GUDHI 2.2.0 as released by upstream in a tarball.upstream/2.2.0

59 files changed, 502 insertions, 156 deletions

diff --git a/example/Alpha_complex/CMakeLists.txt b/example/Alpha_complex/CMakeLists.txt
index 5bf553e9..2fc62452 100644
--- a/example/Alpha_complex/CMakeLists.txt
+++ b/example/Alpha_complex/CMakeLists.txt
@@ -1,4 +1,3 @@
-cmake_minimum_required(VERSION 2.6)
 project(Alpha_complex_examples)
 
 # need CGAL 4.7
diff --git a/example/Bitmap_cubical_complex/CMakeLists.txt b/example/Bitmap_cubical_complex/CMakeLists.txt
index 99304aa4..dc659f2d 100644
--- a/example/Bitmap_cubical_complex/CMakeLists.txt
+++ b/example/Bitmap_cubical_complex/CMakeLists.txt
@@ -1,4 +1,3 @@
-cmake_minimum_required(VERSION 2.6)
 project(Bitmap_cubical_complex_examples)
 
 add_executable ( Random_bitmap_cubical_complex Random_bitmap_cubical_complex.cpp )
diff --git a/example/Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp b/example/Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp
index f70558f2..6eb24040 100644
--- a/example/Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp
+++ b/example/Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Pawel Dlotko
  *
- *    Copyright (C) 2015  INRIA Saclay (France)
+ *    Copyright (C) 2015 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
diff --git a/example/Bottleneck_distance/CMakeLists.txt b/example/Bottleneck_distance/CMakeLists.txt
index 6095d6eb..c6f10127 100644
--- a/example/Bottleneck_distance/CMakeLists.txt
+++ b/example/Bottleneck_distance/CMakeLists.txt
@@ -1,4 +1,3 @@
-cmake_minimum_required(VERSION 2.6)
 project(Bottleneck_distance_examples)
 
 if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
diff --git a/example/Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp b/example/Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp
index fd164b22..1e27887c 100644
--- a/example/Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp
+++ b/example/Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2017  INRIA
+ *    Copyright (C) 2017 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
diff --git a/example/Bottleneck_distance/bottleneck_basic_example.cpp b/example/Bottleneck_distance/bottleneck_basic_example.cpp
index d0ca4e20..3df7d12d 100644
--- a/example/Bottleneck_distance/bottleneck_basic_example.cpp
+++ b/example/Bottleneck_distance/bottleneck_basic_example.cpp
@@ -4,7 +4,7 @@
  *
  *    Authors:       Francois Godi, small modifications by Pawel Dlotko
  *
- *    Copyright (C) 2015  INRIA
+ *    Copyright (C) 2015 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
diff --git a/example/Cech_complex/CMakeLists.txt b/example/Cech_complex/CMakeLists.txt
new file mode 100644
index 00000000..ab391215
--- /dev/null
+++ b/example/Cech_complex/CMakeLists.txt
@@ -0,0 +1,16 @@
+cmake_minimum_required(VERSION 2.6)
+project(Cech_complex_examples)
+
+add_executable ( Cech_complex_example_step_by_step cech_complex_step_by_step.cpp )
+target_link_libraries(Cech_complex_example_step_by_step ${Boost_PROGRAM_OPTIONS_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(Cech_complex_example_step_by_step ${TBB_LIBRARIES})
+endif()
+add_test(NAME Cech_complex_utility_from_rips_on_tore_3D COMMAND $<TARGET_FILE:Cech_complex_example_step_by_step>
+    "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-r" "0.25" "-d" "3")
+
+add_executable ( Cech_complex_example_from_points cech_complex_example_from_points.cpp)
+if (TBB_FOUND)
+  target_link_libraries(Cech_complex_example_from_points ${TBB_LIBRARIES})
+endif()
+add_test(NAME Cech_complex_example_from_points COMMAND $<TARGET_FILE:Cech_complex_example_from_points>)
diff --git a/example/Cech_complex/cech_complex_example_from_points.cpp b/example/Cech_complex/cech_complex_example_from_points.cpp
new file mode 100644
index 00000000..3cc5a4df
--- /dev/null
+++ b/example/Cech_complex/cech_complex_example_from_points.cpp
@@ -0,0 +1,54 @@
+#include <gudhi/Cech_complex.h>
+#include <gudhi/Simplex_tree.h>
+
+#include <iostream>
+#include <string>
+#include <vector>
+#include <array>
+
+int main() {
+  // Type definitions
+  using Point_cloud = std::vector<std::array<double, 2>>;
+  using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
+  using Filtration_value = Simplex_tree::Filtration_value;
+  using Cech_complex = Gudhi::cech_complex::Cech_complex<Simplex_tree, Point_cloud>;
+
+  Point_cloud points;
+  points.push_back({1., 0.});                  // 0
+  points.push_back({0., 1.});                  // 1
+  points.push_back({2., 1.});                  // 2
+  points.push_back({3., 2.});                  // 3
+  points.push_back({0., 3.});                  // 4
+  points.push_back({3. + std::sqrt(3.), 3.});  // 5
+  points.push_back({1., 4.});                  // 6
+  points.push_back({3., 4.});                  // 7
+  points.push_back({2., 4. + std::sqrt(3.)});  // 8
+  points.push_back({0., 4.});                  // 9
+  points.push_back({-0.5, 2.});                // 10
+
+  // ----------------------------------------------------------------------------
+  // Init of a Cech complex from points
+  // ----------------------------------------------------------------------------
+  Filtration_value max_radius = 1.;
+  Cech_complex cech_complex_from_points(points, max_radius);
+
+  Simplex_tree stree;
+  cech_complex_from_points.create_complex(stree, 2);
+  // ----------------------------------------------------------------------------
+  // Display information about the one skeleton Cech complex
+  // ----------------------------------------------------------------------------
+  std::cout << "Cech complex is of dimension " << stree.dimension() << " - " << stree.num_simplices() << " simplices - "
+            << stree.num_vertices() << " vertices." << std::endl;
+
+  std::cout << "Iterator on Cech complex simplices in the filtration order, with [filtration value]:" << std::endl;
+  for (auto f_simplex : stree.filtration_simplex_range()) {
+    std::cout << "   ( ";
+    for (auto vertex : stree.simplex_vertex_range(f_simplex)) {
+      std::cout << vertex << " ";
+    }
+    std::cout << ") -> "
+              << "[" << stree.filtration(f_simplex) << "] ";
+    std::cout << std::endl;
+  }
+  return 0;
+}
diff --git a/example/Cech_complex/cech_complex_example_from_points_for_doc.txt b/example/Cech_complex/cech_complex_example_from_points_for_doc.txt
new file mode 100644
index 00000000..be0afc76
--- /dev/null
+++ b/example/Cech_complex/cech_complex_example_from_points_for_doc.txt
@@ -0,0 +1,31 @@
+Iterator on Cech complex simplices in the filtration order, with [filtration value]:
+   ( 0 ) -> [0]
+   ( 1 ) -> [0]
+   ( 2 ) -> [0]
+   ( 3 ) -> [0]
+   ( 4 ) -> [0]
+   ( 5 ) -> [0]
+   ( 6 ) -> [0]
+   ( 7 ) -> [0]
+   ( 8 ) -> [0]
+   ( 9 ) -> [0]
+   ( 10 ) -> [0]
+   ( 9 4 ) -> [0.5]
+   ( 9 6 ) -> [0.5]
+   ( 10 1 ) -> [0.559017]
+   ( 10 4 ) -> [0.559017]
+   ( 1 0 ) -> [0.707107]
+   ( 2 0 ) -> [0.707107]
+   ( 3 2 ) -> [0.707107]
+   ( 6 4 ) -> [0.707107]
+   ( 9 6 4 ) -> [0.707107]
+   ( 2 1 ) -> [1]
+   ( 2 1 0 ) -> [1]
+   ( 4 1 ) -> [1]
+   ( 5 3 ) -> [1]
+   ( 7 3 ) -> [1]
+   ( 7 5 ) -> [1]
+   ( 7 6 ) -> [1]
+   ( 8 6 ) -> [1]
+   ( 8 7 ) -> [1]
+   ( 10 4 1 ) -> [1]
diff --git a/example/Cech_complex/cech_complex_step_by_step.cpp b/example/Cech_complex/cech_complex_step_by_step.cpp
new file mode 100644
index 00000000..d2dc8b65
--- /dev/null
+++ b/example/Cech_complex/cech_complex_step_by_step.cpp
@@ -0,0 +1,166 @@
+/*    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) 2018 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/graph_simplicial_complex.h>
+#include <gudhi/distance_functions.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Points_off_io.h>
+
+#include <gudhi/Miniball.hpp>
+
+#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<>;
+using Simplex_handle = Simplex_tree::Simplex_handle;
+using Filtration_value = Simplex_tree::Filtration_value;
+using Point = std::vector<double>;
+using Points_off_reader = Gudhi::Points_off_reader<Point>;
+using Proximity_graph = Gudhi::Proximity_graph<Simplex_tree>;
+
+class Cech_blocker {
+ private:
+  using Point_cloud = std::vector<Point>;
+  using Point_iterator = Point_cloud::const_iterator;
+  using Coordinate_iterator = Point::const_iterator;
+  using Min_sphere = Gudhi::Miniball::Miniball<Gudhi::Miniball::CoordAccessor<Point_iterator, Coordinate_iterator>>;
+
+ public:
+  bool operator()(Simplex_handle sh) {
+    std::vector<Point> points;
+    for (auto vertex : simplex_tree_.simplex_vertex_range(sh)) {
+      points.push_back(point_cloud_[vertex]);
+#ifdef DEBUG_TRACES
+      std::cout << "#(" << vertex << ")#";
+#endif  // DEBUG_TRACES
+    }
+    Filtration_value radius = Gudhi::Minimal_enclosing_ball_radius()(points);
+#ifdef DEBUG_TRACES
+    std::cout << "radius = " << radius << " - " << (radius > max_radius_) << std::endl;
+#endif  // DEBUG_TRACES
+    simplex_tree_.assign_filtration(sh, radius);
+    return (radius > max_radius_);
+  }
+  Cech_blocker(Simplex_tree& simplex_tree, Filtration_value max_radius, const std::vector<Point>& point_cloud)
+      : simplex_tree_(simplex_tree), max_radius_(max_radius), point_cloud_(point_cloud) {
+    dimension_ = point_cloud_[0].size();
+  }
+
+ private:
+  Simplex_tree simplex_tree_;
+  Filtration_value max_radius_;
+  std::vector<Point> point_cloud_;
+  int dimension_;
+};
+
+void program_options(int argc, char* argv[], std::string& off_file_points, Filtration_value& max_radius, int& dim_max);
+
+int main(int argc, char* argv[]) {
+  std::string off_file_points;
+  Filtration_value max_radius;
+  int dim_max;
+
+  program_options(argc, argv, off_file_points, max_radius, dim_max);
+
+  // Extract the points from the file filepoints
+  Points_off_reader off_reader(off_file_points);
+
+  // Compute the proximity graph of the points
+  Proximity_graph prox_graph = Gudhi::compute_proximity_graph<Simplex_tree>(off_reader.get_point_cloud(), max_radius,
+                                                                            Gudhi::Minimal_enclosing_ball_radius());
+
+  // 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_with_blockers(dim_max, Cech_blocker(st, max_radius, off_reader.get_point_cloud()));
+
+  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();
+
+#if DEBUG_TRACES
+  std::cout << "********************************************************************\n";
+  std::cout << "* The complex contains " << st.num_simplices() << " simplices - dimension=" << st.dimension() << "\n";
+  std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n";
+  for (auto f_simplex : st.filtration_simplex_range()) {
+    std::cout << "   "
+              << "[" << st.filtration(f_simplex) << "] ";
+    for (auto vertex : st.simplex_vertex_range(f_simplex)) {
+      std::cout << static_cast<int>(vertex) << " ";
+    }
+    std::cout << std::endl;
+  }
+#endif  // DEBUG_TRACES
+
+  return 0;
+}
+
+void program_options(int argc, char* argv[], std::string& off_file_points, Filtration_value& max_radius, int& dim_max) {
+  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")(
+      "max-radius,r",
+      po::value<Filtration_value>(&max_radius)->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.");
+
+  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 << "Construct a Cech complex defined on a set of input points.\n \n";
+
+    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
+    std::cout << visible << std::endl;
+    std::abort();
+  }
+}
diff --git a/example/Contraction/CMakeLists.txt b/example/Contraction/CMakeLists.txt
index a92d1685..582b7ab8 100644
--- a/example/Contraction/CMakeLists.txt
+++ b/example/Contraction/CMakeLists.txt
@@ -1,4 +1,3 @@
-cmake_minimum_required(VERSION 2.6)
 project(Contraction_examples)
 
 add_executable(RipsContraction Rips_contraction.cpp)
diff --git a/example/Contraction/Garland_heckbert.cpp b/example/Contraction/Garland_heckbert.cpp
index 2b0dc973..08dd932e 100644
--- a/example/Contraction/Garland_heckbert.cpp
+++ b/example/Contraction/Garland_heckbert.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-M�diterran�e (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
diff --git a/example/Contraction/Garland_heckbert/Error_quadric.h b/example/Contraction/Garland_heckbert/Error_quadric.h
index e7dafaa0..8bd9b545 100644
--- a/example/Contraction/Garland_heckbert/Error_quadric.h
+++ b/example/Contraction/Garland_heckbert/Error_quadric.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-M�diterran�e (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
diff --git a/example/Contraction/Rips_contraction.cpp b/example/Contraction/Rips_contraction.cpp
index 501b0e87..7f9b150a 100644
--- a/example/Contraction/Rips_contraction.cpp
+++ b/example/Contraction/Rips_contraction.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (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
diff --git a/example/Nerve_GIC/CMakeLists.txt b/example/Nerve_GIC/CMakeLists.txt
index f2626927..fdecf86e 100644
--- a/example/Nerve_GIC/CMakeLists.txt
+++ b/example/Nerve_GIC/CMakeLists.txt
@@ -1,4 +1,3 @@
-cmake_minimum_required(VERSION 2.6)
 project(Nerve_GIC_examples)
 
 if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
@@ -17,10 +16,13 @@ if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
   file(COPY "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
   add_test(NAME Nerve_GIC_example_CoordGIC COMMAND $<TARGET_FILE:CoordGIC>
-      "tore3D_1307.off" "0")
+      "${CMAKE_CURRENT_BINARY_DIR}/tore3D_1307.off" "0")
 
   add_test(NAME Nerve_GIC_example_FuncGIC COMMAND $<TARGET_FILE:FuncGIC>
-      "lucky_cat.off"
-      "lucky_cat_PCA1")
+      "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat.off"
+      "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat_PCA1")
+
+  install(TARGETS CoordGIC DESTINATION bin)
+  install(TARGETS FuncGIC DESTINATION bin)
 
 endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
diff --git a/example/Nerve_GIC/CoordGIC.cpp b/example/Nerve_GIC/CoordGIC.cpp
index c92cf235..73edae18 100644
--- a/example/Nerve_GIC/CoordGIC.cpp
+++ b/example/Nerve_GIC/CoordGIC.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Mathieu Carrière
  *
- *    Copyright (C) 2017  INRIA
+ *    Copyright (C) 2017 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 +66,9 @@ int main(int argc, char **argv) {
 
     GIC.find_simplices();
 
+    GIC.compute_distribution(10);
+    GIC.compute_p_value();
+
     GIC.plot_DOT();
 
     Gudhi::Simplex_tree<> stree;
diff --git a/example/Nerve_GIC/FuncGIC.cpp b/example/Nerve_GIC/FuncGIC.cpp
index cb0f0d63..1f5de999 100644
--- a/example/Nerve_GIC/FuncGIC.cpp
+++ b/example/Nerve_GIC/FuncGIC.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Mathieu Carrière
  *
- *    Copyright (C) 2017  INRIA
+ *    Copyright (C) 2017 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
diff --git a/example/Persistence_representations/CMakeLists.txt b/example/Persistence_representations/CMakeLists.txt
index eb3258f8..33558df3 100644
--- a/example/Persistence_representations/CMakeLists.txt
+++ b/example/Persistence_representations/CMakeLists.txt
@@ -1,27 +1,28 @@
-cmake_minimum_required(VERSION 2.6)
 project(Persistence_representations_example)
 
 add_executable ( Persistence_representations_example_landscape_on_grid persistence_landscape_on_grid.cpp )
 add_test(NAME Persistence_representations_example_landscape_on_grid
     COMMAND $<TARGET_FILE:Persistence_representations_example_landscape_on_grid>)
+install(TARGETS Persistence_representations_example_landscape_on_grid DESTINATION bin)
 
 add_executable ( Persistence_representations_example_landscape persistence_landscape.cpp )
 add_test(NAME Persistence_representations_example_landscape
     COMMAND $<TARGET_FILE:Persistence_representations_example_landscape>)
+install(TARGETS Persistence_representations_example_landscape DESTINATION bin)
 
 add_executable ( Persistence_representations_example_intervals persistence_intervals.cpp )
 add_test(NAME Persistence_representations_example_intervals
     COMMAND $<TARGET_FILE:Persistence_representations_example_intervals>
     "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers")
+install(TARGETS Persistence_representations_example_intervals DESTINATION bin)
 
 add_executable ( Persistence_representations_example_vectors persistence_vectors.cpp )
 add_test(NAME Persistence_representations_example_vectors
     COMMAND $<TARGET_FILE:Persistence_representations_example_vectors>)
+install(TARGETS Persistence_representations_example_vectors DESTINATION bin)
 
 add_executable ( Persistence_representations_example_heat_maps persistence_heat_maps.cpp )
 add_test(NAME Persistence_representations_example_heat_maps
     COMMAND $<TARGET_FILE:Persistence_representations_example_heat_maps>)
-
-
-
+install(TARGETS Persistence_representations_example_heat_maps DESTINATION bin)
 
diff --git a/example/Persistence_representations/persistence_heat_maps.cpp b/example/Persistence_representations/persistence_heat_maps.cpp
index 2a472ac6..323b57e9 100644
--- a/example/Persistence_representations/persistence_heat_maps.cpp
+++ b/example/Persistence_representations/persistence_heat_maps.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Pawel Dlotko
  *
- *    Copyright (C) 2016  INRIA (France)
+ *    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
diff --git a/example/Persistence_representations/persistence_intervals.cpp b/example/Persistence_representations/persistence_intervals.cpp
index c1ceb458..b5dcf25c 100644
--- a/example/Persistence_representations/persistence_intervals.cpp
+++ b/example/Persistence_representations/persistence_intervals.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Pawel Dlotko
  *
- *    Copyright (C) 2016  INRIA (France)
+ *    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
diff --git a/example/Persistence_representations/persistence_landscape.cpp b/example/Persistence_representations/persistence_landscape.cpp
index 400a9ae1..27542cf7 100644
--- a/example/Persistence_representations/persistence_landscape.cpp
+++ b/example/Persistence_representations/persistence_landscape.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Pawel Dlotko
  *
- *    Copyright (C) 2016  INRIA (France)
+ *    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
diff --git a/example/Persistence_representations/persistence_landscape_on_grid.cpp b/example/Persistence_representations/persistence_landscape_on_grid.cpp
index b201b397..0f471a67 100644
--- a/example/Persistence_representations/persistence_landscape_on_grid.cpp
+++ b/example/Persistence_representations/persistence_landscape_on_grid.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Pawel Dlotko
  *
- *    Copyright (C) 2016  INRIA (France)
+ *    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
diff --git a/example/Persistence_representations/persistence_vectors.cpp b/example/Persistence_representations/persistence_vectors.cpp
index 834ae644..072e530d 100644
--- a/example/Persistence_representations/persistence_vectors.cpp
+++ b/example/Persistence_representations/persistence_vectors.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Pawel Dlotko
  *
- *    Copyright (C) 2016  INRIA (France)
+ *    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
diff --git a/example/Persistent_cohomology/CMakeLists.txt b/example/Persistent_cohomology/CMakeLists.txt
index 18e2913b..0f731519 100644
--- a/example/Persistent_cohomology/CMakeLists.txt
+++ b/example/Persistent_cohomology/CMakeLists.txt
@@ -1,4 +1,3 @@
-cmake_minimum_required(VERSION 2.6)
 project(Persistent_cohomology_examples)
 
 add_executable(plain_homology plain_homology.cpp)
diff --git a/example/Persistent_cohomology/custom_persistence_sort.cpp b/example/Persistent_cohomology/custom_persistence_sort.cpp
index 64f2a4dc..35366144 100644
--- a/example/Persistent_cohomology/custom_persistence_sort.cpp
+++ b/example/Persistent_cohomology/custom_persistence_sort.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
diff --git a/example/Persistent_cohomology/persistence_from_file.cpp b/example/Persistent_cohomology/persistence_from_file.cpp
index eafa3fd5..c40434a4 100644
--- a/example/Persistent_cohomology/persistence_from_file.cpp
+++ b/example/Persistent_cohomology/persistence_from_file.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
diff --git a/example/Persistent_cohomology/persistence_from_simple_simplex_tree.cpp b/example/Persistent_cohomology/persistence_from_simple_simplex_tree.cpp
index 8ef479d4..ffccfd86 100644
--- a/example/Persistent_cohomology/persistence_from_simple_simplex_tree.cpp
+++ b/example/Persistent_cohomology/persistence_from_simple_simplex_tree.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2014  INRIA
+ *    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
diff --git a/example/Persistent_cohomology/plain_homology.cpp b/example/Persistent_cohomology/plain_homology.cpp
index a5ae09c8..a2256060 100644
--- a/example/Persistent_cohomology/plain_homology.cpp
+++ b/example/Persistent_cohomology/plain_homology.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Marc Glisse
  *
- *    Copyright (C) 2015  INRIA Saclay - Ile-de-France (France)
+ *    Copyright (C) 2015 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
diff --git a/example/Persistent_cohomology/rips_multifield_persistence.cpp b/example/Persistent_cohomology/rips_multifield_persistence.cpp
index dae36ed2..626ec2ef 100644
--- a/example/Persistent_cohomology/rips_multifield_persistence.cpp
+++ b/example/Persistent_cohomology/rips_multifield_persistence.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Clément Maria
  *
- *    Copyright (C) 2014  INRIA
+ *    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
diff --git a/example/Persistent_cohomology/rips_persistence_step_by_step.cpp b/example/Persistent_cohomology/rips_persistence_step_by_step.cpp
index c1de0ef8..7c81fcfb 100644
--- a/example/Persistent_cohomology/rips_persistence_step_by_step.cpp
+++ b/example/Persistent_cohomology/rips_persistence_step_by_step.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
diff --git a/example/Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp b/example/Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp
index 9618f278..c7607dce 100644
--- a/example/Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp
+++ b/example/Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Clément Maria, Marc Glisse
  *
- *    Copyright (C) 2014  INRIA
+ *    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
diff --git a/example/Rips_complex/CMakeLists.txt b/example/Rips_complex/CMakeLists.txt
index 2940f164..e7772bdb 100644
--- a/example/Rips_complex/CMakeLists.txt
+++ b/example/Rips_complex/CMakeLists.txt
@@ -1,4 +1,3 @@
-cmake_minimum_required(VERSION 2.6)
 project(Rips_complex_examples)
 
 # Point cloud
@@ -11,17 +10,29 @@ add_executable ( Rips_complex_example_one_skeleton_from_distance_matrix example_
 
 add_executable ( Rips_complex_example_from_csv_distance_matrix example_rips_complex_from_csv_distance_matrix_file.cpp )
 
+# Sparse rips from points
+add_executable ( Rips_complex_example_sparse example_sparse_rips.cpp )
+
+# Correlation matrix
+add_executable (  Rips_complex_example_one_skeleton_rips_from_correlation_matrix example_one_skeleton_rips_from_correlation_matrix.cpp )
+
 if (TBB_FOUND)
   target_link_libraries(Rips_complex_example_from_off ${TBB_LIBRARIES})
   target_link_libraries(Rips_complex_example_one_skeleton_from_points ${TBB_LIBRARIES})
   target_link_libraries(Rips_complex_example_one_skeleton_from_distance_matrix ${TBB_LIBRARIES})
   target_link_libraries(Rips_complex_example_from_csv_distance_matrix ${TBB_LIBRARIES})
+  target_link_libraries(Rips_complex_example_sparse ${TBB_LIBRARIES})
+  target_link_libraries(Rips_complex_example_one_skeleton_rips_from_correlation_matrix ${TBB_LIBRARIES})
 endif()
 
 add_test(NAME Rips_complex_example_one_skeleton_from_points
     COMMAND $<TARGET_FILE:Rips_complex_example_one_skeleton_from_points>)
 add_test(NAME Rips_complex_example_one_skeleton_from_distance_matrix
     COMMAND $<TARGET_FILE:Rips_complex_example_one_skeleton_from_distance_matrix>)
+add_test(NAME Rips_complex_example_sparse
+    COMMAND $<TARGET_FILE:Rips_complex_example_sparse>)
+add_test(NAME Rips_complex_example_one_skeleton_rips_from_correlation_matrix
+    COMMAND $<TARGET_FILE:Rips_complex_example_one_skeleton_rips_from_correlation_matrix>)
 
 add_test(NAME Rips_complex_example_from_off_doc_12_1 COMMAND $<TARGET_FILE:Rips_complex_example_from_off>
     "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "12.0" "1" "${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt")
@@ -57,3 +68,4 @@ install(TARGETS Rips_complex_example_from_off DESTINATION bin)
 install(TARGETS Rips_complex_example_one_skeleton_from_points DESTINATION bin)
 install(TARGETS Rips_complex_example_one_skeleton_from_distance_matrix DESTINATION bin)
 install(TARGETS Rips_complex_example_from_csv_distance_matrix DESTINATION bin)
+install(TARGETS Rips_complex_example_one_skeleton_rips_from_correlation_matrix DESTINATION bin)
diff --git a/example/Rips_complex/example_one_skeleton_rips_from_correlation_matrix.cpp b/example/Rips_complex/example_one_skeleton_rips_from_correlation_matrix.cpp
new file mode 100644
index 00000000..05bacb9f
--- /dev/null
+++ b/example/Rips_complex/example_one_skeleton_rips_from_correlation_matrix.cpp
@@ -0,0 +1,81 @@
+#include <gudhi/Rips_complex.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/distance_functions.h>
+
+#include <iostream>
+#include <string>
+#include <vector>
+#include <limits>  // for std::numeric_limits
+
+int main() {
+  // Type definitions
+  using Simplex_tree = Gudhi::Simplex_tree<>;
+  using Filtration_value = Simplex_tree::Filtration_value;
+  using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
+  using Distance_matrix = std::vector<std::vector<Filtration_value>>;
+
+  // User defined correlation matrix is:
+  // |1     0.06  0.23  0.01  0.89|
+  // |0.06  1     0.74  0.01  0.61|
+  // |0.23  0.74  1     0.72  0.03|
+  // |0.01  0.01  0.72  1     0.7 |
+  // |0.89  0.61  0.03  0.7   1   |
+
+  Distance_matrix correlations;
+  correlations.push_back({});
+  correlations.push_back({0.06});
+  correlations.push_back({0.23, 0.74});
+  correlations.push_back({0.01, 0.01, 0.72});
+  correlations.push_back({0.89, 0.61, 0.03, 0.7});
+
+  // ----------------------------------------------------------------------------
+  // Convert correlation matrix to a distance matrix:
+  // ----------------------------------------------------------------------------
+  double threshold = 0;
+  for (size_t i = 0; i != correlations.size(); ++i) {
+    for (size_t j = 0; j != correlations[i].size(); ++j) {
+      // Here we check if our data comes from corelation matrix.
+      if ((correlations[i][j] < -1) || (correlations[i][j] > 1)) {
+        std::cerr << "The input matrix is not a correlation matrix. The program will now terminate.\n";
+        throw "The input matrix is not a correlation matrix. The program will now terminate.\n";
+      }
+      correlations[i][j] = 1 - correlations[i][j];
+      // Here we make sure that we will get the treshold value equal to maximal
+      // distance in the matrix.
+      if (correlations[i][j] > threshold) threshold = correlations[i][j];
+    }
+  }
+
+  //-----------------------------------------------------------------------------
+  // Now the correlation matrix is a distance matrix and can be processed further.
+  //-----------------------------------------------------------------------------
+  Distance_matrix distances = correlations;
+
+  Rips_complex rips_complex_from_points(distances, threshold);
+
+  Simplex_tree stree;
+  rips_complex_from_points.create_complex(stree, 1);
+  // ----------------------------------------------------------------------------
+  // Display information about the one skeleton Rips complex. Note that
+  // the filtration displayed here comes from the distance matrix computed
+  // above, which is 1 - initial correlation matrix. Only this way, we obtain
+  // a complex with filtration. If a correlation matrix is used instead, we would
+  // have a reverse filtration (i.e. filtration of boundary of each simplex S
+  // is greater or equal to the filtration of S).
+  // ----------------------------------------------------------------------------
+  std::cout << "Rips complex is of dimension " << stree.dimension() << " - " << stree.num_simplices() << " simplices - "
+            << stree.num_vertices() << " vertices." << std::endl;
+
+  std::cout << "Iterator on Rips complex simplices in the filtration order, with [filtration value]:" << std::endl;
+  for (auto f_simplex : stree.filtration_simplex_range()) {
+    std::cout << "   ( ";
+    for (auto vertex : stree.simplex_vertex_range(f_simplex)) {
+      std::cout << vertex << " ";
+    }
+    std::cout << ") -> "
+              << "[" << stree.filtration(f_simplex) << "] ";
+    std::cout << std::endl;
+  }
+
+  return 0;
+}
diff --git a/example/Rips_complex/example_sparse_rips.cpp b/example/Rips_complex/example_sparse_rips.cpp
new file mode 100644
index 00000000..1c95b48c
--- /dev/null
+++ b/example/Rips_complex/example_sparse_rips.cpp
@@ -0,0 +1,30 @@
+#include <gudhi/Sparse_rips_complex.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/distance_functions.h>
+
+#include <iostream>
+#include <vector>
+
+int main() {
+  using Point = std::vector<double>;
+  using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
+  using Filtration_value = Simplex_tree::Filtration_value;
+  using Sparse_rips = Gudhi::rips_complex::Sparse_rips_complex<Filtration_value>;
+
+  Point points[] = {{1.0, 1.0}, {7.0, 0.0}, {4.0, 6.0}, {9.0, 6.0}, {0.0, 14.0}, {2.0, 19.0}, {9.0, 17.0}};
+
+  // ----------------------------------------------------------------------------
+  // Init from Euclidean points
+  // ----------------------------------------------------------------------------
+  double epsilon = 2;  // very rough, no guarantees
+  Sparse_rips sparse_rips(points, Gudhi::Euclidean_distance(), epsilon);
+
+  Simplex_tree stree;
+  sparse_rips.create_complex(stree, 10);
+
+  // ----------------------------------------------------------------------------
+  // Display information about the complex
+  // ----------------------------------------------------------------------------
+  std::cout << "Sparse Rips complex is of dimension " << stree.dimension() << " - " << stree.num_simplices()
+            << " simplices - " << stree.num_vertices() << " vertices." << std::endl;
+}
diff --git a/example/Rips_complex/one_skeleton_rips_from_correlation_matrix_for_doc.txt b/example/Rips_complex/one_skeleton_rips_from_correlation_matrix_for_doc.txt
new file mode 100644
index 00000000..640d7083
--- /dev/null
+++ b/example/Rips_complex/one_skeleton_rips_from_correlation_matrix_for_doc.txt
@@ -0,0 +1,17 @@
+Rips complex is of dimension 1 - 15 simplices - 5 vertices.
+Iterator on Rips complex simplices in the filtration order, with [filtration value]:
+   ( 0 ) -> [0] 
+   ( 1 ) -> [0] 
+   ( 2 ) -> [0] 
+   ( 3 ) -> [0] 
+   ( 4 ) -> [0] 
+   ( 4 0 ) -> [0.11] 
+   ( 2 1 ) -> [0.26] 
+   ( 3 2 ) -> [0.28] 
+   ( 4 3 ) -> [0.3] 
+   ( 4 1 ) -> [0.39] 
+   ( 2 0 ) -> [0.77] 
+   ( 1 0 ) -> [0.94] 
+   ( 4 2 ) -> [0.97] 
+   ( 3 0 ) -> [0.99] 
+   ( 3 1 ) -> [0.99] 
diff --git a/example/Simplex_tree/CMakeLists.txt b/example/Simplex_tree/CMakeLists.txt
index b33b2d05..857e8518 100644
--- a/example/Simplex_tree/CMakeLists.txt
+++ b/example/Simplex_tree/CMakeLists.txt
@@ -1,4 +1,3 @@
-cmake_minimum_required(VERSION 2.6)
 project(Simplex_tree_examples)
 
 add_executable ( Simplex_tree_example_from_cliques_of_graph simplex_tree_from_cliques_of_graph.cpp )
diff --git a/example/Simplex_tree/cech_complex_cgal_mini_sphere_3d.cpp b/example/Simplex_tree/cech_complex_cgal_mini_sphere_3d.cpp
index 9bd51106..08ed74bb 100644
--- a/example/Simplex_tree/cech_complex_cgal_mini_sphere_3d.cpp
+++ b/example/Simplex_tree/cech_complex_cgal_mini_sphere_3d.cpp
@@ -2,9 +2,9 @@
  *    (Geometric Understanding in Higher Dimensions) is a generic C++
  *    library for computational topology.
  *
- *    Author(s):       Clément Maria
+ *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+ *    Copyright (C) 2017 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
diff --git a/example/Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp b/example/Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp
index d8289ba9..290a9d9b 100644
--- a/example/Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp
+++ b/example/Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.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
diff --git a/example/Simplex_tree/graph_expansion_with_blocker.cpp b/example/Simplex_tree/graph_expansion_with_blocker.cpp
index 0d458cbd..f39de31f 100644
--- a/example/Simplex_tree/graph_expansion_with_blocker.cpp
+++ b/example/Simplex_tree/graph_expansion_with_blocker.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2014
+ *    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
@@ -29,33 +29,33 @@ using Simplex_handle = Simplex_tree::Simplex_handle;
 
 int main(int argc, char* const argv[]) {
   // Construct the Simplex Tree with a 1-skeleton graph example
-  Simplex_tree simplexTree;
+  Simplex_tree stree;
 
-  simplexTree.insert_simplex({0, 1}, 0.);
-  simplexTree.insert_simplex({0, 2}, 1.);
-  simplexTree.insert_simplex({0, 3}, 2.);
-  simplexTree.insert_simplex({1, 2}, 3.);
-  simplexTree.insert_simplex({1, 3}, 4.);
-  simplexTree.insert_simplex({2, 3}, 5.);
-  simplexTree.insert_simplex({2, 4}, 6.);
-  simplexTree.insert_simplex({3, 6}, 7.);
-  simplexTree.insert_simplex({4, 5}, 8.);
-  simplexTree.insert_simplex({4, 6}, 9.);
-  simplexTree.insert_simplex({5, 6}, 10.);
-  simplexTree.insert_simplex({6}, 10.);
+  stree.insert_simplex({0, 1}, 0.);
+  stree.insert_simplex({0, 2}, 1.);
+  stree.insert_simplex({0, 3}, 2.);
+  stree.insert_simplex({1, 2}, 3.);
+  stree.insert_simplex({1, 3}, 4.);
+  stree.insert_simplex({2, 3}, 5.);
+  stree.insert_simplex({2, 4}, 6.);
+  stree.insert_simplex({3, 6}, 7.);
+  stree.insert_simplex({4, 5}, 8.);
+  stree.insert_simplex({4, 6}, 9.);
+  stree.insert_simplex({5, 6}, 10.);
+  stree.insert_simplex({6}, 10.);
 
-  simplexTree.expansion_with_blockers(3, [&](Simplex_handle sh) {
+  stree.expansion_with_blockers(3, [&](Simplex_handle sh) {
     bool result = false;
     std::cout << "Blocker on [";
     // User can loop on the vertices from the given simplex_handle i.e.
-    for (auto vertex : simplexTree.simplex_vertex_range(sh)) {
+    for (auto vertex : stree.simplex_vertex_range(sh)) {
       // We block the expansion, if the vertex '6' is in the given list of vertices
       if (vertex == 6) result = true;
       std::cout << vertex << ", ";
     }
-    std::cout << "] ( " << simplexTree.filtration(sh);
+    std::cout << "] ( " << stree.filtration(sh);
     // User can re-assign a new filtration value directly in the blocker (default is the maximal value of boudaries)
-    simplexTree.assign_filtration(sh, simplexTree.filtration(sh) + 1.);
+    stree.assign_filtration(sh, stree.filtration(sh) + 1.);
 
     std::cout << " + 1. ) = " << result << std::endl;
 
@@ -63,13 +63,13 @@ int main(int argc, char* const argv[]) {
   });
 
   std::cout << "********************************************************************\n";
-  std::cout << "* The complex contains " << simplexTree.num_simplices() << " simplices";
-  std::cout << "   - dimension " << simplexTree.dimension() << "\n";
+  std::cout << "* The complex contains " << stree.num_simplices() << " simplices";
+  std::cout << "   - dimension " << stree.dimension() << "\n";
   std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n";
-  for (auto f_simplex : simplexTree.filtration_simplex_range()) {
+  for (auto f_simplex : stree.filtration_simplex_range()) {
     std::cout << "   "
-              << "[" << simplexTree.filtration(f_simplex) << "] ";
-    for (auto vertex : simplexTree.simplex_vertex_range(f_simplex)) std::cout << "(" << vertex << ")";
+              << "[" << stree.filtration(f_simplex) << "] ";
+    for (auto vertex : stree.simplex_vertex_range(f_simplex)) std::cout << "(" << vertex << ")";
     std::cout << std::endl;
   }
 
diff --git a/example/Simplex_tree/mini_simplex_tree.cpp b/example/Simplex_tree/mini_simplex_tree.cpp
index 19e45361..e7c7177f 100644
--- a/example/Simplex_tree/mini_simplex_tree.cpp
+++ b/example/Simplex_tree/mini_simplex_tree.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Marc Glisse
  *
- *    Copyright (C) 2015  INRIA Saclay - Ile-de-France (France)
+ *    Copyright (C) 2015 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
diff --git a/example/Simplex_tree/simple_simplex_tree.cpp b/example/Simplex_tree/simple_simplex_tree.cpp
index 828977c2..d71b5608 100644
--- a/example/Simplex_tree/simple_simplex_tree.cpp
+++ b/example/Simplex_tree/simple_simplex_tree.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2014
+ *    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
diff --git a/example/Simplex_tree/simplex_tree_from_cliques_of_graph.cpp b/example/Simplex_tree/simplex_tree_from_cliques_of_graph.cpp
index d1b8b2de..6d70f3d1 100644
--- a/example/Simplex_tree/simplex_tree_from_cliques_of_graph.cpp
+++ b/example/Simplex_tree/simplex_tree_from_cliques_of_graph.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Clément Maria
  *
- *    Copyright (C) 2014  INRIA
+ *    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
diff --git a/example/Skeleton_blocker/CMakeLists.txt b/example/Skeleton_blocker/CMakeLists.txt
index de70f089..0e5d2f11 100644
--- a/example/Skeleton_blocker/CMakeLists.txt
+++ b/example/Skeleton_blocker/CMakeLists.txt
@@ -1,4 +1,3 @@
-cmake_minimum_required(VERSION 2.6)
 project(Skeleton_blocker_examples)
 
 add_executable(Skeleton_blocker_example_from_simplices Skeleton_blocker_from_simplices.cpp)
diff --git a/example/Skeleton_blocker/Skeleton_blocker_from_simplices.cpp b/example/Skeleton_blocker/Skeleton_blocker_from_simplices.cpp
index 076c6a53..f288e39c 100644
--- a/example/Skeleton_blocker/Skeleton_blocker_from_simplices.cpp
+++ b/example/Skeleton_blocker/Skeleton_blocker_from_simplices.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA
+ *    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
diff --git a/example/Skeleton_blocker/Skeleton_blocker_iteration.cpp b/example/Skeleton_blocker/Skeleton_blocker_iteration.cpp
index 08ff0264..4d008450 100644
--- a/example/Skeleton_blocker/Skeleton_blocker_iteration.cpp
+++ b/example/Skeleton_blocker/Skeleton_blocker_iteration.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA
+ *    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
diff --git a/example/Skeleton_blocker/Skeleton_blocker_link.cpp b/example/Skeleton_blocker/Skeleton_blocker_link.cpp
index 58322038..2ec72128 100644
--- a/example/Skeleton_blocker/Skeleton_blocker_link.cpp
+++ b/example/Skeleton_blocker/Skeleton_blocker_link.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA
+ *    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
diff --git a/example/Spatial_searching/CMakeLists.txt b/example/Spatial_searching/CMakeLists.txt
index 4cf3d863..0f799987 100644
--- a/example/Spatial_searching/CMakeLists.txt
+++ b/example/Spatial_searching/CMakeLists.txt
@@ -1,4 +1,3 @@
-cmake_minimum_required(VERSION 2.6)
 project(Spatial_searching_examples)
 
 if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/example/Subsampling/CMakeLists.txt b/example/Subsampling/CMakeLists.txt
index 34400b1e..f26d107f 100644
--- a/example/Subsampling/CMakeLists.txt
+++ b/example/Subsampling/CMakeLists.txt
@@ -1,4 +1,3 @@
-cmake_minimum_required(VERSION 2.6)
 project(Subsampling_examples)
 
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/example/Tangential_complex/CMakeLists.txt b/example/Tangential_complex/CMakeLists.txt
index 16d1339d..af0dac51 100644
--- a/example/Tangential_complex/CMakeLists.txt
+++ b/example/Tangential_complex/CMakeLists.txt
@@ -1,4 +1,3 @@
-cmake_minimum_required(VERSION 2.6)
 project(Tangential_complex_examples)
 
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/example/Witness_complex/CMakeLists.txt b/example/Witness_complex/CMakeLists.txt
index a8231392..3d838c0d 100644
--- a/example/Witness_complex/CMakeLists.txt
+++ b/example/Witness_complex/CMakeLists.txt
@@ -1,4 +1,3 @@
-cmake_minimum_required(VERSION 2.6)
 project(Witness_complex_examples)
 
 add_executable ( Witness_complex_example_nearest_landmark_table example_nearest_landmark_table.cpp )
diff --git a/example/Witness_complex/example_nearest_landmark_table.cpp b/example/Witness_complex/example_nearest_landmark_table.cpp
index b8594212..acaf7c54 100644
--- a/example/Witness_complex/example_nearest_landmark_table.cpp
+++ b/example/Witness_complex/example_nearest_landmark_table.cpp
@@ -1,25 +1,3 @@
-/*    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):       Siargey Kachanovich
- *
- *    Copyright (C) 2016  INRIA (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/>.
- */
-
 #define BOOST_PARAMETER_MAX_ARITY 12
 
 #include <gudhi/Simplex_tree.h>
diff --git a/example/Witness_complex/example_strong_witness_complex_off.cpp b/example/Witness_complex/example_strong_witness_complex_off.cpp
index 346bef6d..19f73836 100644
--- a/example/Witness_complex/example_strong_witness_complex_off.cpp
+++ b/example/Witness_complex/example_strong_witness_complex_off.cpp
@@ -1,25 +1,3 @@
-/*    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):       Siargey Kachanovich
- *
- *    Copyright (C) 2016  INRIA (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/Euclidean_strong_witness_complex.h>
 #include <gudhi/pick_n_random_points.h>
diff --git a/example/Witness_complex/example_witness_complex_sphere.cpp b/example/Witness_complex/example_witness_complex_sphere.cpp
index a6e9b11a..9e3c972d 100644
--- a/example/Witness_complex/example_witness_complex_sphere.cpp
+++ b/example/Witness_complex/example_witness_complex_sphere.cpp
@@ -1,25 +1,3 @@
-/*    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):       Siargey Kachanovich
- *
- *    Copyright (C) 2016  INRIA (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/>.
- */
-
 #define BOOST_PARAMETER_MAX_ARITY 12
 
 #include <gudhi/Simplex_tree.h>
diff --git a/example/Witness_complex/generators.h b/example/Witness_complex/generators.h
index 7df43db5..4b755daa 100644
--- a/example/Witness_complex/generators.h
+++ b/example/Witness_complex/generators.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Siargey Kachanovich
  *
- *    Copyright (C) 2015  INRIA Sophia Antipolis-Méditerranée (France)
+ *    Copyright (C) 2015 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
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_
-#define EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_
+#ifndef GENERATORS_H_
+#define GENERATORS_H_
 
 #include <CGAL/Epick_d.h>
 #include <CGAL/point_generators_d.h>
@@ -163,4 +163,4 @@ void generate_points_torus(Point_Vector& W, int nbP, int dim) {
   }
 }
 
-#endif  // EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_
+#endif  // GENERATORS_H_
diff --git a/example/common/CMakeLists.txt b/example/common/CMakeLists.txt
index afe865d4..04015cdc 100644
--- a/example/common/CMakeLists.txt
+++ b/example/common/CMakeLists.txt
@@ -1,13 +1,21 @@
-cmake_minimum_required(VERSION 2.6)
 project(Common_examples)
 
 add_executable ( vector_double_off_reader example_vector_double_points_off_reader.cpp )
 target_link_libraries(vector_double_off_reader ${CGAL_LIBRARY})
+file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 add_test(NAME Common_example_vector_double_off_reader COMMAND $<TARGET_FILE:vector_double_off_reader>
-    "${CMAKE_SOURCE_DIR}/data/points/SO3_10000.off")
+    "alphacomplexdoc.off")
 
 install(TARGETS vector_double_off_reader DESTINATION bin)
 
+if (DIFF_PATH)
+  # Do not forget to copy test results files in current binary dir
+  file(COPY "vectordoubleoffreader_result.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+
+  add_test(Common_example_vector_double_off_reader_diff_files ${DIFF_PATH}
+      ${CMAKE_CURRENT_BINARY_DIR}/vectordoubleoffreader_result.txt ${CMAKE_CURRENT_BINARY_DIR}/alphacomplexdoc.off.txt)
+endif()
+
 if(CGAL_FOUND)
   add_executable ( cgal_3D_off_reader example_CGAL_3D_points_off_reader.cpp )
   target_link_libraries(cgal_3D_off_reader ${CGAL_LIBRARY})
diff --git a/example/common/example_CGAL_3D_points_off_reader.cpp b/example/common/example_CGAL_3D_points_off_reader.cpp
index 665b7a29..4658d8d5 100644
--- a/example/common/example_CGAL_3D_points_off_reader.cpp
+++ b/example/common/example_CGAL_3D_points_off_reader.cpp
@@ -20,12 +20,12 @@ int main(int argc, char **argv) {
     usage(argv[0]);
   }
 
-  std::string offInputFile(argv[1]);
+  std::string off_input_file(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);
+  Gudhi::Points_3D_off_reader<Point_3> off_reader(off_input_file);
   // Check the read operation was correct
   if (!off_reader.is_valid()) {
-    std::cerr << "Unable to read file " << offInputFile << std::endl;
+    std::cerr << "Unable to read file " << off_input_file << std::endl;
     usage(argv[0]);
   }
 
diff --git a/example/common/example_CGAL_points_off_reader.cpp b/example/common/example_CGAL_points_off_reader.cpp
index 8c6a6b54..f45683a5 100644
--- a/example/common/example_CGAL_points_off_reader.cpp
+++ b/example/common/example_CGAL_points_off_reader.cpp
@@ -22,12 +22,12 @@ int main(int argc, char **argv) {
     usage(argv[0]);
   }
 
-  std::string offInputFile(argv[1]);
+  std::string off_input_file(argv[1]);
   // Read the OFF file (input file name given as parameter) and triangulate points
-  Gudhi::Points_off_reader<Point_d> off_reader(offInputFile);
+  Gudhi::Points_off_reader<Point_d> off_reader(off_input_file);
   // Check the read operation was correct
   if (!off_reader.is_valid()) {
-    std::cerr << "Unable to read file " << offInputFile << std::endl;
+    std::cerr << "Unable to read file " << off_input_file << std::endl;
     usage(argv[0]);
   }
 
diff --git a/example/common/example_vector_double_points_off_reader.cpp b/example/common/example_vector_double_points_off_reader.cpp
index 8aecb26e..5093da85 100644
--- a/example/common/example_vector_double_points_off_reader.cpp
+++ b/example/common/example_vector_double_points_off_reader.cpp
@@ -17,25 +17,27 @@ int main(int argc, char **argv) {
     usage(argv[0]);
   }
 
-  std::string offInputFile(argv[1]);
+  std::string off_input_file(argv[1]);
   // Read the OFF file (input file name given as parameter) and triangulate points
-  Gudhi::Points_off_reader<Point_d> off_reader(offInputFile);
+  Gudhi::Points_off_reader<Point_d> off_reader(off_input_file);
   // Check the read operation was correct
   if (!off_reader.is_valid()) {
-    std::cerr << "Unable to read file " << offInputFile << std::endl;
+    std::cerr << "Unable to read file " << off_input_file << std::endl;
     usage(argv[0]);
   }
 
   // Retrieve the triangulation
   std::vector<Point_d> point_cloud = off_reader.get_point_cloud();
 
+  std::ofstream output_file(off_input_file + ".txt");
   int n {0};
   for (auto point : point_cloud) {
-    std::cout << "Point[" << n << "] = ";
+    output_file << "Point[" << n << "] = ";
     for (std::size_t i {0}; i < point.size(); i++)
-      std::cout << point[i] << " ";
-    std::cout << "\n";
+      output_file << point[i] << " ";
+    output_file << "\n";
     ++n;
   }
+  output_file.close();
   return 0;
 }
diff --git a/example/common/cgaloffreader_result.txt b/example/common/vectordoubleoffreader_result.txt
index 1deb8dbd..1deb8dbd 100644
--- a/example/common/cgaloffreader_result.txt
+++ b/example/common/vectordoubleoffreader_result.txt