Add of src/common/include/gudhi/Points_3D_off_io.h to read specific 3D OFF Files for CGAL Point_3

Add an example to read 3D OFF Files for CGAL Point_3
Modify alpha_complex_3d_persistence.cpp to read OFF files
Add periodic_alpha_complex_3d_persistence.cpp in Persistent_cohomology examples
Add info about new examples in README


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/periodic_alpha_complex_3d@1116 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 6b423b598869a0f4f9c62d93c93b69efd93c0161

10 files changed, 686 insertions, 33 deletions

diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index 2f94ed15..ee6ba541 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -53,8 +53,14 @@ if(GMPXX_FOUND AND GMP_FOUND)
   if(CGAL_FOUND)
     add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp)
     target_link_libraries(alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY})
+
+    add_executable(periodic_alpha_complex_3d_persistence periodic_alpha_complex_3d_persistence.cpp)
+    target_link_libraries(periodic_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY})
+    add_test(periodic_alpha_complex_3d_persistence_2_0 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off 2 0)
+
     if (TBB_FOUND)
       target_link_libraries(alpha_complex_3d_persistence ${TBB_RELEASE_LIBRARY})
+      target_link_libraries(periodic_alpha_complex_3d_persistence ${TBB_RELEASE_LIBRARY})
     endif()
     add_test(alpha_complex_3d_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 2 0.5)
 
@@ -65,7 +71,7 @@ if(GMPXX_FOUND AND GMP_FOUND)
       if (EIGEN3_FOUND)
         message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
         include( ${EIGEN3_USE_FILE} )
-      
+
         add_executable (alpha_complex_persistence alpha_complex_persistence.cpp)
         target_link_libraries(alpha_complex_persistence  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
         if (TBB_FOUND)
diff --git a/src/Persistent_cohomology/example/README b/src/Persistent_cohomology/example/README
index 8c71ccf5..92b80c76 100644
--- a/src/Persistent_cohomology/example/README
+++ b/src/Persistent_cohomology/example/README
@@ -4,13 +4,13 @@ cd /path-to-example/
 cmake .
 make
 
-
-Example of use :
+***********************************************************************************************************************
+Example of use of RIPS:
 
 Computation of the persistent homology with Z/2Z coefficients of the Rips complex on points 
 sampling a Klein bottle:
 
-./rips_persistence ../../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -m 100
+./rips_persistence ../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -m 100
 
 output:
 210  0 0 inf
@@ -29,7 +29,7 @@ where
 
 with Z/3Z coefficients:
 
-./rips_persistence ../../../data/points/Kl.txt -r 0.25 -d 3 -p 3 -m 100
+./rips_persistence ../../data/points/Kl.txt -r 0.25 -d 3 -p 3 -m 100
 
 output:
 3  0 0 inf
@@ -37,7 +37,7 @@ output:
 
 and the computation with Z/2Z and Z/3Z coefficients simultaneously:
 
-./rips_multifield_persistence ../../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 3 -m 100
+./rips_multifield_persistence ../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 3 -m 100
 
 output:
 6  0 0 inf
@@ -47,10 +47,96 @@ output:
 
 and finally the computation with all Z/pZ for 2 <= p <= 71 (20 first prime numbers):
 
- ./rips_multifield_persistence ../../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 71 -m 100
+ ./rips_multifield_persistence ../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 71 -m 100
 
 output:
 557940830126698960967415390  0 0 inf
 557940830126698960967415390  1 0.0702103 inf
 2  1 0.0702103 inf
 2  2 0.159992 inf
+
+***********************************************************************************************************************
+Example of use of ALPHA:
+
+For a more verbose mode, please run cmake with option "DEBUG_TRACES=TRUE" and recompile the programs.
+
+1) 3D special case
+------------------
+Computation of the persistent homology with Z/2Z coefficients of the alpha complex on points 
+sampling a torus 3D:
+
+./alpha_complex_3d_persistence ../../data/points/tore3D_300.off 2 0.45
+
+output:
+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 
+
+Here we retrieve expected Betti numbers on a tore 3D:
+Betti numbers[0] = 1
+Betti numbers[1] = 2
+Betti numbers[2] = 1
+
+N.B.: alpha_complex_3d_persistence accepts only OFF files in 3D dimension.
+
+2) d-Dimension case
+-------------------
+Computation of the persistent homology with Z/2Z coefficients of the alpha complex on points 
+sampling a torus 3D:
+
+./alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off
+
+output:
+Alpha complex is of dimension 3 - 9273 simplices - 300 vertices.
+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 
+
+Here we retrieve expected Betti numbers on a tore 3D:
+Betti numbers[0] = 1
+Betti numbers[1] = 2
+Betti numbers[2] = 1
+
+N.B.: alpha_complex_persistence accepts OFF files in d-Dimension.
+
+3) 3D periodic special case
+---------------------------
+./periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off 2 0.0
+
+output:
+Periodic Delaunay computed.
+Simplex_tree dim: 3
+2  0 0.0866025 inf 
+2  1 0.0866025 inf 
+2  1 0.0866025 inf 
+2  1 0.0866025 inf 
+2  2 0.0866025 inf 
+2  2 0.0866025 inf 
+2  2 0.0866025 inf 
+
+N.B.: periodic_alpha_complex_3d_persistence accepts only OFF files in 3D dimension. In this example, the periodic cube
+is hard coded to { x = [0,1]; y = [0,1]; z = [0,1] }
+
+***********************************************************************************************************************
+Example of use of PLAIN HOMOLOGY:
+
+This example computes the plain homology of the following simplicial complex without filtration values:
+  /* Complex to build. */
+  /*    1   3          */
+  /*    o---o          */
+  /*   /X\ /           */
+  /*  o---o   o        */
+  /*  2   0   4        */
+
+./plain_homology 
+
+output:
+2  0 0 inf 
+2  0 0 inf 
+2  1 0 inf 
+
+Here we retrieve the 2 entities {0,1,2,3} and {4} (Betti numbers[0] = 2) and the hole in {0,1,3} (Betti numbers[1] = 1)
\ No newline at end of file
diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
index 01497c7c..48fbb91a 100644
--- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
@@ -20,9 +20,9 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <gudhi/graph_simplicial_complex.h>
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Points_3D_off_io.h>
 #include <boost/variant.hpp>
 
 #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
@@ -139,20 +139,18 @@ int main(int argc, char * const argv[]) {
   }
 
   // Read points from file
-  std::string filegraph = argv[1];
-  std::list<Point_3> lp;
-  std::ifstream is(filegraph.c_str());
-  int n;
-  is >> n;
-#ifdef DEBUG_TRACES
-  std::cout << "Reading " << n << " points " << std::endl;
-#endif  // DEBUG_TRACES
-  Point_3 p;
-  for (; n > 0; n--) {
-    is >> p;
-    lp.push_back(p);
+  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();
+
   // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode.
   Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL);
 #ifdef DEBUG_TRACES
diff --git a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
index 8f9f077c..17fb84d2 100644
--- a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
@@ -29,7 +29,7 @@ int main(int argc, char **argv) {
   // ----------------------------------------------------------------------------
   // Init of an alpha complex from an OFF file
   // ----------------------------------------------------------------------------
-  typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel;
+  using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
   Gudhi::alphacomplex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_points, alpha_square_max_value);
 
   // ----------------------------------------------------------------------------
diff --git a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
new file mode 100644
index 00000000..e9425066
--- /dev/null
+++ b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
@@ -0,0 +1,303 @@
+/*    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 Saclay (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Points_3D_off_io.h>
+#include <boost/variant.hpp>
+
+#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
+#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/iterator.h>
+
+#include <fstream>
+#include <cmath>
+#include <string>
+#include <tuple>
+#include <map>
+#include <utility>
+#include <list>
+#include <vector>
+
+// Traits
+using K = CGAL::Exact_predicates_inexact_constructions_kernel;
+using PK = CGAL::Periodic_3_Delaunay_triangulation_traits_3<K>;
+// Vertex type
+using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>;
+using Vb = CGAL::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::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 P3DT3 = CGAL::Periodic_3_Delaunay_triangulation_3<PK,Tds>;
+using Alpha_shape_3 = CGAL::Alpha_shape_3<P3DT3>;
+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 Cell_handle = Alpha_shape_3::Cell_handle;
+using Facet = Alpha_shape_3::Facet;
+using Edge_3 = Alpha_shape_3::Edge;
+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 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 >;
+
+Vertex_list from(const Cell_handle& ch) {
+  Vertex_list the_list;
+  for (auto i = 0; i < 4; i++) {
+#ifdef DEBUG_TRACES
+    std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl;
+#endif  // DEBUG_TRACES
+    the_list.push_back(ch->vertex(i));
+  }
+  return the_list;
+}
+
+Vertex_list from(const Facet& fct) {
+  Vertex_list the_list;
+  for (auto i = 0; i < 4; i++) {
+    if (fct.second != i) {
+#ifdef DEBUG_TRACES
+      std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl;
+#endif  // DEBUG_TRACES
+      the_list.push_back(fct.first->vertex(i));
+    }
+  }
+  return the_list;
+}
+
+Vertex_list from(const Edge_3& edg) {
+  Vertex_list the_list;
+  for (auto i = 0; i < 4; i++) {
+    if ((edg.second == i) || (edg.third == i)) {
+#ifdef DEBUG_TRACES
+      std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl;
+#endif  // DEBUG_TRACES
+      the_list.push_back(edg.first->vertex(i));
+    }
+  }
+  return the_list;
+}
+
+Vertex_list from(const Alpha_shape_3::Vertex_handle& vh) {
+  Vertex_list the_list;
+#ifdef DEBUG_TRACES
+  std::cout << "from vertex=" << vh->point() << std::endl;
+#endif  // DEBUG_TRACES
+  the_list.push_back(vh);
+  return the_list;
+}
+
+void usage(char * const progName) {
+  std::cerr << "Usage: " << progName <<
+      " path_to_file_graph 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 != 4) {
+    std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
+    usage(argv[0]);
+  }
+
+  int coeff_field_characteristic = 0;
+  int returnedScanValue = sscanf(argv[2], "%d", &coeff_field_characteristic);
+  if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) {
+    std::cerr << "Error: " << argv[2] << " is not correct\n";
+    usage(argv[0]);
+  }
+
+  Filtration_value min_persistence = 0.0;
+  returnedScanValue = sscanf(argv[3], "%lf", &min_persistence);
+  if ((returnedScanValue == EOF) || (min_persistence < -1.0)) {
+    std::cerr << "Error: " << argv[3] << " is not correct\n";
+    usage(argv[0]);
+  }
+
+  // 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();
+  
+  // Define the periodic cube
+  P3DT3 pdt(PK::Iso_cuboid_3(0,0,0,1,1,1));
+  // Heuristic for inserting large point sets (if pts is reasonably large)
+  pdt.insert(lp.begin(), lp.end(), true);
+  // As pdt won't be modified anymore switch to 1-sheeted cover if possible
+  if (pdt.is_triangulation_in_1_sheet()) pdt.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(pdt, 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);
+      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);
+      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);
+      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)) {
+      count_vertices++;
+      vertex_list = from(*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;
+  }
+  simplex_tree.set_filtration(filtration_max);
+  simplex_tree.set_dimension(dim_max);
+
+#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() << " ";
+  std::cout << "  filtration = " << simplex_tree.filtration() << std::endl << std::endl;
+#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);
+  // 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/common/example/CGAL_3D_points_off_reader.cpp b/src/common/example/CGAL_3D_points_off_reader.cpp
new file mode 100644
index 00000000..d48bb17d
--- /dev/null
+++ b/src/common/example/CGAL_3D_points_off_reader.cpp
@@ -0,0 +1,41 @@
+#include <gudhi/Points_3D_off_io.h>
+
+#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
+
+#include <iostream>
+#include <string>
+#include <vector>
+
+using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel;
+using Point_3 = Kernel::Point_3;
+
+void usage(char * const progName) {
+  std::cerr << "Usage: " << progName << " inputFile.off" << std::endl;
+  exit(-1);
+}
+
+int main(int argc, char **argv) {
+  if (argc != 2) {
+    std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl;
+    usage(argv[0]);
+  }
+
+  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> point_cloud = off_reader.get_point_cloud();
+
+  int n {0};
+  for (auto point : point_cloud) {
+    ++n;
+    std::cout << "Point[" << n << "] = (" << point[0] << ", " << point[1] << ", " << point[2] << ")\n";
+  }
+  return 0;
+}
diff --git a/src/common/example/CGAL_points_off_reader.cpp b/src/common/example/CGAL_points_off_reader.cpp
index 45e9f1e6..997b47c1 100644
--- a/src/common/example/CGAL_points_off_reader.cpp
+++ b/src/common/example/CGAL_points_off_reader.cpp
@@ -8,17 +8,19 @@
 #include <string>
 #include <vector>
 
-typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel;
-typedef typename Kernel::Point_d Point_d;
+using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
+using Point_d = typename Kernel::Point_d;
 
-void usage(int argc, char * const progName) {
-  std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl;
+void usage(char * const progName) {
   std::cerr << "Usage: " << progName << " inputFile.off" << std::endl;
   exit(-1);
 }
 
 int main(int argc, char **argv) {
-  if (argc != 2) usage(argc, (argv[0] - 1));
+  if (argc != 2) {
+    std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl;
+    usage(argv[0]);
+  }
 
   std::string offInputFile(argv[1]);
   // Read the OFF file (input file name given as parameter) and triangulate points
@@ -26,16 +28,16 @@ int main(int argc, char **argv) {
   // Check the read operation was correct
   if (!off_reader.is_valid()) {
     std::cerr << "Unable to read file " << offInputFile << std::endl;
-    exit(-1);
+    usage(argv[0]);
   }
 
   // Retrieve the triangulation
   std::vector<Point_d> point_cloud = off_reader.get_point_cloud();
 
-  int n = 0;
+  int n {0};
   for (auto point : point_cloud) {
     std::cout << "Point[" << n << "] = ";
-    for (int i = 0; i < point.dimension(); i++)
+    for (int i {0}; i < point.dimension(); i++)
       std::cout << point[i] << " ";
     std::cout << "\n";
     ++n;
diff --git a/src/common/example/CMakeLists.txt b/src/common/example/CMakeLists.txt
index 5aeaa8c6..ee6c9058 100644
--- a/src/common/example/CMakeLists.txt
+++ b/src/common/example/CMakeLists.txt
@@ -3,6 +3,10 @@ project(GUDHIDelaunayTriangulationOffFileReadWrite)
 
 # need CGAL 4.7
 if(CGAL_FOUND)
+  add_executable ( cgal3Doffreader CGAL_3D_points_off_reader.cpp )
+  target_link_libraries(cgal3Doffreader  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+  add_test(cgal3Doffreader ${CMAKE_CURRENT_BINARY_DIR}/cgaloffreader ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
+
   if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
     find_package(Eigen3 3.1.0)
     if (EIGEN3_FOUND)
diff --git a/src/common/include/gudhi/Points_3D_off_io.h b/src/common/include/gudhi/Points_3D_off_io.h
new file mode 100644
index 00000000..02e6f910
--- /dev/null
+++ b/src/common/include/gudhi/Points_3D_off_io.h
@@ -0,0 +1,206 @@
+/*    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) 2015  INRIA Saclay (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+#ifndef POINTS_3D_OFF_IO_H_
+#define POINTS_3D_OFF_IO_H_
+
+#include <gudhi/Off_reader.h>
+
+#include <string>
+#include <vector>
+#include <fstream>
+#include <map>
+
+namespace Gudhi {
+
+/** 
+ * @brief OFF file visitor implementation according to Off_reader in order to read points from an OFF file.
+ */
+template<typename Point_3>
+class Points_3D_off_visitor_reader {
+ private:
+  std::vector<Point_3> point_cloud_;
+  bool valid_;
+
+ public:
+
+  /** @brief Off_reader visitor init implementation. 
+   * 
+   * The init parameters are set from OFF file header.
+   * Dimension value is required and the value must be 3.
+   *
+   * @param[in] dim space dimension of vertices.
+   * @param[in] num_vertices number of vertices in the OFF file (not used).
+   * @param[in] num_faces number of faces in the OFF file (not used).
+   * @param[in] num_edges number of edges in the OFF file (not used).
+   */
+  void init(int dim, int num_vertices, int num_faces, int num_edges) {
+#ifdef DEBUG_TRACES
+    std::cout << "Points_3D_off_visitor_reader::init - dim=" << dim << " - num_vertices=" <<
+        num_vertices << " - num_faces=" << num_faces << " - num_edges=" << num_edges << std::endl;
+#endif  // DEBUG_TRACES
+    if (dim == 3) {
+      valid_ = true;
+    } else {
+      valid_ = false;
+      std::cerr << "Points_3D_off_reader::Points_3D_off_reader cannot read OFF files in dimension " << dim << "\n";
+    }
+
+    if (num_faces > 0) {
+      std::cerr << "Points_3D_off_visitor_reader::init faces are not taken into account from OFF file for Points.\n";
+    }
+    if (num_edges > 0) {
+      std::cerr << "Points_3D_off_visitor_reader::init edges are not taken into account from OFF file for Points.\n";
+    }
+  }
+
+  /** @brief Off_reader visitor point implementation. 
+   * 
+   * The point function is called on each vertex line from OFF file.
+   * This function inserts the vertex in the vector of points.
+   *
+   * @param[in] point vector of vertex coordinates.
+   * 
+   * @details
+   * Point_3 must have a constructor with the following form:
+   * 
+   * @code template<class InputIterator > Point_3::Point_3(double x, double y, double z) @endcode
+   */
+  void point(const std::vector<double>& point) {
+    if (valid_) {
+#ifdef DEBUG_TRACES
+      std::cout << "Points_3D_off_visitor_reader::point ";
+      for (auto coordinate : point) {
+        std::cout << coordinate << " | ";
+      }
+      std::cout << std::endl;
+#endif  // DEBUG_TRACES
+      // Fill the point cloud
+      point_cloud_.push_back(Point_3(point[0], point[1], point[2]));
+    }
+  }
+
+  // Off_reader visitor maximal_face implementation - Only points are read
+
+  void maximal_face(const std::vector<int>& face) { }
+
+  // Off_reader visitor done implementation - Only points are read
+
+  void done() { }
+
+  /** @brief Point cloud getter.
+   *
+   * @return The point cloud.
+   */
+  const std::vector<Point_3>& get_point_cloud() const {
+    return point_cloud_;
+  }
+
+  /** @brief Returns if the OFF file read operation was successful or not.
+   *
+   * @return OFF file read status.
+   */
+  bool is_valid() const {
+    return valid_;
+  }
+};
+
+/** 
+ * \@brief OFF file reader implementation in order to read dimension 3 points from an OFF file.
+ * 
+ * @details
+ * This class is using the Points_3D_off_visitor_reader to visit the OFF file according to Off_reader.
+ * 
+ * Point_3 must have a constructor with the following form:
+ * 
+ * @code template<class InputIterator > Point_3::Point_3(double x, double y, double z) @endcode
+ * 
+ * @section Example
+ *
+ * This example loads points from an OFF file and builds a vector of CGAL points in dimension 3.
+ * Then, it is asked to display the points.
+ * 
+ * Asserts
+ * 
+ * @include common/CGAL_Points_3D_off_reader.cpp
+ * 
+ * When launching:
+ * 
+ * @code $> ./cgal3Doffreader ../../data/points/alphacomplexdoc.off
+ * @endcode
+ *
+ * the program output is:
+ * 
+ * @include common/cgal3Doffreader_result.txt
+ */
+template<typename Point_3>
+class Points_3D_off_reader {
+ public:
+
+  /** @brief Reads the OFF file and constructs a vector of points from the points
+   * that are in the OFF file.
+   *
+   * @param[in] name_file OFF file to read.
+   * 
+   * @post Check with is_valid() function to see if read operation was successful.
+   */
+  Points_3D_off_reader(const std::string& name_file)
+      : valid_(false) {
+    std::ifstream stream(name_file);
+    if (stream.is_open()) {
+      Off_reader off_reader(stream);
+      Points_3D_off_visitor_reader<Point_3> off_visitor;
+      valid_ = off_reader.read(off_visitor);
+      valid_ = valid_ && off_visitor.is_valid();
+      if (valid_) {
+        point_cloud = off_visitor.get_point_cloud();
+      }
+    } else {
+      std::cerr << "Points_3D_off_reader::Points_3D_off_reader could not open file " << name_file << "\n";
+    }
+  }
+
+  /** @brief Returns if the OFF file read operation was successful or not.
+   *
+   * @return OFF file read status.
+   */
+  bool is_valid() const {
+    return valid_;
+  }
+
+  /** @brief Point cloud getter.
+   *
+   * @return point_cloud.
+   */
+  const std::vector<Point_3>& get_point_cloud() const {
+    return point_cloud;
+  }
+
+ private:
+  /** @brief point_cloud.*/
+  std::vector<Point_3> point_cloud;
+  /** @brief OFF file read status.*/
+  bool valid_;
+};
+
+} // namespace Gudhi
+
+#endif  // POINTS_3D_OFF_IO_H_
diff --git a/src/common/include/gudhi/Points_off_io.h b/src/common/include/gudhi/Points_off_io.h
index 77f36be2..74b49386 100644
--- a/src/common/include/gudhi/Points_off_io.h
+++ b/src/common/include/gudhi/Points_off_io.h
@@ -43,7 +43,7 @@ class Points_off_visitor_reader {
   /** \brief Off_reader visitor init implementation. 
    * 
    * The init parameters are set from OFF file header.
-   * Dimension value is required in order to construct Alpha complex.
+   * Dimension value is required in order to construct a vector of points.
    *
    * @param[in] dim space dimension of vertices.
    * @param[in] num_vertices number of vertices in the OFF file (not used).
@@ -63,12 +63,19 @@ class Points_off_visitor_reader {
     }
   }
 
-  /** \brief Off_reader visitor point implementation. 
+  /** @brief Off_reader visitor point implementation. 
    * 
    * The point function is called on each vertex line from OFF file.
-   * This function inserts the vertex in the Alpha complex.
+   * This function inserts the vertex in the vector of points.
    *
    * @param[in] point vector of vertex coordinates.
+   * 
+   * @details
+   * Point_d must have a constructor with the following form:
+   * 
+   * @code template<class InputIterator > Point_d::Point_d(int d, InputIterator first, InputIterator last) @endcode
+   * 
+   * where d is the point dimension. 		
    */
   void point(const std::vector<double>& point) {
 #ifdef DEBUG_TRACES
@@ -127,7 +134,7 @@ class Points_off_visitor_reader {
 template<typename Point_d>
 class Points_off_reader {
  public:
-  /** \brief Reads the OFF file and constructs the Alpha complex from the points
+  /** \brief Reads the OFF file and constructs a vector of points from the points
    * that are in the OFF file.
    *
    * @param[in] name_file OFF file to read.