Merge last trunk modifications

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_3d_fix@2169 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: f8526767e8002cb106f46b8eeb93442b596786de

12 files changed, 504 insertions, 365 deletions

diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index 758bd6b1..d2a84b1e 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -1,19 +1,21 @@
 cmake_minimum_required(VERSION 2.6)
 project(Persistent_cohomology_examples)
 
-# problem with Visual Studio link on Boost program_options
-add_definitions( -DBOOST_ALL_NO_LIB )
-add_definitions( -DBOOST_ALL_DYN_LINK )
-
 add_executable(plain_homology plain_homology.cpp)
 target_link_libraries(plain_homology ${Boost_SYSTEM_LIBRARY})
 
 add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp)
 target_link_libraries(persistence_from_simple_simplex_tree ${Boost_SYSTEM_LIBRARY})
 
+add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp)
+target_link_libraries(rips_distance_matrix_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
 add_executable(rips_persistence rips_persistence.cpp)
 target_link_libraries(rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
+add_executable(rips_persistence_step_by_step rips_persistence_step_by_step.cpp)
+target_link_libraries(rips_persistence_step_by_step ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
 add_executable(rips_persistence_via_boundary_matrix rips_persistence_via_boundary_matrix.cpp)
 target_link_libraries(rips_persistence_via_boundary_matrix ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
@@ -23,15 +25,19 @@ target_link_libraries(persistence_from_file ${Boost_SYSTEM_LIBRARY} ${Boost_PROG
 if (TBB_FOUND)
   target_link_libraries(plain_homology ${TBB_LIBRARIES})
   target_link_libraries(persistence_from_simple_simplex_tree ${TBB_LIBRARIES})
+  target_link_libraries(rips_distance_matrix_persistence ${TBB_LIBRARIES})
   target_link_libraries(rips_persistence ${TBB_LIBRARIES})
+  target_link_libraries(rips_persistence_step_by_step ${TBB_LIBRARIES})
   target_link_libraries(rips_persistence_via_boundary_matrix ${TBB_LIBRARIES})
   target_link_libraries(persistence_from_file ${TBB_LIBRARIES})
 endif()
 
 add_test(plain_homology ${CMAKE_CURRENT_BINARY_DIR}/plain_homology)
 add_test(persistence_from_simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_simple_simplex_tree 1 0)
-add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.16 -d 3 -p 3 -m 100)
-add_test(rips_persistence_via_boundary_matrix_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence_via_boundary_matrix ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.16 -d 3 -p 3 -m 100)
+add_test(rips_distance_matrix ${CMAKE_CURRENT_BINARY_DIR}/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_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3)
+add_test(rips_persistence_step_by_step_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence_step_by_step ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3)
+add_test(rips_persistence_via_boundary_matrix_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence_via_boundary_matrix ${CMAKE_SOURCE_DIR}/data/points/Kl.off -r 0.16 -d 3 -p 3 -m 100)
 add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc -p 2 -m 0)
 add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc -p 3 -m 100)
    
@@ -39,14 +45,10 @@ if(GMP_FOUND)
    if(GMPXX_FOUND)
       add_executable(rips_multifield_persistence rips_multifield_persistence.cpp )
       target_link_libraries(rips_multifield_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
-      add_executable ( performance_rips_persistence performance_rips_persistence.cpp )
-      target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
       if (TBB_FOUND)
         target_link_libraries(rips_multifield_persistence ${TBB_LIBRARIES})
-        target_link_libraries(performance_rips_persistence ${TBB_LIBRARIES})
       endif(TBB_FOUND)
-
-   add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 2 -q 71 -m 100)
+   add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2 -q 71)
    endif(GMPXX_FOUND)
 endif(GMP_FOUND)
 
diff --git a/src/Persistent_cohomology/example/README b/src/Persistent_cohomology/example/README
index 7803e5ab..2ac79398 100644
--- a/src/Persistent_cohomology/example/README
+++ b/src/Persistent_cohomology/example/README
@@ -10,13 +10,13 @@ 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/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2
 
 output:
-210  0 0 inf
-210  1 0.0702103 inf
-2  1 0.0702103 inf
-2  2 0.159992 inf
+2  0 0 inf 
+2  1 0.0983494 inf 
+2  1 0.104347 inf 
+2  2 0.138335 inf 
 
 
 Every line is of this format: p1*...*pr   dim b d
@@ -29,31 +29,45 @@ where
 
 with Z/3Z coefficients:
 
-./rips_persistence ../../data/points/Kl.txt -r 0.25 -d 3 -p 3 -m 100
+./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3
 
 output:
-3  0 0 inf
-3  1 0.0702103 inf
+3  0 0 inf 
+3  1 0.0983494 inf 
+3  1 0.104347 inf 
+3  2 0.138335 inf 
 
 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/tore3D_1307.off -r 0.25 -m 0.12 -d 3 -p 2 -q 3
 
 output:
-6  0 0 inf
-6  1 0.0702103 inf
-2  1 0.0702103 inf
-2  2 0.159992 inf
+6  0 0 inf 
+6  1 0.0983494 inf 
+6  1 0.104347 inf 
+6  2 0.138335 inf 
+6  0 0 0.122545 
+6  0 0 0.121171 
+6  0 0 0.120964 
+6  0 0 0.12057 
+6  0 0 0.12047 
+6  0 0 0.120414 
 
 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.off -r 0.25 -m 0.5 -d 3 -p 2 -q 71
 
 output:
-557940830126698960967415390  0 0 inf
-557940830126698960967415390  1 0.0702103 inf
-2  1 0.0702103 inf
-2  2 0.159992 inf
+557940830126698960967415390  0 0 inf 
+557940830126698960967415390  1 0.0983494 inf 
+557940830126698960967415390  1 0.104347 inf 
+557940830126698960967415390  2 0.138335 inf 
+557940830126698960967415390  0 0 0.122545 
+557940830126698960967415390  0 0 0.121171 
+557940830126698960967415390  0 0 0.120964 
+557940830126698960967415390  0 0 0.12057 
+557940830126698960967415390  0 0 0.12047 
+557940830126698960967415390  0 0 0.120414 
 
 ***********************************************************************************************************************
 Example of use of ALPHA:
diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
index b5084e5b..371acede 100644
--- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/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
@@ -66,6 +66,7 @@ typedef std::list<Alpha_shape_3::Vertex_handle> Vertex_list;
 
 // gudhi type definition
 typedef Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence> ST;
+typedef ST::Filtration_value Filtration_value;
 typedef ST::Vertex_handle Simplex_tree_vertex;
 typedef std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex > Alpha_shape_simplex_tree_map;
 typedef std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex> Alpha_shape_simplex_tree_pair;
@@ -88,7 +89,7 @@ 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], "%lf", &min_persistence);
+  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]);
diff --git a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
index 2412569a..9e84e91f 100644
--- a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
@@ -11,6 +11,9 @@
 #include <string>
 #include <limits>  // for numeric_limits
 
+using Simplex_tree = Gudhi::Simplex_tree<>;
+using Filtration_value = Simplex_tree::Filtration_value;
+
 void program_options(int argc, char * argv[]
                      , std::string & off_file_points
                      , std::string & output_file_diag
@@ -34,7 +37,7 @@ int main(int argc, char **argv) {
   using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
   Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_points);
 
-  Gudhi::Simplex_tree<> simplex;
+  Simplex_tree simplex;
   if (alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) {
     // ----------------------------------------------------------------------------
     // Display information about the alpha complex
@@ -48,7 +51,7 @@ int main(int argc, char **argv) {
 
     std::cout << "Simplex_tree dim: " << simplex.dimension() << std::endl;
     // Compute the persistence diagram of the complex
-    Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::Simplex_tree<>,
+    Gudhi::persistent_cohomology::Persistent_cohomology< Simplex_tree,
         Gudhi::persistent_cohomology::Field_Zp > pcoh(simplex);
     // initializes the coefficient field for homology
     pcoh.init_coefficients(coeff_field_characteristic);
diff --git a/src/Persistent_cohomology/example/performance_rips_persistence.cpp b/src/Persistent_cohomology/example/performance_rips_persistence.cpp
deleted file mode 100644
index b4d282ac..00000000
--- a/src/Persistent_cohomology/example/performance_rips_persistence.cpp
+++ /dev/null
@@ -1,214 +0,0 @@
-/*    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):       Clément Maria
- *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (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/reader_utils.h>
-#include <gudhi/graph_simplicial_complex.h>
-#include <gudhi/distance_functions.h>
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Persistent_cohomology.h>
-#include <gudhi/Persistent_cohomology/Multi_field.h>
-#include <gudhi/Hasse_complex.h>
-
-#include <chrono>
-#include <string>
-#include <vector>
-
-using namespace Gudhi;
-using namespace Gudhi::persistent_cohomology;
-
-/* Compute the persistent homology of the complex cpx with coefficients in Z/pZ. */
-template< typename FilteredComplex>
-void timing_persistence(FilteredComplex & cpx
-                        , int p);
-
-/* Compute multi-field persistent homology of the complex cpx with coefficients in
- * Z/rZ for all prime number r in [p;q].*/
-template< typename FilteredComplex>
-void timing_persistence(FilteredComplex & cpx
-                        , int p
-                        , int q);
-
-/* Timings for the computation of persistent homology with different 
- * representations of a Rips complex and different coefficient fields. The 
- * Rips complex is built on a set of 10000 points sampling a Klein bottle embedded 
- * in dimension 5.
- * We represent complexes with a simplex tree and 
- * with a Hasse diagram. The Hasse diagram represents explicitly all 
- * codimension 1 incidence relations in the complex, and hence leads to 
- * a faster computation of persistence because boundaries are precomputed. 
- * Hovewer, the simplex tree may be constructed directly from a point cloud and
- * is more compact.
- * We compute persistent homology with coefficient fields Z/2Z and Z/1223Z.
- * We present also timings for the computation of multi-field persistent 
- * homology in all fields Z/rZ for r prime between 2 and 1223.
- */
-int main(int argc, char * argv[]) {
-  std::chrono::time_point<std::chrono::system_clock> start, end;
-  int elapsed_sec;
-  {
-
-  std::string filepoints = "../../../data/points/Kl.txt";
-  Filtration_value threshold = 0.27;
-  int dim_max = 3;
-  int p = 2;
-  int q = 1223;
-
-  // Extract the points from the file filepoints
-  typedef std::vector<double> Point_t;
-  std::vector< Point_t > points;
-  read_points(filepoints, points);
-
-  // Compute the proximity graph of the points
-  start = std::chrono::system_clock::now();
-  Graph_t prox_graph = compute_proximity_graph(points, threshold
-                                               , euclidean_distance<Point_t>);
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "Compute Rips graph in " << elapsed_sec << " ms.\n";
-
-  // Construct the Rips complex in a Simplex Tree
-  Simplex_tree<Simplex_tree_options_fast_persistence> st;
-  start = std::chrono::system_clock::now();
-
-  // insert the proximity graph in the simplex tree
-  st.insert_graph(prox_graph);
-  // expand the graph until dimension dim_max
-  st.expansion(dim_max);
-
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "Compute Rips complex in " << elapsed_sec << " ms.\n";
-  std::cout << "  - dimension           = " << st.dimension() << std::endl;
-  std::cout << "  - number of simplices = " << st.num_simplices() << std::endl;
-
-  // Sort the simplices in the order of the filtration
-  start = std::chrono::system_clock::now();
-  st.initialize_filtration();
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "Order the simplices of the filtration in " << elapsed_sec << " ms.\n";
-
-  // Copy the keys inside the simplices
-  start = std::chrono::system_clock::now();
-  {
-    int count = 0;
-    for (auto sh : st.filtration_simplex_range())
-      st.assign_key(sh, count++);
-  }
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "Copied the keys inside the simplices in " << elapsed_sec << " ms.\n";
-
-  // Convert the simplex tree into a hasse diagram
-  start = std::chrono::system_clock::now();
-  Hasse_complex<> hcpx(st);
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "Convert the simplex tree into a Hasse diagram in " << elapsed_sec << " ms.\n";
-
-
-  std::cout << "Timings when using a simplex tree: \n";
-  timing_persistence(st, p);
-  timing_persistence(st, q);
-  timing_persistence(st, p, q);
-
-  std::cout << "Timings when using a Hasse complex: \n";
-  timing_persistence(hcpx, p);
-  timing_persistence(hcpx, q);
-  timing_persistence(hcpx, p, q);
-
-  start = std::chrono::system_clock::now();
-  }
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "Running the complex destructors in " << elapsed_sec << " ms.\n";
-  return 0;
-}
-
-template< typename FilteredComplex>
-void
-timing_persistence(FilteredComplex & cpx
-                   , int p) {
-  std::chrono::time_point<std::chrono::system_clock> start, end;
-  int elapsed_sec;
-  {
-  start = std::chrono::system_clock::now();
-  Persistent_cohomology< FilteredComplex, Field_Zp > pcoh(cpx);
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "  Initialize pcoh in " << elapsed_sec << " ms.\n";
-  // initializes the coefficient field for homology
-  start = std::chrono::system_clock::now();
-  pcoh.init_coefficients(p);
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "  Initialize the coefficient field in " << elapsed_sec << " ms.\n";
-
-  start = std::chrono::system_clock::now();
-
-  pcoh.compute_persistent_cohomology(INFINITY);
-
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "  Compute persistent homology in Z/" << p << "Z in " << elapsed_sec << " ms.\n";
-  start = std::chrono::system_clock::now();
-  }
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "  Run the persistence destructors in " << elapsed_sec << " ms.\n";
-}
-
-template< typename FilteredComplex>
-void
-timing_persistence(FilteredComplex & cpx
-                   , int p
-                   , int q) {
-  std::chrono::time_point<std::chrono::system_clock> start, end;
-  int elapsed_sec;
-  {
-  start = std::chrono::system_clock::now();
-  Persistent_cohomology< FilteredComplex, Multi_field > pcoh(cpx);
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "  Initialize pcoh in " << elapsed_sec << " ms.\n";
-  // initializes the coefficient field for homology
-  start = std::chrono::system_clock::now();
-  pcoh.init_coefficients(p, q);
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "  Initialize the coefficient field in " << elapsed_sec << " ms.\n";
-  // compute persistent homology, disgarding persistent features of life shorter than min_persistence
-
-  start = std::chrono::system_clock::now();
-
-  pcoh.compute_persistent_cohomology(INFINITY);
-
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "  Compute multi-field persistent homology in all coefficient fields Z/pZ "
-      << "with p in [" << p << ";" << q << "] in " << elapsed_sec << " ms.\n";
-  start = std::chrono::system_clock::now();
-  }
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "  Run the persistence destructors in " << elapsed_sec << " ms.\n";
-}
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 a199fea1..dbc42706 100644
--- a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/periodic_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>
 
 // Traits
 using K = CGAL::Exact_predicates_inexact_constructions_kernel;
@@ -70,6 +71,7 @@ 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>;
@@ -136,19 +138,8 @@ int main(int argc, char * const argv[]) {
     usage(argv[0]);
   }
 
-  int coeff_field_characteristic = 0;
-  int returnedScanValue = sscanf(argv[3], "%d", &coeff_field_characteristic);
-  if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) {
-    std::cerr << "Error: " << argv[3] << " is not correct\n";
-    usage(argv[0]);
-  }
-
-  Filtration_value min_persistence = 0.0;
-  returnedScanValue = sscanf(argv[4], "%lf", &min_persistence);
-  if ((returnedScanValue == EOF) || (min_persistence < -1.0)) {
-    std::cerr << "Error: " << argv[4] << " is not correct\n";
-    usage(argv[0]);
-  }
+  int coeff_field_characteristic = atoi(argv[3]);
+  Filtration_value min_persistence = strtof(argv[4], nullptr);
 
   // Read points from file
   std::string offInputFile(argv[1]);
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 ba772f04..7ca9410a 100644
--- a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
+++ b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (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
@@ -29,13 +29,12 @@
 #include <utility>
 #include <vector>
 
-using namespace Gudhi;
-using namespace Gudhi::persistent_cohomology;
-
-typedef std::vector< Vertex_handle > typeVectorVertex;
-typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
-typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
-typedef Simplex_tree<> typeST;
+// Types definition
+using Simplex_tree = Gudhi::Simplex_tree<>;
+using Filtration_value = Simplex_tree::Filtration_value;
+using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp >;
+using typeVectorVertex = std::vector< Simplex_tree::Vertex_handle >;
 
 void usage(char * const progName) {
   std::cerr << "Usage: " << progName << " coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
@@ -66,7 +65,7 @@ int main(int argc, char * const argv[]) {
   // TEST OF INSERTION
   std::cout << "********************************************************************" << std::endl;
   std::cout << "TEST OF INSERTION" << std::endl;
-  typeST st;
+  Simplex_tree st;
 
   // ++ FIRST
   std::cout << "   - INSERT (0,1,2)" << std::endl;
@@ -166,7 +165,7 @@ int main(int argc, char * const argv[]) {
   std::cout << "**************************************************************" << std::endl;
 
   // Compute the persistence diagram of the complex
-  persistent_cohomology::Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh(st);
+  Persistent_cohomology pcoh(st);
   // initializes the coefficient field for homology
   pcoh.init_coefficients(coeff_field_characteristic);
 
diff --git a/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp b/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp
new file mode 100644
index 00000000..8517e7f6
--- /dev/null
+++ b/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp
@@ -0,0 +1,144 @@
+/*    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):       Pawel Dlotko, Vincent Rouvreau
+ *
+ *    Copyright (C) 2016  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 <gudhi/Rips_complex.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/reader_utils.h>
+
+#include <boost/program_options.hpp>
+
+#include <string>
+#include <vector>
+#include <limits>  // infinity
+
+// Types definition
+using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
+using Filtration_value = Simplex_tree::Filtration_value;
+using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
+using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp >;
+using Distance_matrix = std::vector<std::vector<Filtration_value>>;
+
+void program_options(int argc, char * argv[]
+                     , std::string & csv_matrix_file
+                     , std::string & filediag
+                     , Filtration_value & threshold
+                     , int & dim_max
+                     , int & p
+                     , Filtration_value & min_persistence);
+
+int main(int argc, char * argv[]) {
+  std::string csv_matrix_file;
+  std::string filediag;
+  Filtration_value threshold;
+  int dim_max;
+  int p;
+  Filtration_value min_persistence;
+
+  program_options(argc, argv, csv_matrix_file, filediag, threshold, dim_max, p, min_persistence);
+
+  Distance_matrix distances = read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file);
+  Rips_complex rips_complex_from_file(distances, threshold);
+
+  // Construct the Rips complex in a Simplex Tree
+  Simplex_tree simplex_tree;
+
+  rips_complex_from_file.create_complex(simplex_tree, dim_max);
+  std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
+  std::cout << "   and has dimension " << simplex_tree.dimension() << " \n";
+
+  // Sort the simplices in the order of the filtration
+  simplex_tree.initialize_filtration();
+
+  // Compute the persistence diagram of the complex
+  Persistent_cohomology pcoh(simplex_tree);
+  // initializes the coefficient field for homology
+  pcoh.init_coefficients(p);
+
+  pcoh.compute_persistent_cohomology(min_persistence);
+
+  // Output the diagram in filediag
+  if (filediag.empty()) {
+    pcoh.output_diagram();
+  } else {
+    std::ofstream out(filediag);
+    pcoh.output_diagram(out);
+    out.close();
+  }
+  return 0;
+}
+
+void program_options(int argc, char * argv[]
+                     , std::string & csv_matrix_file
+                     , std::string & filediag
+                     , 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 ';'.");
+
+  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");
+
+  po::positional_options_description pos;
+  pos.add("input-file", 1);
+
+  po::options_description all;
+  all.add(visible).add(hidden);
+
+  po::variables_map vm;
+  po::store(po::command_line_parser(argc, argv).
+            options(all).positional(pos).run(), vm);
+  po::notify(vm);
+
+  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 set of distance 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";
+    std::cout << "b and d are respectively the birth and death of the feature and \n";
+    std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
+
+    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
+    std::cout << visible << std::endl;
+    std::abort();
+  }
+}
diff --git a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
index c5cd775d..7674b5a5 100644
--- a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Clément Maria
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (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
@@ -20,26 +20,29 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <gudhi/reader_utils.h>
-#include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/Rips_complex.h>
 #include <gudhi/distance_functions.h>
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Persistent_cohomology.h>
 #include <gudhi/Persistent_cohomology/Multi_field.h>
+#include <gudhi/Points_off_io.h>
 
 #include <boost/program_options.hpp>
 
 #include <string>
 #include <vector>
 
-using namespace Gudhi;
-using namespace Gudhi::persistent_cohomology;
-
-typedef int Vertex_handle;
-typedef double Filtration_value;
+// Types definition
+using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
+using Filtration_value = Simplex_tree::Filtration_value;
+using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
+using Multi_field = Gudhi::persistent_cohomology::Multi_field;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Multi_field >;
+using Point = std::vector<double>;
+using Points_off_reader = Gudhi::Points_off_reader<Point>;
 
 void program_options(int argc, char * argv[]
-                     , std::string & filepoints
+                     , std::string & off_file_points
                      , std::string & filediag
                      , Filtration_value & threshold
                      , int & dim_max
@@ -48,7 +51,7 @@ void program_options(int argc, char * argv[]
                      , Filtration_value & min_persistence);
 
 int main(int argc, char * argv[]) {
-  std::string filepoints;
+  std::string off_file_points;
   std::string filediag;
   Filtration_value threshold;
   int dim_max;
@@ -56,33 +59,26 @@ int main(int argc, char * argv[]) {
   int max_p;
   Filtration_value min_persistence;
 
-  program_options(argc, argv, filepoints, filediag, threshold, dim_max, min_p, max_p, min_persistence);
-
-  // Extract the points from the file filepoints
-  typedef std::vector<double> Point_t;
-  std::vector< Point_t > points;
-  read_points(filepoints, points);
+  program_options(argc, argv, off_file_points, filediag, threshold, dim_max, min_p, max_p, min_persistence);
 
-  // Compute the proximity graph of the points
-  Graph_t prox_graph = compute_proximity_graph(points, threshold
-                                               , euclidean_distance<Point_t>);
+  Points_off_reader off_reader(off_file_points);
+  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Euclidean_distance());
 
   // Construct the Rips complex in a Simplex Tree
-  typedef Simplex_tree<Simplex_tree_options_fast_persistence> ST;
-  ST st;
-  // insert the proximity graph in the simplex tree
-  st.insert_graph(prox_graph);
-  // expand the graph until dimension dim_max
-  st.expansion(dim_max);
+  Simplex_tree simplex_tree;
+
+  rips_complex_from_file.create_complex(simplex_tree, dim_max);
+  std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
+  std::cout << "   and has dimension " << simplex_tree.dimension() << " \n";
 
   // Sort the simplices in the order of the filtration
-  st.initialize_filtration();
+  simplex_tree.initialize_filtration();
 
   // Compute the persistence diagram of the complex
-  Persistent_cohomology<ST, Multi_field > pcoh(st);
+  Persistent_cohomology pcoh(simplex_tree);
   // initializes the coefficient field for homology
   pcoh.init_coefficients(min_p, max_p);
-  // compute persistent homology, disgarding persistent features of life shorter than min_persistence
+
   pcoh.compute_persistent_cohomology(min_persistence);
 
   // Output the diagram in filediag
@@ -98,7 +94,7 @@ int main(int argc, char * argv[]) {
 }
 
 void program_options(int argc, char * argv[]
-                     , std::string & filepoints
+                     , std::string & off_file_points
                      , std::string & filediag
                      , Filtration_value & threshold
                      , int & dim_max
@@ -108,8 +104,8 @@ void program_options(int argc, char * argv[]
   namespace po = boost::program_options;
   po::options_description hidden("Hidden options");
   hidden.add_options()
-      ("input-file", po::value<std::string>(&filepoints),
-       "Name of file containing a point set. Format is one point per line:   X1 ... Xd \n");
+      ("input-file", po::value<std::string>(&off_file_points),
+       "Name of an OFF file containing a point set.\n");
 
   po::options_description visible("Allowed options");
   visible.add_options()
diff --git a/src/Persistent_cohomology/example/rips_persistence.cpp b/src/Persistent_cohomology/example/rips_persistence.cpp
index cab49395..c6378de7 100644
--- a/src/Persistent_cohomology/example/rips_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Clément Maria
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (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
@@ -20,11 +20,11 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <gudhi/reader_utils.h>
-#include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/Rips_complex.h>
 #include <gudhi/distance_functions.h>
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Points_off_io.h>
 
 #include <boost/program_options.hpp>
 
@@ -32,14 +32,17 @@
 #include <vector>
 #include <limits>  // infinity
 
-using namespace Gudhi;
-using namespace Gudhi::persistent_cohomology;
-
-typedef int Vertex_handle;
-typedef double Filtration_value;
+// Types definition
+using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
+using Filtration_value = Simplex_tree::Filtration_value;
+using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
+using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp >;
+using Point = std::vector<double>;
+using Points_off_reader = Gudhi::Points_off_reader<Point>;
 
 void program_options(int argc, char * argv[]
-                     , std::string & filepoints
+                     , std::string & off_file_points
                      , std::string & filediag
                      , Filtration_value & threshold
                      , int & dim_max
@@ -47,40 +50,30 @@ void program_options(int argc, char * argv[]
                      , Filtration_value & min_persistence);
 
 int main(int argc, char * argv[]) {
-  std::string filepoints;
+  std::string off_file_points;
   std::string filediag;
   Filtration_value threshold;
   int dim_max;
   int p;
   Filtration_value min_persistence;
 
-  program_options(argc, argv, filepoints, filediag, threshold, dim_max, p, min_persistence);
-
-  // Extract the points from the file filepoints
-  typedef std::vector<double> Point_t;
-  std::vector< Point_t > points;
-  read_points(filepoints, points);
+  program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence);
 
-  // Compute the proximity graph of the points
-  Graph_t prox_graph = compute_proximity_graph(points, threshold
-                                               , euclidean_distance<Point_t>);
+  Points_off_reader off_reader(off_file_points);
+  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Euclidean_distance());
 
   // Construct the Rips complex in a Simplex Tree
-  typedef Simplex_tree<Simplex_tree_options_fast_persistence> ST;
-  ST st;
-  // insert the proximity graph in the simplex tree
-  st.insert_graph(prox_graph);
-  // expand the graph until dimension dim_max
-  st.expansion(dim_max);
+  Simplex_tree simplex_tree;
 
-  std::cout << "The complex contains " << st.num_simplices() << " simplices \n";
-  std::cout << "   and has dimension " << st.dimension() << " \n";
+  rips_complex_from_file.create_complex(simplex_tree, dim_max);
+  std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
+  std::cout << "   and has dimension " << simplex_tree.dimension() << " \n";
 
   // Sort the simplices in the order of the filtration
-  st.initialize_filtration();
+  simplex_tree.initialize_filtration();
 
   // Compute the persistence diagram of the complex
-  persistent_cohomology::Persistent_cohomology<ST, Field_Zp > pcoh(st);
+  Persistent_cohomology pcoh(simplex_tree);
   // initializes the coefficient field for homology
   pcoh.init_coefficients(p);
 
@@ -99,7 +92,7 @@ int main(int argc, char * argv[]) {
 }
 
 void program_options(int argc, char * argv[]
-                     , std::string & filepoints
+                     , std::string & off_file_points
                      , std::string & filediag
                      , Filtration_value & threshold
                      , int & dim_max
@@ -108,15 +101,16 @@ void program_options(int argc, char * argv[]
   namespace po = boost::program_options;
   po::options_description hidden("Hidden options");
   hidden.add_options()
-      ("input-file", po::value<std::string>(&filepoints),
-       "Name of file containing a point set. Format is one point per line:   X1 ... Xd ");
+      ("input-file", po::value<std::string>(&off_file_points),
+       "Name of an OFF file containing a point set.\n");
 
   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()),
+      ("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.")
diff --git a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp
new file mode 100644
index 00000000..b159c62e
--- /dev/null
+++ b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp
@@ -0,0 +1,217 @@
+/*    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):       Clément Maria
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (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/graph_simplicial_complex.h>
+#include <gudhi/distance_functions.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Points_off_io.h>
+
+#include <boost/program_options.hpp>
+
+#include <string>
+#include <vector>
+#include <limits>  // infinity
+#include <utility>  // for pair
+#include <map>
+
+// ----------------------------------------------------------------------------
+// rips_persistence_step_by_step is an example of each step that is required to
+// build a Rips over a Simplex_tree. Please refer to rips_persistence to see
+// how to do the same thing with the Rips_complex wrapper for less detailed
+// steps.
+// ----------------------------------------------------------------------------
+
+// Types definition
+using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
+using Vertex_handle = Simplex_tree::Vertex_handle;
+using Filtration_value = Simplex_tree::Filtration_value;
+using Graph_t = boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS
+, boost::property < vertex_filtration_t, Filtration_value >
+, boost::property < edge_filtration_t, Filtration_value >
+>;
+using Edge_t = std::pair< Vertex_handle, Vertex_handle >;
+
+template< typename InputPointRange, typename Distance >
+Graph_t compute_proximity_graph(InputPointRange &points, Filtration_value threshold, Distance distance);
+
+using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp >;
+using Point = std::vector<double>;
+using Points_off_reader = Gudhi::Points_off_reader<Point>;
+
+void program_options(int argc, char * argv[]
+                     , std::string & off_file_points
+                     , std::string & filediag
+                     , Filtration_value & threshold
+                     , int & dim_max
+                     , int & p
+                     , Filtration_value & min_persistence);
+
+int main(int argc, char * argv[]) {
+  std::string off_file_points;
+  std::string filediag;
+  Filtration_value threshold;
+  int dim_max;
+  int p;
+  Filtration_value min_persistence;
+
+  program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence);
+
+  // Extract the points from the file filepoints
+  Points_off_reader off_reader(off_file_points);
+
+  // Compute the proximity graph of the points
+  Graph_t prox_graph = compute_proximity_graph(off_reader.get_point_cloud(), threshold
+                                               , Euclidean_distance());
+
+  // Construct the Rips complex in a Simplex Tree
+  Simplex_tree st;
+  // insert the proximity graph in the simplex tree
+  st.insert_graph(prox_graph);
+  // expand the graph until dimension dim_max
+  st.expansion(dim_max);
+
+  std::cout << "The complex contains " << st.num_simplices() << " simplices \n";
+  std::cout << "   and has dimension " << st.dimension() << " \n";
+
+  // Sort the simplices in the order of the filtration
+  st.initialize_filtration();
+
+  // Compute the persistence diagram of the complex
+  Persistent_cohomology pcoh(st);
+  // initializes the coefficient field for homology
+  pcoh.init_coefficients(p);
+
+  pcoh.compute_persistent_cohomology(min_persistence);
+
+  // Output the diagram in filediag
+  if (filediag.empty()) {
+    pcoh.output_diagram();
+  } else {
+    std::ofstream out(filediag);
+    pcoh.output_diagram(out);
+    out.close();
+  }
+
+  return 0;
+}
+
+void program_options(int argc, char * argv[]
+                     , std::string & off_file_points
+                     , std::string & filediag
+                     , 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>(&off_file_points),
+       "Name of an OFF file containing a point set.\n");
+
+  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");
+
+  po::positional_options_description pos;
+  pos.add("input-file", 1);
+
+  po::options_description all;
+  all.add(visible).add(hidden);
+
+  po::variables_map vm;
+  po::store(po::command_line_parser(argc, argv).
+            options(all).positional(pos).run(), vm);
+  po::notify(vm);
+
+  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 set of input points.\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";
+    std::cout << "b and d are respectively the birth and death of the feature and \n";
+    std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
+
+    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
+    std::cout << visible << std::endl;
+    std::abort();
+  }
+}
+
+/** Output the proximity graph of the points.
+ *
+ * If points contains n elements, the proximity graph is the graph
+ * with n vertices, and an edge [u,v] iff the distance function between
+ * points u and v is smaller than threshold.
+ *
+ * The type PointCloud furnishes .begin() and .end() methods, that return
+ * iterators with value_type Point.
+ */
+template< typename InputPointRange, typename Distance >
+Graph_t compute_proximity_graph(InputPointRange &points, Filtration_value threshold, Distance distance) {
+  std::vector< Edge_t > edges;
+  std::vector< Filtration_value > edges_fil;
+
+  Vertex_handle idx_u, idx_v;
+  Filtration_value fil;
+  idx_u = 0;
+  for (auto it_u = points.begin(); it_u != points.end(); ++it_u) {
+    idx_v = idx_u + 1;
+    for (auto it_v = it_u + 1; it_v != points.end(); ++it_v, ++idx_v) {
+      fil = distance(*it_u, *it_v);
+      if (fil <= threshold) {
+        edges.emplace_back(idx_u, idx_v);
+        edges_fil.push_back(fil);
+      }
+    }
+    ++idx_u;
+  }
+
+  Graph_t skel_graph(edges.begin()
+                     , edges.end()
+                     , edges_fil.begin()
+                     , idx_u);  // number of points labeled from 0 to idx_u-1
+
+  auto vertex_prop = boost::get(vertex_filtration_t(), skel_graph);
+
+  boost::graph_traits<Graph_t>::vertex_iterator vi, vi_end;
+  for (std::tie(vi, vi_end) = boost::vertices(skel_graph);
+       vi != vi_end; ++vi) {
+    boost::put(vertex_prop, *vi, 0.);
+  }
+
+  return skel_graph;
+}
diff --git a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
index 4c6656f5..63da9847 100644
--- a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
@@ -4,8 +4,7 @@
  *
  *    Author(s):       Clément Maria, Marc Glisse
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France),
- *                  2015  INRIA Saclay Île de 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
@@ -21,12 +20,12 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <gudhi/reader_utils.h>
-#include <gudhi/graph_simplicial_complex.h>
-#include <gudhi/distance_functions.h>
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Rips_complex.h>
 #include <gudhi/Hasse_complex.h>
+#include <gudhi/Points_off_io.h>
+#include <gudhi/distance_functions.h>
 
 #include <boost/program_options.hpp>
 
@@ -44,14 +43,16 @@
 //                                                            //
 ////////////////////////////////////////////////////////////////
 
-using namespace Gudhi;
-using namespace Gudhi::persistent_cohomology;
-
-typedef int Vertex_handle;
-typedef double Filtration_value;
+// Types definition
+using Simplex_tree = Gudhi::Simplex_tree<>;
+using Filtration_value = Simplex_tree::Filtration_value;
+using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
+using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
+using Point = std::vector<double>;
+using Points_off_reader = Gudhi::Points_off_reader<Point>;
 
 void program_options(int argc, char * argv[]
-                     , std::string & filepoints
+                     , std::string & off_file_points
                      , std::string & filediag
                      , Filtration_value & threshold
                      , int & dim_max
@@ -59,30 +60,21 @@ void program_options(int argc, char * argv[]
                      , Filtration_value & min_persistence);
 
 int main(int argc, char * argv[]) {
-  std::string filepoints;
+  std::string off_file_points;
   std::string filediag;
   Filtration_value threshold;
   int dim_max;
   int p;
   Filtration_value min_persistence;
 
-  program_options(argc, argv, filepoints, filediag, threshold, dim_max, p, min_persistence);
-
-  // Extract the points from the file filepoints
-  typedef std::vector<double> Point_t;
-  std::vector< Point_t > points;
-  read_points(filepoints, points);
+  program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence);
 
-  // Compute the proximity graph of the points
-  Graph_t prox_graph = compute_proximity_graph(points, threshold
-                                               , euclidean_distance<Point_t>);
+  Points_off_reader off_reader(off_file_points);
+  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Euclidean_distance());
 
   // Construct the Rips complex in a Simplex Tree
-  Simplex_tree<>& st = *new Simplex_tree<>;
-  // insert the proximity graph in the simplex tree
-  st.insert_graph(prox_graph);
-  // expand the graph until dimension dim_max
-  st.expansion(dim_max);
+  Simplex_tree& st = *new Simplex_tree;
+  rips_complex_from_file.create_complex(st, dim_max);
 
   std::cout << "The complex contains " << st.num_simplices() << " simplices \n";
   std::cout << "   and has dimension " << st.dimension() << " \n";
@@ -99,7 +91,7 @@ int main(int argc, char * argv[]) {
     st.assign_key(sh, count++);
 
   // Convert to a more convenient representation.
-  Hasse_complex<> hcpx(st);
+  Gudhi::Hasse_complex<> hcpx(st);
 
 #ifdef GUDHI_USE_TBB
   ts.terminate();
@@ -109,7 +101,7 @@ int main(int argc, char * argv[]) {
   delete &st;
 
   // Compute the persistence diagram of the complex
-  persistent_cohomology::Persistent_cohomology< Hasse_complex<>, Field_Zp > pcoh(hcpx);
+  Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::Hasse_complex<>, Field_Zp > pcoh(hcpx);
   // initializes the coefficient field for homology
   pcoh.init_coefficients(p);
 
@@ -126,7 +118,7 @@ int main(int argc, char * argv[]) {
 }
 
 void program_options(int argc, char * argv[]
-                     , std::string & filepoints
+                     , std::string & off_file_points
                      , std::string & filediag
                      , Filtration_value & threshold
                      , int & dim_max
@@ -135,7 +127,7 @@ void program_options(int argc, char * argv[]
   namespace po = boost::program_options;
   po::options_description hidden("Hidden options");
   hidden.add_options()
-      ("input-file", po::value<std::string>(&filepoints),
+      ("input-file", po::value<std::string>(&off_file_points),
        "Name of file containing a point set. Format is one point per line:   X1 ... Xd ");
 
   po::options_description visible("Allowed options", 100);