Merge last trunk modifications

Comment some bad code
Try to cythonize rips from correlation matrix


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@2858 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 3b9bcdfdeae247ed5486e20cb62f2812fdd14b0d

13 files changed, 444 insertions, 159 deletions

diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
index ece5e6c3..1b8ff95a 100644
--- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
+++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
@@ -202,10 +202,10 @@ and a weights file.
 \code $> ./weighted_alpha_complex_3d_persistence ../../data/points/tore3D_300.off
 ../../data/points/tore3D_300.weights 2 0.45 \endcode
 \code Simplex_tree dim: 3
-2  -0 0 inf
-2  1 0.0682162 1.0001
-2  1 0.0934117 1.00003
-2  2 0.56444 1.03938 \endcode
+2  0 -1 inf
+2  1 -0.931784 0.000103311
+2  1 -0.906588 2.60165e-05
+2  2 -0.43556 0.0393798 \endcode
 
 \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
 Persistent_cohomology/alpha_complex_persistence.cpp</a> computes the persistent homology with
@@ -221,7 +221,8 @@ Simplex_tree dim: 3
 \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
 Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a> computes the persistent homology with
 \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the periodic alpha complex on points sampling from an OFF file.
-\code $> ./periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off 3 1.0 \endcode
+\code $> ./periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off
+../../data/points/iso_cuboid_3_in_0_1.txt 3 1.0 \endcode
 \code Periodic Delaunay computed.
 Simplex_tree dim: 3
 3  0 0 inf 
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index 926cef6b..80e5647d 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -39,8 +39,8 @@ add_test(NAME Persistent_cohomology_example_from_simple_simplex_tree COMMAND $<T
     "1" "0")
 add_test(NAME Persistent_cohomology_example_from_rips_distance_matrix COMMAND $<TARGET_FILE:rips_distance_matrix_persistence>
     "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" "-r" "1.0" "-d" "3" "-p" "3" "-m" "0")
-add_test(rips_distance_matrix ${CMAKE_CURRENT_BINARY_DIR}/rips_distance_matrix_persistence
-    ${CMAKE_SOURCE_DIR}/data/correlation_matrix/full_correlation_matrix.csv.csv -r 1.0 -d 3 -p 3 -m 0)
+add_test(NAME Persistent_cohomology_example_from_rips_correlation_matrix COMMAND $<TARGET_FILE:rips_correlation_matrix_persistence>
+    "${CMAKE_SOURCE_DIR}/data/correlation_matrix/lower_triangular_correlation_matrix.csv" "-c" "0.3" "-d" "3" "-p" "3" "-m" "0")
 add_test(NAME Persistent_cohomology_example_from_rips_on_tore_3D COMMAND $<TARGET_FILE:rips_persistence>
     "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3")
 add_test(NAME Persistent_cohomology_example_from_rips_step_by_step_on_tore_3D COMMAND $<TARGET_FILE:rips_persistence_step_by_step>
@@ -55,6 +55,7 @@ add_test(NAME Persistent_cohomology_example_from_file_3_3_100 COMMAND $<TARGET_F
 install(TARGETS plain_homology DESTINATION bin)
 install(TARGETS persistence_from_simple_simplex_tree DESTINATION bin)
 install(TARGETS rips_distance_matrix_persistence DESTINATION bin)
+install(TARGETS rips_correlation_matrix_persistence DESTINATION bin)
 install(TARGETS rips_persistence DESTINATION bin)
 install(TARGETS rips_persistence_step_by_step DESTINATION bin)
 install(TARGETS rips_persistence_via_boundary_matrix DESTINATION bin)
@@ -79,24 +80,18 @@ if(CGAL_FOUND)
   target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY})
   add_executable(exact_alpha_complex_3d_persistence exact_alpha_complex_3d_persistence.cpp)
   target_link_libraries(exact_alpha_complex_3d_persistence ${CGAL_LIBRARY})
-  add_executable(weighted_alpha_complex_3d_persistence weighted_alpha_complex_3d_persistence.cpp)
-  target_link_libraries(weighted_alpha_complex_3d_persistence ${CGAL_LIBRARY})
 
   if (TBB_FOUND)
     target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES})
     target_link_libraries(exact_alpha_complex_3d_persistence ${TBB_LIBRARIES})
-    target_link_libraries(weighted_alpha_complex_3d_persistence ${TBB_LIBRARIES})
   endif(TBB_FOUND)
   add_test(NAME Persistent_cohomology_example_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
       "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "2" "0.45")
   add_test(NAME Persistent_cohomology_example_exact_alpha_complex_3d COMMAND $<TARGET_FILE:exact_alpha_complex_3d_persistence>
       "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "2" "0.45")
-  add_test(NAME Persistent_cohomology_example_weighted_alpha_complex_3d COMMAND $<TARGET_FILE:weighted_alpha_complex_3d_persistence>
-      "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.weights" "2" "0.45")
 
   install(TARGETS alpha_complex_3d_persistence DESTINATION bin)
   install(TARGETS exact_alpha_complex_3d_persistence DESTINATION bin)
-  install(TARGETS weighted_alpha_complex_3d_persistence DESTINATION bin)
 
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
     add_executable (alpha_complex_persistence alpha_complex_persistence.cpp)
@@ -117,7 +112,7 @@ if(CGAL_FOUND)
     add_test(NAME Persistent_cohomology_example_alpha_complex COMMAND $<TARGET_FILE:alpha_complex_persistence>
         "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45")
     add_test(NAME Persistent_cohomology_example_periodic_alpha_complex_3d COMMAND $<TARGET_FILE:periodic_alpha_complex_3d_persistence>
-        "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" "2" "0")
+        "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" "3" "1.0")
     add_test(NAME Persistent_cohomology_example_custom_persistence_sort COMMAND $<TARGET_FILE:custom_persistence_sort>)
 
     install(TARGETS alpha_complex_persistence DESTINATION bin)
@@ -125,4 +120,31 @@ if(CGAL_FOUND)
     install(TARGETS custom_persistence_sort 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)
+
+  add_executable(weighted_alpha_complex_3d_persistence weighted_alpha_complex_3d_persistence.cpp)
+  target_link_libraries(weighted_alpha_complex_3d_persistence ${CGAL_LIBRARY})
+  if (TBB_FOUND)
+    target_link_libraries(weighted_alpha_complex_3d_persistence ${TBB_LIBRARIES})
+  endif(TBB_FOUND)
+
+  install(TARGETS weighted_alpha_complex_3d_persistence DESTINATION bin)
+
+  add_test(NAME Persistent_cohomology_example_weighted_alpha_complex_3d COMMAND $<TARGET_FILE:weighted_alpha_complex_3d_persistence>
+      "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.weights" "2" "0.45")
+
 endif(CGAL_FOUND)
diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_helper.h b/src/Persistent_cohomology/example/alpha_complex_3d_helper.h
index 7865e4ec..6b3b7d5d 100644
--- a/src/Persistent_cohomology/example/alpha_complex_3d_helper.h
+++ b/src/Persistent_cohomology/example/alpha_complex_3d_helper.h
@@ -23,7 +23,7 @@
 #ifndef ALPHA_COMPLEX_3D_HELPER_H_
 #define ALPHA_COMPLEX_3D_HELPER_H_
 
-template<class Vertex_list, class Cell_handle>
+template <class Vertex_list, class Cell_handle>
 Vertex_list from_cell(const Cell_handle& ch) {
   Vertex_list the_list;
   for (auto i = 0; i < 4; i++) {
@@ -35,7 +35,7 @@ Vertex_list from_cell(const Cell_handle& ch) {
   return the_list;
 }
 
-template<class Vertex_list, class Facet>
+template <class Vertex_list, class Facet>
 Vertex_list from_facet(const Facet& fct) {
   Vertex_list the_list;
   for (auto i = 0; i < 4; i++) {
@@ -49,7 +49,7 @@ Vertex_list from_facet(const Facet& fct) {
   return the_list;
 }
 
-template<class Vertex_list, class Edge_3>
+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++) {
@@ -63,7 +63,7 @@ Vertex_list from_edge(const Edge_3& edg) {
   return the_list;
 }
 
-template<class Vertex_list, class Vertex_handle>
+template <class Vertex_list, class Vertex_handle>
 Vertex_list from_vertex(const Vertex_handle& vh) {
   Vertex_list the_list;
 #ifdef DEBUG_TRACES
diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
index f63ff0f6..26196a6f 100644
--- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
@@ -39,6 +39,7 @@
 #include <utility>
 #include <list>
 #include <vector>
+#include <cstdlib>
 
 #include "alpha_complex_3d_helper.h"
 
@@ -56,10 +57,10 @@ using Point_3 = Kernel::Point_3;
 // filtration with alpha values needed type definition
 using Alpha_value_type = Alpha_shape_3::FT;
 using Object = CGAL::Object;
-using Dispatch = CGAL::Dispatch_output_iterator<
-          CGAL::cpp11::tuple<Object, Alpha_value_type>,
-          CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >,
-          std::back_insert_iterator< std::vector<Alpha_value_type> > > >;
+using Dispatch =
+    CGAL::Dispatch_output_iterator<CGAL::cpp11::tuple<Object, Alpha_value_type>,
+                                   CGAL::cpp11::tuple<std::back_insert_iterator<std::vector<Object> >,
+                                                      std::back_insert_iterator<std::vector<Alpha_value_type> > > >;
 using Cell_handle = Alpha_shape_3::Cell_handle;
 using Facet = Alpha_shape_3::Facet;
 using Edge_3 = Alpha_shape_3::Edge;
@@ -70,19 +71,19 @@ using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>;
 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_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 Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>;
+using Persistent_cohomology =
+    Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>;
 
 void usage(const std::string& progName) {
-  std::cerr << "Usage:\n" << progName << " path_to_OFF_file coeff_field_characteristic[integer " <<
-               "> 0] min_persistence[float >= -1.0]\n";
-  std::cerr << "  path_to_OFF_file is the path to your points cloud in OFF format.\n";
+  std::cerr << "Usage: " << progName
+            << " path_to_the_OFF_file coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
   exit(-1);
 }
 
-int main(int argc, char * const argv[]) {
+int main(int argc, char* const argv[]) {
   // program args management
   if (argc != 4) {
     std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
@@ -90,13 +91,7 @@ int main(int argc, char * const argv[]) {
   }
 
   int coeff_field_characteristic = atoi(argv[2]);
-
-  Filtration_value min_persistence = 0.0;
-  int returnedScanValue = sscanf(argv[3], "%f", &min_persistence);
-  if ((returnedScanValue == EOF) || (min_persistence < -1.0)) {
-    std::cerr << "Error: " << argv[3] << " is not correct\n";
-    usage(argv[0]);
-  }
+  Filtration_value min_persistence = strtof(argv[3], nullptr);
 
   // Read points from file
   std::string offInputFile(argv[1]);
@@ -143,28 +138,28 @@ int main(int argc, char * const 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);
     }
@@ -203,7 +198,6 @@ int main(int argc, char * const 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;
@@ -211,7 +205,6 @@ int main(int argc, char * const argv[]) {
   std::cout << "facets \t\t" << count_facets << std::endl;
   std::cout << "cells \t\t" << count_cells << std::endl;
 
-
   std::cout << "Information of the Simplex Tree: " << std::endl;
   std::cout << "  Number of vertices = " << simplex_tree.num_vertices() << " ";
   std::cout << "  Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
@@ -230,7 +223,7 @@ int main(int argc, char * const 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/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp
index 09561d03..2e2bfd2f 100644
--- a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/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
@@ -39,6 +39,7 @@
 #include <utility>
 #include <list>
 #include <vector>
+#include <cstdlib>
 
 #include "alpha_complex_3d_helper.h"
 
@@ -57,10 +58,10 @@ using Point_3 = Kernel::Point_3;
 // filtration with alpha values needed type definition
 using Alpha_value_type = Alpha_shape_3::FT;
 using Object = CGAL::Object;
-using Dispatch = CGAL::Dispatch_output_iterator<
-          CGAL::cpp11::tuple<Object, Alpha_value_type>,
-          CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >,
-          std::back_insert_iterator< std::vector<Alpha_value_type> > > >;
+using Dispatch =
+    CGAL::Dispatch_output_iterator<CGAL::cpp11::tuple<Object, Alpha_value_type>,
+                                   CGAL::cpp11::tuple<std::back_insert_iterator<std::vector<Object> >,
+                                                      std::back_insert_iterator<std::vector<Alpha_value_type> > > >;
 using Cell_handle = Alpha_shape_3::Cell_handle;
 using Facet = Alpha_shape_3::Facet;
 using Edge_3 = Alpha_shape_3::Edge;
@@ -71,19 +72,19 @@ using Vertex_list = std::list<Vertex_handle>;
 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_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 Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>;
+using Persistent_cohomology =
+    Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>;
 
-void usage(char * const progName) {
-  std::cerr << "Usage:\n" << progName << " path_to_OFF_file coeff_field_characteristic[integer " <<
-               "> 0] min_persistence[float >= -1.0]\n";
-  std::cerr << "  path_to_OFF_file is the path to your points cloud in OFF format.\n";
+void usage(const std::string& progName) {
+  std::cerr << "Usage: " << progName
+            << " path_to_the_OFF_file coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
   exit(-1);
 }
 
-int main(int argc, char * const argv[]) {
+int main(int argc, char* const argv[]) {
   // program args management
   if (argc != 4) {
     std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
@@ -91,13 +92,7 @@ int main(int argc, char * const argv[]) {
   }
 
   int coeff_field_characteristic = atoi(argv[2]);
-
-  Filtration_value min_persistence = 0.0;
-  int returnedScanValue = sscanf(argv[3], "%f", &min_persistence);
-  if ((returnedScanValue == EOF) || (min_persistence < -1.0)) {
-    std::cerr << "Error: " << argv[3] << " is not correct\n";
-    usage(argv[0]);
-  }
+  Filtration_value min_persistence = strtof(argv[3], nullptr);
 
   // Read points from file
   std::string offInputFile(argv[1]);
@@ -144,28 +139,28 @@ int main(int argc, char * const 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);
     }
@@ -205,7 +200,6 @@ int main(int argc, char * const 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;
@@ -213,7 +207,6 @@ int main(int argc, char * const argv[]) {
   std::cout << "facets \t\t" << count_facets << std::endl;
   std::cout << "cells \t\t" << count_cells << std::endl;
 
-
   std::cout << "Information of the Simplex Tree: " << std::endl;
   std::cout << "  Number of vertices = " << simplex_tree.num_vertices() << " ";
   std::cout << "  Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
@@ -232,7 +225,7 @@ int main(int argc, char * const 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/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
index 8140a3c5..c6d3e236 100644
--- a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
@@ -63,10 +63,10 @@ using Point_3 = PK::Point_3;
 // filtration with alpha values needed type definition
 using Alpha_value_type = Alpha_shape_3::FT;
 using Object = CGAL::Object;
-using Dispatch = CGAL::Dispatch_output_iterator<
-    CGAL::cpp11::tuple<Object, Alpha_value_type>,
-    CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >,
-    std::back_insert_iterator< std::vector<Alpha_value_type> > > >;
+using Dispatch =
+    CGAL::Dispatch_output_iterator<CGAL::cpp11::tuple<Object, Alpha_value_type>,
+                                   CGAL::cpp11::tuple<std::back_insert_iterator<std::vector<Object> >,
+                                                      std::back_insert_iterator<std::vector<Alpha_value_type> > > >;
 using Cell_handle = Alpha_shape_3::Cell_handle;
 using Facet = Alpha_shape_3::Facet;
 using Edge_3 = Alpha_shape_3::Edge;
@@ -77,27 +77,19 @@ using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>;
 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_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 >;
-
-void usage(char * const progName) {
-  std::cerr << "Usage:\n" << progName << " path_to_OFF_file path_to_iso_cuboid_3_file coeff_field_characteristic[" <<
-               "integer > 0] min_persistence[float >= -1.0]\n" <<
-               "  path_to_OFF_file is the path to your points cloud in OFF format.\n" <<
-               "  path_to_iso_cuboid_3_file is the path to the iso cuboid file with the following format :\n" <<
-               "    x_min y_min z_min x_max y_max z_max\n" <<
-               "  In this example, the periodic cube will be " <<
-               "{ x = [x_min,x_max]; y = [y_min,y_max]; z = [z_min,z_max] }.\n" <<
-               "  For more information, please refer to\n" <<
-               "    https://doc.cgal.org/latest/Kernel_23/classCGAL_1_1Iso__cuboid__3.html\n";
+using Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>;
+using Persistent_cohomology =
+    Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>;
 
+void usage(const std::string& progName) {
+  std::cerr << "Usage: " << progName << " path_to_the_OFF_file path_to_iso_cuboid_3_file "
+                                        "coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
   exit(-1);
 }
 
-int main(int argc, char * const argv[]) {
+int main(int argc, char* const argv[]) {
   // program args management
   if (argc != 5) {
     std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
@@ -168,29 +160,28 @@ int main(int argc, char * const 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);
     }
@@ -216,7 +207,7 @@ int main(int argc, char * const 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
@@ -229,7 +220,6 @@ int main(int argc, char * const 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;
@@ -237,7 +227,6 @@ int main(int argc, char * const argv[]) {
   std::cout << "facets \t\t" << count_facets << std::endl;
   std::cout << "cells \t\t" << count_cells << std::endl;
 
-
   std::cout << "Information of the Simplex Tree: " << std::endl;
   std::cout << "  Number of vertices = " << simplex_tree.num_vertices() << " ";
   std::cout << "  Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
diff --git a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
index 8214d66a..8ef479d4 100644
--- a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
+++ b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
@@ -142,7 +142,6 @@ int main(int argc, char * const argv[]) {
   /*   An edge [11,6]         */
   /*   An edge [10,12,2]      */
 
-  st.set_dimension(2);
 
   std::cout << "The complex contains " << st.num_simplices() << " simplices - " << st.num_vertices() << " vertices "
       << std::endl;
diff --git a/src/Persistent_cohomology/example/plain_homology.cpp b/src/Persistent_cohomology/example/plain_homology.cpp
index 50f692f2..a5ae09c8 100644
--- a/src/Persistent_cohomology/example/plain_homology.cpp
+++ b/src/Persistent_cohomology/example/plain_homology.cpp
@@ -64,8 +64,6 @@ int main() {
   st.insert_simplex_and_subfaces(edge03);
   st.insert_simplex(edge13);
   st.insert_simplex(vertex4);
-  // FIXME: Remove this line
-  st.set_dimension(2);
 
   // Sort the simplices in the order of the filtration
   st.initialize_filtration();
diff --git a/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp b/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp
index 6f12dada..94d5b8d4 100644
--- a/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp
@@ -68,8 +68,8 @@ int main(int argc, char* argv[]) {
     }
   }
 
-  //If the treshold, being minimal corelation is in the range [0,1], 
-  //change it to 1-threshold
+  // If the threshold, being minimal correlation is in the range [0,1],
+  // change it to 1-threshold
   if ( ( threshold>=0 ) && ( threshold<=1 ) )
   {
 	  threshold = 1-threshold;
@@ -95,7 +95,7 @@ int main(int argc, char* argv[]) {
   pcoh.compute_persistent_cohomology(min_persistence);
     
   
-  //invert the persistence diagram 
+  // invert the persistence diagram
   auto pairs = pcoh.get_persistent_pairs();
   std::vector< intervals_common > processed_persistence_intervals;
   processed_persistence_intervals.reserve( pairs.size() );
@@ -128,34 +128,34 @@ void program_options(int argc, char* argv[], std::string& csv_matrix_file, std::
                      Filtration_value& threshold, int& dim_max, int& p, Filtration_value& min_persistence) {
   namespace po = boost::program_options;
   po::options_description hidden("Hidden options");
-  hidden.add_options()(
-      "input-file", po::value<std::string>(&csv_matrix_file),
-      "Name of file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'.");
+  // hidden.add_options()(
+  //     "input-file", po::value<std::string>(&csv_matrix_file),
+  //     "Name of file containing a correlation matrix. Can be square or lower triangular matrix. Separator is ';'.");
   hidden.add_options()
       ("input-file", po::value<std::string>(&csv_matrix_file),
-       "Name of file containing a corelation matrix. Can be square or lower triangular matrix. Separator is ';'.");
+       "Name of file containing a correlation matrix. Can be square or lower triangular matrix. Separator is ';'.");
 
   po::options_description visible("Allowed options", 100);
-  visible.add_options()("help,h", "produce help message")(
-      "output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
-      "Name of file in which the persistence diagram is written. Default print in std::cout")(
-      "max-edge-length,r",
-      po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
-      "Maximal length of an edge for the Rips complex construction.")(
-      "cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
-      "Maximal dimension of the Rips complex we want to compute.")(
-      "field-charac,p", po::value<int>(&p)->default_value(11),
-      "Characteristic p of the coefficient field Z/pZ for computing homology.")(
-      "min-persistence,m", po::value<Filtration_value>(&min_persistence),
-      "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length "
-      "intervals");
+  // visible.add_options()("help,h", "produce help message")(
+  //     "output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
+  //     "Name of file in which the persistence diagram is written. Default print in std::cout")(
+  //     "max-edge-length,r",
+  //     po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
+  //     "Maximal length of an edge for the Rips complex construction.")(
+  //     "cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
+  //     "Maximal dimension of the Rips complex we want to compute.")(
+  //     "field-charac,p", po::value<int>(&p)->default_value(11),
+  //     "Characteristic p of the coefficient field Z/pZ for computing homology.")(
+  //     "min-persistence,m", po::value<Filtration_value>(&min_persistence),
+  //     "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length "
+  //     "intervals");
   visible.add_options()
       ("help,h", "produce help message")
       ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
        "Name of file in which the persistence diagram is written. Default print in std::cout")
-      ("min-edge-corelation,c",
+      ("min-edge-correlation,c",
        po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
-       "Minimal corelation of an edge for the Rips complex construction.")
+       "Minimal correlation of an edge for the Rips complex construction.")
       ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
        "Maximal dimension of the Rips complex we want to compute.")
       ("field-charac,p", po::value<int>(&p)->default_value(11),
@@ -176,7 +176,7 @@ void program_options(int argc, char* argv[], std::string& csv_matrix_file, std::
   if (vm.count("help") || !vm.count("input-file")) {
     std::cout << std::endl;
     std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
-    std::cout << "of a Rips complex defined on a corelation matrix.\n \n";
+    std::cout << "of a Rips complex defined on a correlation matrix.\n \n";
     std::cout << "The output diagram contains one bar per line, written with the convention: \n";
     std::cout << "   p   dim b d \n";
     std::cout << "where dim is the dimension of the homological feature,\n";
diff --git a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
index 72268511..249a7ece 100644
--- a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
@@ -26,12 +26,17 @@
 #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/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>
@@ -44,26 +49,44 @@
 
 #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;
-using Dispatch = CGAL::Dispatch_output_iterator<
-          CGAL::cpp11::tuple<Object, Alpha_value_type>,
-          CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >,
-          std::back_insert_iterator< std::vector<Alpha_value_type> > > >;
+using Dispatch =
+    CGAL::Dispatch_output_iterator<CGAL::cpp11::tuple<Object, Alpha_value_type>,
+                                   CGAL::cpp11::tuple<std::back_insert_iterator<std::vector<Object> >,
+                                                      std::back_insert_iterator<std::vector<Alpha_value_type> > > >;
 using Cell_handle = Alpha_shape_3::Cell_handle;
 using Facet = Alpha_shape_3::Facet;
 using Edge_3 = Alpha_shape_3::Edge;
@@ -74,24 +97,19 @@ using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>;
 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_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 >;
-
-void usage(char * const progName) {
-  std::cerr << "Usage:\n" << progName << " path_to_OFF_file path_to_weight_file coeff_field_characteristic[integer " <<
-               "> 0] min_persistence[float >= -1.0]\n";
-  std::cerr << "  path_to_OFF_file is the path to your points cloud in OFF format.\n";
-  std::cerr << "  path_to_weight_file is the path to the weights of your points cloud (one value per line.)\n";
-  std::cerr << "  Weights values are explained on CGAL documentation:\n";
-  std::cerr << "    https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title0\n";
-  std::cerr << "    https://doc.cgal.org/latest/Triangulation_3/index.html#Triangulation3secclassRegulartriangulation\n";
+using Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>;
+using Persistent_cohomology =
+    Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>;
+
+void usage(const std::string& progName) {
+  std::cerr << "Usage: " << progName << " path_to_the_OFF_file path_to_weight_file coeff_field_characteristic[integer > "
+                                        "0] min_persistence[float >= -1.0]\n";
   exit(-1);
 }
 
-int main(int argc, char * const argv[]) {
+int main(int argc, char* const argv[]) {
   // program args management
   if (argc != 5) {
     std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
@@ -167,29 +185,28 @@ int main(int argc, char * const 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);
     }
@@ -215,7 +232,7 @@ int main(int argc, char * const 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
@@ -228,7 +245,6 @@ int main(int argc, char * const 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;
@@ -236,7 +252,6 @@ int main(int argc, char * const argv[]) {
   std::cout << "facets \t\t" << count_facets << std::endl;
   std::cout << "cells \t\t" << count_cells << std::endl;
 
-
   std::cout << "Information of the Simplex Tree: " << std::endl;
   std::cout << "  Number of vertices = " << simplex_tree.num_vertices() << " ";
   std::cout << "  Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
diff --git a/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp
new file mode 100644
index 00000000..13634ff7
--- /dev/null
+++ b/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp
@@ -0,0 +1,281 @@
+/*    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):       Vincent Rouvreau
+ *
+ *    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
+ *    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 <boost/variant.hpp>
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Points_3D_off_io.h>
+
+#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
+#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/iterator.h>
+
+#include <fstream>
+#include <cmath>
+#include <string>
+#include <tuple>
+#include <map>
+#include <utility>
+#include <list>
+#include <vector>
+#include <cstdlib>
+
+#include "alpha_complex_3d_helper.h"
+
+// Traits
+using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel;
+using PK = CGAL::Periodic_3_regular_triangulation_traits_3<Kernel>;
+
+// Vertex type
+using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>;
+using Vb = CGAL::Regular_triangulation_vertex_base_3<PK,DsVb>;
+using AsVb = CGAL::Alpha_shape_vertex_base_3<PK,Vb>;
+// Cell type
+using DsCb = CGAL::Periodic_3_triangulation_ds_cell_base_3<>;
+using Cb = CGAL::Regular_triangulation_cell_base_3<PK,DsCb>;
+using AsCb = CGAL::Alpha_shape_cell_base_3<PK,Cb>;
+using Tds = CGAL::Triangulation_data_structure_3<AsVb,AsCb>;
+using P3RT3 = CGAL::Periodic_3_regular_triangulation_3<PK,Tds>;
+using Alpha_shape_3 = CGAL::Alpha_shape_3<P3RT3>;
+
+using Point_3 = P3RT3::Bare_point;
+using Weighted_point_3 = P3RT3::Weighted_point;
+
+// filtration with alpha values needed type definition
+using Alpha_value_type = Alpha_shape_3::FT;
+using Object = CGAL::Object;
+using Dispatch =
+    CGAL::Dispatch_output_iterator<CGAL::cpp11::tuple<Object, Alpha_value_type>,
+                                   CGAL::cpp11::tuple<std::back_insert_iterator<std::vector<Object> >,
+                                                      std::back_insert_iterator<std::vector<Alpha_value_type> > > >;
+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>;
+
+// 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>;
+
+void usage(const std::string& progName) {
+  std::cerr << "Usage: " << progName << " path_to_the_OFF_file path_to_weight_file path_to_the_cuboid_file "
+                                        "coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
+  exit(-1);
+}
+
+int main(int argc, char* const argv[]) {
+  // program args management
+  if (argc != 6) {
+    std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
+    usage(argv[0]);
+  }
+
+  int coeff_field_characteristic = atoi(argv[4]);
+  Filtration_value min_persistence = strtof(argv[5], nullptr);
+
+  // Read points from file
+  std::string offInputFile(argv[1]);
+  // Read the OFF file (input file name given as parameter) and triangulate points
+  Gudhi::Points_3D_off_reader<Point_3> off_reader(offInputFile);
+  // Check the read operation was correct
+  if (!off_reader.is_valid()) {
+    std::cerr << "Unable to read file " << offInputFile << std::endl;
+    usage(argv[0]);
+  }
+
+  // Retrieve the triangulation
+  std::vector<Point_3> lp = off_reader.get_point_cloud();
+
+  // Read weights information from file
+  std::ifstream weights_ifstr(argv[2]);
+  std::vector<Weighted_point_3> wp;
+  if (weights_ifstr.good()) {
+    double weight = 0.0;
+    std::size_t index = 0;
+    wp.reserve(lp.size());
+    // Attempt read the weight in a double format, return false if it fails
+    while ((weights_ifstr >> weight) && (index < lp.size())) {
+      wp.push_back(Weighted_point_3(lp[index], weight));
+      index++;
+    }
+    if (index != lp.size()) {
+      std::cerr << "Bad number of weights in file " << argv[2] << std::endl;
+      usage(argv[0]);
+    }
+  } else {
+    std::cerr << "Unable to read file " << argv[2] << std::endl;
+    usage(argv[0]);
+  }
+
+  // Read iso_cuboid_3 information from file
+  std::ifstream iso_cuboid_str(argv[3]);
+  double x_min, y_min, z_min, x_max, y_max, z_max;
+  if (iso_cuboid_str.good()) {
+    iso_cuboid_str >> x_min >> y_min >> z_min >> x_max >> y_max >> z_max;
+  } else {
+    std::cerr << "Unable to read file " << argv[3] << std::endl;
+    usage(argv[0]);
+  }
+
+  // Define the periodic cube
+  P3RT3 prt(PK::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max));
+  // Heuristic for inserting large point sets (if pts is reasonably large)
+  prt.insert(wp.begin(), wp.end(), true);
+  // As prt won't be modified anymore switch to 1-sheeted cover if possible
+  if (prt.is_triangulation_in_1_sheet()) prt.convert_to_1_sheeted_covering();
+  std::cout << "Periodic Delaunay computed." << std::endl;
+
+  // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode
+  // Maybe need to set it to GENERAL mode
+  Alpha_shape_3 as(prt, 0, Alpha_shape_3::GENERAL);
+
+  // filtration with alpha values from alpha shape
+  std::vector<Object> the_objects;
+  std::vector<Alpha_value_type> the_alpha_values;
+
+  Dispatch disp = CGAL::dispatch_output<Object, Alpha_value_type>(std::back_inserter(the_objects),
+                                                                  std::back_inserter(the_alpha_values));
+
+  as.filtration_with_alpha_values(disp);
+#ifdef DEBUG_TRACES
+  std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl;
+#endif  // DEBUG_TRACES
+
+  Alpha_shape_3::size_type count_vertices = 0;
+  Alpha_shape_3::size_type count_edges = 0;
+  Alpha_shape_3::size_type count_facets = 0;
+  Alpha_shape_3::size_type count_cells = 0;
+
+  // Loop on objects vector
+  Vertex_list vertex_list;
+  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;
+    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()) {
+        // alpha shape not found
+        Simplex_tree_vertex vertex = map_cgal_simplex_tree.size();
+#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));
+      } 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);
+      }
+    }
+    // Construction of the simplex_tree
+    Filtration_value filtr = /*std::sqrt*/ (*the_alpha_value_iterator);
+#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;
+  }
+
+#ifdef DEBUG_TRACES
+  std::cout << "vertices \t\t" << count_vertices << std::endl;
+  std::cout << "edges \t\t" << count_edges << std::endl;
+  std::cout << "facets \t\t" << count_facets << std::endl;
+  std::cout << "cells \t\t" << count_cells << std::endl;
+
+  std::cout << "Information of the Simplex Tree: " << std::endl;
+  std::cout << "  Number of vertices = " << simplex_tree.num_vertices() << " ";
+  std::cout << "  Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
+  std::cout << "  Dimension = " << simplex_tree.dimension() << " ";
+#endif  // DEBUG_TRACES
+
+#ifdef DEBUG_TRACES
+  std::cout << "Iterator on vertices: " << std::endl;
+  for (auto vertex : simplex_tree.complex_vertex_range()) {
+    std::cout << vertex << " ";
+  }
+#endif  // DEBUG_TRACES
+
+  // Sort the simplices in the order of the filtration
+  simplex_tree.initialize_filtration();
+
+  std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl;
+  // Compute the persistence diagram of the complex
+  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();
+
+  return 0;
+}
diff --git a/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp b/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp
index da418034..0a08d200 100644
--- a/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp
+++ b/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp
@@ -62,8 +62,6 @@ BOOST_AUTO_TEST_CASE( plain_homology_betti_numbers )
   st.insert_simplex_and_subfaces(edge04);
   st.insert_simplex(edge14);
   st.insert_simplex(vertex5);
-  // FIXME: Remove this line
-  st.set_dimension(3);
 
   // Sort the simplices in the order of the filtration
   st.initialize_filtration();
@@ -170,8 +168,6 @@ BOOST_AUTO_TEST_CASE( betti_numbers )
   st.insert_simplex_and_subfaces(edge04, 2.0);
   st.insert_simplex(edge14, 2.0);
   st.insert_simplex(vertex5, 1.0);
-  // FIXME: Remove this line
-  st.set_dimension(3);
 
   // Sort the simplices in the order of the filtration
   st.initialize_filtration();
diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
index f53987b6..a1c106d5 100644
--- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
+++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
@@ -196,8 +196,6 @@ BOOST_AUTO_TEST_CASE( persistence_constructor_exception )
   // To make number of simplices = 255
   const short simplex_0[] = {0, 1, 2, 3, 4, 5, 6, 7};
   st.insert_simplex_and_subfaces(simplex_0);
-  // FIXME: Remove this line
-  st.set_dimension(8);
 
   // Sort the simplices in the order of the filtration
   st.initialize_filtration();