@
 
 #include <boost/program_options.hpp>
 #include <boost/variant.hpp>
+#include <boost/container/static_vector.hpp>
 
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Persistent_cohomology.h>
@@ -38,7 +39,6 @@
 #include <tuple>
 #include <map>
 #include <utility>
-#include <list>
 #include <vector>
 #include <cstdlib>
 
@@ -66,14 +66,13 @@ using Cell_handle = Alpha_shape_3::Cell_handle;
 using Facet = Alpha_shape_3::Facet;
 using Edge_3 = Alpha_shape_3::Edge;
 using Vertex_handle = Alpha_shape_3::Vertex_handle;
-using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>;
+using Vertex_list = boost::container::static_vector<Alpha_shape_3::Vertex_handle, 4>;
 
 // gudhi type definition
 using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
 using Filtration_value = ST::Filtration_value;
 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 Persistent_cohomology =
     Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>;
@@ -97,7 +96,7 @@ int main(int argc, char **argv) {
     exit(-1);
   }
 
-  // Retrieve the triangulation
+  // Retrieve the points
   std::vector<Point_3> lp = off_reader.get_point_cloud();
 
   // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode.
@@ -128,37 +127,23 @@ int main(int argc, char **argv) {
   ST simplex_tree;
   Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
   std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
-  int dim_max = 0;
-  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)) {
       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)) {
       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)) {
       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)) {
       count_vertices++;
       vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
     }
     // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
-    Simplex_tree_vector_vertex the_simplex_tree;
+    Simplex_tree_vector_vertex the_simplex;
     for (auto the_alpha_shape_vertex : vertex_list) {
       Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
       if (the_map_iterator == map_cgal_simplex_tree.end()) {
@@ -167,15 +152,15 @@ int main(int argc, char **argv) {
 #ifdef DEBUG_TRACES
         std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl;
 #endif  // DEBUG_TRACES
-        the_simplex_tree.push_back(vertex);
-        map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex));
+        the_simplex.push_back(vertex);
+        map_cgal_simplex_tree.emplace(the_alpha_shape_vertex, vertex);
       } else {
         // alpha shape found
         Simplex_tree_vertex vertex = the_map_iterator->second;
 #ifdef DEBUG_TRACES
         std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
 #endif  // DEBUG_TRACES
-        the_simplex_tree.push_back(vertex);
+        the_simplex.push_back(vertex);
       }
     }
     // Construction of the simplex_tree
@@ -183,14 +168,10 @@ int main(int argc, char **argv) {
 #ifdef DEBUG_TRACES
     std::cout << "filtration = " << filtr << std::endl;
 #endif  // DEBUG_TRACES
-    if (filtr > filtration_max) {
-      filtration_max = filtr;
-    }
-    simplex_tree.insert_simplex(the_simplex_tree, filtr);
-    if (the_alpha_value_iterator != the_alpha_values.end())
-      ++the_alpha_value_iterator;
-    else
-      std::cout << "This shall not happen" << std::endl;
+    simplex_tree.insert_simplex(the_simplex, filtr);
+    GUDHI_CHECK(the_alpha_value_iterator != the_alpha_values.end(),
+        "CGAL provided more simplices than values");
+    ++the_alpha_value_iterator;
   }
 
 #ifdef DEBUG_TRACES
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 9a266418..3b9a2ae0 100644
--- a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp
@@ -38,7 +38,6 @@
 #include <tuple>
 #include <map>
 #include <utility>
-#include <list>
 #include <vector>
 #include <cstdlib>
 
@@ -67,14 +66,13 @@ using Cell_handle = Alpha_shape_3::Cell_handle;
 using Facet = Alpha_shape_3::Facet;
 using Edge_3 = Alpha_shape_3::Edge;
 using Vertex_handle = Alpha_shape_3::Vertex_handle;
-using Vertex_list = std::list<Vertex_handle>;
+using Vertex_list = std::vector<Vertex_handle>;
 
 // gudhi type definition
 using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
 using Filtration_value = ST::Filtration_value;
 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 Persistent_cohomology =
     Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>;
@@ -98,7 +96,7 @@ int main(int argc, char **argv) {
     exit(-1);
   }
 
-  // Retrieve the triangulation
+  // Retrieve the points
   std::vector<Point_3> lp = off_reader.get_point_cloud();
 
   // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode.
@@ -129,37 +127,23 @@ int main(int argc, char **argv) {
   ST simplex_tree;
   Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
   std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
-  int dim_max = 0;
-  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)) {
       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)) {
       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)) {
       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)) {
       count_vertices++;
       vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
     }
     // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
-    Simplex_tree_vector_vertex the_simplex_tree;
+    Simplex_tree_vector_vertex the_simplex;
     for (auto the_alpha_shape_vertex : vertex_list) {
       Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
       if (the_map_iterator == map_cgal_simplex_tree.end()) {
@@ -168,15 +152,15 @@ int main(int argc, char **argv) {
 #ifdef DEBUG_TRACES
         std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl;
 #endif  // DEBUG_TRACES
-        the_simplex_tree.push_back(vertex);
-        map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex));
+        the_simplex.push_back(vertex);
+        map_cgal_simplex_tree.emplace(the_alpha_shape_vertex, vertex);
       } else {
         // alpha shape found
         Simplex_tree_vertex vertex = the_map_iterator->second;
 #ifdef DEBUG_TRACES
         std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
 #endif  // DEBUG_TRACES
-        the_simplex_tree.push_back(vertex);
+        the_simplex.push_back(vertex);
       }
     }
     // Construction of the simplex_tree
@@ -185,10 +169,7 @@ int main(int argc, char **argv) {
 #ifdef DEBUG_TRACES
     std::cout << "filtration = " << filtr << std::endl;
 #endif  // DEBUG_TRACES
-    if (filtr > filtration_max) {
-      filtration_max = filtr;
-    }
-    simplex_tree.insert_simplex(the_simplex_tree, filtr);
+    simplex_tree.insert_simplex(the_simplex, filtr);
     if (the_alpha_value_iterator != the_alpha_values.end())
       ++the_alpha_value_iterator;
     else
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 186a58f8..6993b0ad 100644
--- a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp
@@ -39,7 +39,6 @@
 #include <tuple>
 #include <map>
 #include <utility>
-#include <list>
 #include <vector>
 #include <cstdlib>
 
@@ -72,14 +71,13 @@ using Cell_handle = Alpha_shape_3::Cell_handle;
 using Facet = Alpha_shape_3::Facet;
 using Edge_3 = Alpha_shape_3::Edge;
 using Vertex_handle = Alpha_shape_3::Vertex_handle;
-using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>;
+using Vertex_list = std::vector<Alpha_shape_3::Vertex_handle>;
 
 // gudhi type definition
 using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
 using Filtration_value = ST::Filtration_value;
 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 Persistent_cohomology =
     Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>;
@@ -115,7 +113,7 @@ int main(int argc, char **argv) {
     exit(-1);
   }
 
-  // Retrieve the triangulation
+  // Retrieve the points
   std::vector<Point_3> lp = off_reader.get_point_cloud();
 
   // Define the periodic cube
@@ -152,37 +150,23 @@ int main(int argc, char **argv) {
   ST simplex_tree;
   Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
   std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
-  int dim_max = 0;
-  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)) {
       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)) {
       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)) {
       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)) {
       count_vertices++;
       vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
     }
     // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
-    Simplex_tree_vector_vertex the_simplex_tree;
+    Simplex_tree_vector_vertex the_simplex;
     for (auto the_alpha_shape_vertex : vertex_list) {
       Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
       if (the_map_iterator == map_cgal_simplex_tree.end()) {
@@ -191,15 +175,15 @@ int main(int argc, char **argv) {
 #ifdef DEBUG_TRACES
         std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl;
 #endif  // DEBUG_TRACES
-        the_simplex_tree.push_back(vertex);
-        map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex));
+        the_simplex.push_back(vertex);
+        map_cgal_simplex_tree.emplace(the_alpha_shape_vertex, vertex);
       } else {
         // alpha shape found
         Simplex_tree_vertex vertex = the_map_iterator->second;
 #ifdef DEBUG_TRACES
         std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
 #endif  // DEBUG_TRACES
-        the_simplex_tree.push_back(vertex);
+        the_simplex.push_back(vertex);
       }
     }
     // Construction of the simplex_tree
@@ -207,10 +191,7 @@ int main(int argc, char **argv) {
 #ifdef DEBUG_TRACES
     std::cout << "filtration = " << filtr << std::endl;
 #endif  // DEBUG_TRACES
-    if (filtr > filtration_max) {
-      filtration_max = filtr;
-    }
-    simplex_tree.insert_simplex(the_simplex_tree, filtr);
+    simplex_tree.insert_simplex(the_simplex, filtr);
     if (the_alpha_value_iterator != the_alpha_values.end())
       ++the_alpha_value_iterator;
     else
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 0e73a99b..f46f1a58 100644
--- a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp
@@ -44,7 +44,6 @@
 #include <tuple>
 #include <map>
 #include <utility>
-#include <list>
 #include <vector>
 #include <cstdlib>
 
@@ -92,14 +91,13 @@ using Cell_handle = Alpha_shape_3::Cell_handle;
 using Facet = Alpha_shape_3::Facet;
 using Edge_3 = Alpha_shape_3::Edge;
 using Vertex_handle = Alpha_shape_3::Vertex_handle;
-using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>;
+using Vertex_list = std::vector<Alpha_shape_3::Vertex_handle>;
 
 // gudhi type definition
 using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
 using Filtration_value = ST::Filtration_value;
 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 Persistent_cohomology =
     Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>;
@@ -125,7 +123,7 @@ int main(int argc, char **argv) {
     exit(-1);
   }
 
-  // Retrieve the triangulation
+  // Retrieve the points
   std::vector<Point_3> lp = off_reader.get_point_cloud();
 
   // Read weights information from file
@@ -177,37 +175,23 @@ int main(int argc, char **argv) {
   ST simplex_tree;
   Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
   std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
-  int dim_max = 0;
-  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)) {
       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)) {
       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)) {
       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)) {
       count_vertices++;
       vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
     }
     // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
-    Simplex_tree_vector_vertex the_simplex_tree;
+    Simplex_tree_vector_vertex the_simplex;
     for (auto the_alpha_shape_vertex : vertex_list) {
       Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
       if (the_map_iterator == map_cgal_simplex_tree.end()) {
@@ -216,15 +200,15 @@ int main(int argc, char **argv) {
 #ifdef DEBUG_TRACES
         std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl;
 #endif  // DEBUG_TRACES
-        the_simplex_tree.push_back(vertex);
-        map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex));
+        the_simplex.push_back(vertex);
+        map_cgal_simplex_tree.emplace(the_alpha_shape_vertex, vertex);
       } else {
         // alpha shape found
         Simplex_tree_vertex vertex = the_map_iterator->second;
 #ifdef DEBUG_TRACES
         std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
 #endif  // DEBUG_TRACES
-        the_simplex_tree.push_back(vertex);
+        the_simplex.push_back(vertex);
       }
     }
     // Construction of the simplex_tree
@@ -232,10 +216,7 @@ int main(int argc, char **argv) {
 #ifdef DEBUG_TRACES
     std::cout << "filtration = " << filtr << std::endl;
 #endif  // DEBUG_TRACES
-    if (filtr > filtration_max) {
-      filtration_max = filtr;
-    }
-    simplex_tree.insert_simplex(the_simplex_tree, filtr);
+    simplex_tree.insert_simplex(the_simplex, filtr);
     if (the_alpha_value_iterator != the_alpha_values.end())
       ++the_alpha_value_iterator;
     else
diff --git a/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp
index 13634ff7..282b9180 100644
--- a/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp
@@ -38,7 +38,6 @@
 #include <tuple>
 #include <map>
 #include <utility>
-#include <list>
 #include <vector>
 #include <cstdlib>
 
@@ -74,14 +73,13 @@ using Cell_handle = Alpha_shape_3::Cell_handle;
 using Facet = Alpha_shape_3::Facet;
 using Edge_3 = Alpha_shape_3::Edge;
 using Vertex_handle = Alpha_shape_3::Vertex_handle;
-using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>;
+using Vertex_list = std::vector<Alpha_shape_3::Vertex_handle>;
 
 // gudhi type definition
 using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
 using Filtration_value = ST::Filtration_value;
 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 Persistent_cohomology =
     Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>;
@@ -112,7 +110,7 @@ int main(int argc, char* const argv[]) {
     usage(argv[0]);
   }
 
-  // Retrieve the triangulation
+  // Retrieve the points
   std::vector<Point_3> lp = off_reader.get_point_cloud();
 
   // Read weights information from file
@@ -180,37 +178,23 @@ int main(int argc, char* const argv[]) {
   ST simplex_tree;
   Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
   std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
-  int dim_max = 0;
-  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)) {
       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)) {
       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)) {
       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)) {
       count_vertices++;
       vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
     }
     // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
-    Simplex_tree_vector_vertex the_simplex_tree;
+    Simplex_tree_vector_vertex the_simplex;
     for (auto the_alpha_shape_vertex : vertex_list) {
       Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
       if (the_map_iterator == map_cgal_simplex_tree.end()) {
@@ -219,15 +203,15 @@ int main(int argc, char* const argv[]) {
 #ifdef DEBUG_TRACES
         std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl;
 #endif  // DEBUG_TRACES
-        the_simplex_tree.push_back(vertex);
-        map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex));
+        the_simplex.push_back(vertex);
+        map_cgal_simplex_tree.emplace(the_alpha_shape_vertex, vertex);
       } else {
         // alpha shape found
         Simplex_tree_vertex vertex = the_map_iterator->second;
 #ifdef DEBUG_TRACES
         std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
 #endif  // DEBUG_TRACES
-        the_simplex_tree.push_back(vertex);
+        the_simplex.push_back(vertex);
       }
     }
     // Construction of the simplex_tree
@@ -235,10 +219,7 @@ int main(int argc, char* const argv[]) {
 #ifdef DEBUG_TRACES
     std::cout << "filtration = " << filtr << std::endl;
 #endif  // DEBUG_TRACES
-    if (filtr > filtration_max) {
-      filtration_max = filtr;
-    }
-    simplex_tree.insert_simplex(the_simplex_tree, filtr);
+    simplex_tree.insert_simplex(the_simplex, filtr);
     if (the_alpha_value_iterator != the_alpha_values.end())
       ++the_alpha_value_iterator;
     else