Fix compilation issues

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_module@1596 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 343308ef914e6a6617890f49a55eb0bb8db15ee9

9 files changed, 63 insertions, 269 deletions

diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index d97d1b63..75f3c5d4 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -39,13 +39,9 @@ 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)
    endif(GMPXX_FOUND)
 endif(GMP_FOUND)
diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
index 48fbb91a..f7e8f800 100644
--- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
@@ -64,6 +64,7 @@ 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;
@@ -132,7 +133,7 @@ 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 cb181936..24315144 100644
--- a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
@@ -9,6 +9,8 @@
 #include <string>
 #include <limits>  // for numeric_limits
 
+using Filtration_value = double;
+
 void program_options(int argc, char * argv[]
                      , std::string & off_file_points
                      , std::string & output_file_diag
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..5184ef52 100644
--- a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
@@ -70,6 +70,7 @@ 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>;
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..817aac4d 100644
--- a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
+++ b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
@@ -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</*Gudhi::Simplex_tree_options_fast_persistence*/>;
+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_multifield_persistence.cpp b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
index d4a07bb6..f4adc7a9 100644
--- a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
@@ -25,14 +25,21 @@
 #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>
 
-
-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 & off_file_points
@@ -54,22 +61,22 @@ int main(int argc, char * argv[]) {
 
   program_options(argc, argv, off_file_points, filediag, threshold, dim_max, min_p, max_p, min_persistence);
 
-  Gudhi::rips_complex::Rips_complex<> rips_complex_from_file(off_file_points);
+  Points_off_reader off_reader(off_file_points);
+  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold,
+                                      euclidean_distance<Point>);
 
   // Construct the Rips complex in a Simplex Tree
-  using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
   Simplex_tree simplex_tree;
 
-  if (rips_complex_from_file.create_complex(simplex_tree, threshold, dim_max, euclidean_distance<std::vector<double>>)) {
+  if (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();
   
-    using Multi_field = Gudhi::persistent_cohomology::Multi_field;
     // Compute the persistence diagram of the complex
-    Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Multi_field > pcoh(simplex_tree);
+    Persistent_cohomology pcoh(simplex_tree);
     // initializes the coefficient field for homology
     pcoh.init_coefficients(min_p, max_p);
   
diff --git a/src/Persistent_cohomology/example/rips_persistence.cpp b/src/Persistent_cohomology/example/rips_persistence.cpp
index e3ab5927..97bab14c 100644
--- a/src/Persistent_cohomology/example/rips_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence.cpp
@@ -25,6 +25,7 @@
 #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>
 
@@ -32,7 +33,14 @@
 #include <vector>
 #include <limits>  // infinity
 
-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 & off_file_points
@@ -52,22 +60,22 @@ int main(int argc, char * argv[]) {
 
   program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence);
 
-  Gudhi::rips_complex::Rips_complex<> rips_complex_from_file(off_file_points);
+  Points_off_reader off_reader(off_file_points);
+  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold,
+                                      euclidean_distance<Point>);
 
   // Construct the Rips complex in a Simplex Tree
-  using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
   Simplex_tree simplex_tree;
 
-  if (rips_complex_from_file.create_complex(simplex_tree, threshold, dim_max, euclidean_distance<std::vector<double>>)) {
+  if (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();
   
-    using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
     // Compute the persistence diagram of the complex
-    Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp > pcoh(simplex_tree);
+    Persistent_cohomology pcoh(simplex_tree);
     // initializes the coefficient field for homology
     pcoh.init_coefficients(p);
   
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..991ed4f0 100644
--- a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
@@ -21,12 +21,12 @@
  *    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 +44,16 @@
 //                                                            //
 ////////////////////////////////////////////////////////////////
 
-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 +61,22 @@ 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<Point>);
 
   // 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 +93,7 @@ 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 +103,7 @@ 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 +120,7 @@ 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 +129,7 @@ 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);