Merge last trunk modifications

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@3327 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 85b28237989b93fb4b5f8629a7f28bdb51b9a1b1

26 files changed, 326 insertions, 144 deletions

diff --git a/data/points/Kl.off b/data/points/Kl.off
index 911bcd23..8930a321 100644
--- a/data/points/Kl.off
+++ b/data/points/Kl.off
@@ -1,5 +1,5 @@
-OFF
-10000 0 0
+nOFF
+5 10000 0 0
 0.5 0 0 0 1 
 0.562791 0 0.125333 0 0.998027 
 0.625333 0 0.24869 0 0.992115 
diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h
index 63c6675c..91305032 100644
--- a/src/Alpha_complex/include/gudhi/Alpha_complex.h
+++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h
@@ -34,6 +34,7 @@
 #include <CGAL/Epick_d.h>
 #include <CGAL/Spatial_sort_traits_adapter_d.h>
 #include <CGAL/property_map.h>  // for CGAL::Identity_property_map
+#include <CGAL/NT_converter.h>
 
 #include <iostream>
 #include <vector>
@@ -323,8 +324,9 @@ class Alpha_complex {
             if (f_simplex_dim > 0) {
               // squared_radius function initialization
               Squared_Radius squared_radius = kernel_.compute_squared_radius_d_object();
+              CGAL::NT_converter<typename Geom_traits::FT, Filtration_value> cv;
 
-              alpha_complex_filtration = squared_radius(pointVector.begin(), pointVector.end());
+              alpha_complex_filtration = cv(squared_radius(pointVector.begin(), pointVector.end()));
             }
             complex.assign_filtration(f_simplex, alpha_complex_filtration);
 #ifdef DEBUG_TRACES
diff --git a/src/Alpha_complex/utilities/alphacomplex.md b/src/Alpha_complex/utilities/alphacomplex.md
index aace85d3..ede749a9 100644
--- a/src/Alpha_complex/utilities/alphacomplex.md
+++ b/src/Alpha_complex/utilities/alphacomplex.md
@@ -1,3 +1,13 @@
+---

+layout: page

+title: "Alpha complex"

+meta_title: "Alpha complex"

+teaser: ""

+permalink: /alphacomplex/

+---

+{::comment}

+Leave the lines above as it is required by the web site generator 'Jekyll'

+{:/comment}

 

 

 # Alpha complex #

diff --git a/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md b/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md
index 6e1b2578..a1bb9007 100644
--- a/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md
+++ b/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md
@@ -1,3 +1,13 @@
+---

+layout: page

+title: "Cubical complex"

+meta_title: "Cubical complex"

+teaser: ""

+permalink: /cubicalcomplex/

+---

+{::comment}

+Leave the lines above as it is required by the web site generator 'Jekyll'

+{:/comment}

 

 

 # Cubical complex#

diff --git a/src/Bottleneck_distance/utilities/bottleneckdistance.md b/src/Bottleneck_distance/utilities/bottleneckdistance.md
index 526f5822..f2749acc 100644
--- a/src/Bottleneck_distance/utilities/bottleneckdistance.md
+++ b/src/Bottleneck_distance/utilities/bottleneckdistance.md
@@ -1,3 +1,13 @@
+---

+layout: page

+title: "Bottleneck distance"

+meta_title: "Bottleneck distance"

+teaser: ""

+permalink: /bottleneckdistance/

+---

+{::comment}

+Leave the lines above as it is required by the web site generator 'Jekyll'

+{:/comment}

 

 

 # Bottleneck distance #

diff --git a/src/GudhUI/model/Model.h b/src/GudhUI/model/Model.h
index fc284cc6..072d1185 100644
--- a/src/GudhUI/model/Model.h
+++ b/src/GudhUI/model/Model.h
@@ -74,7 +74,7 @@ class CGAL_geometric_flag_complex_wrapper {
       // std::cout << "size:" << vertices.size() << std::endl;
       for (std::size_t i = 0; i < vertices.size(); ++i)
         for (std::size_t j = i + 1; j < vertices.size(); ++j)
-          complex_.add_edge(Vertex_handle(vertices[i]), Vertex_handle(vertices[j]));
+          complex_.add_edge_without_blockers(Vertex_handle(vertices[i]), Vertex_handle(vertices[j]));
     }
   }
 
diff --git a/src/GudhUI/utils/Critical_points.h b/src/GudhUI/utils/Critical_points.h
index 2a18e079..e7b9ef31 100644
--- a/src/GudhUI/utils/Critical_points.h
+++ b/src/GudhUI/utils/Critical_points.h
@@ -79,7 +79,7 @@ template<typename SkBlComplex> class Critical_points {
     unsigned pos = 0;
     for (Edge e : edges) {
       std::cout << "edge " << pos++ << "/" << edges.size() << "\n";
-      auto eh = filled_complex_.add_edge(e.first, e.second);
+      auto eh = filled_complex_.add_edge_without_blockers(e.first, e.second);
       int is_contractible(is_link_reducible(eh));
 
       switch (is_contractible) {
diff --git a/src/GudhUI/utils/K_nearest_builder.h b/src/GudhUI/utils/K_nearest_builder.h
index 7be0a4f4..4000a331 100644
--- a/src/GudhUI/utils/K_nearest_builder.h
+++ b/src/GudhUI/utils/K_nearest_builder.h
@@ -81,7 +81,7 @@ template<typename SkBlComplex> class K_nearest_builder {
       for (auto it = ++search.begin(); it != search.end(); ++it) {
         Vertex_handle q(std::get<1>(it->first));
         if (p != q && complex_.contains_vertex(p) && complex_.contains_vertex(q))
-          complex_.add_edge(p, q);
+          complex_.add_edge_without_blockers(p, q);
       }
     }
   }
diff --git a/src/GudhUI/utils/Rips_builder.h b/src/GudhUI/utils/Rips_builder.h
index b22f4db6..59b4bee2 100644
--- a/src/GudhUI/utils/Rips_builder.h
+++ b/src/GudhUI/utils/Rips_builder.h
@@ -60,7 +60,7 @@ template<typename SkBlComplex> class Rips_builder {
       std::cout.flush();
       for (auto q = p; ++q != vertices.end(); /**/)
         if (squared_eucl_distance(complex_.point(*p), complex_.point(*q)) < 4 * alpha * alpha)
-          complex_.add_edge(*p, *q);
+          complex_.add_edge_without_blockers(*p, *q);
     }
     std::cout << std::endl;
   }
diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h
index 40ff7a4a..f5b67be6 100644
--- a/src/Nerve_GIC/include/gudhi/GIC.h
+++ b/src/Nerve_GIC/include/gudhi/GIC.h
@@ -23,6 +23,11 @@
 #ifndef GIC_H_
 #define GIC_H_
 
+#ifdef GUDHI_USE_TBB
+#include <tbb/parallel_for.h>
+#include <tbb/mutex.h>
+#endif
+
 #include <gudhi/Debug_utils.h>
 #include <gudhi/graph_simplicial_complex.h>
 #include <gudhi/reader_utils.h>
@@ -99,9 +104,8 @@ class Cover_complex {
   int data_dimension;                           // dimension of input data.
   int n;                                        // number of points.
 
-  std::map<int, double> func;  // function used to compute the output simplicial complex.
-  std::map<int, double>
-      func_color;                 // function used to compute the colors of the nodes of the output simplicial complex.
+  std::vector<double> func;       // function used to compute the output simplicial complex.
+  std::vector<double> func_color; // function used to compute the colors of the nodes of the output simplicial complex.
   bool functional_cover = false;  // whether we use a cover with preimages of a function or not.
 
   Graph one_skeleton_OFF;          // one-skeleton given by the input OFF file (if it exists).
@@ -114,8 +118,8 @@ class Cover_complex {
   Persistence_diagram PD;
   std::vector<double> distribution;
 
-  std::map<int, std::vector<int> >
-      cover;  // function associating to each data point its vectors of cover elements to which it belongs.
+  std::vector<std::vector<int> >
+      cover;  // function associating to each data point the vector of cover elements to which it belongs.
   std::map<int, std::vector<int> >
       cover_back;  // inverse of cover, in order to get the data points associated to a specific cover element.
   std::map<int, double> cover_std;  // standard function (induced by func) used to compute the extended persistence
@@ -140,8 +144,8 @@ class Cover_complex {
 
   // Point comparator
   struct Less {
-    Less(std::map<int, double> func) { Fct = func; }
-    std::map<int, double> Fct;
+    Less(std::vector<double> func) { Fct = func; }
+    std::vector<double> Fct;
     bool operator()(int a, int b) {
       if (Fct[a] == Fct[b])
         return a < b;
@@ -276,6 +280,7 @@ class Cover_complex {
         point_cloud.emplace_back(point.begin(), point.begin() + data_dimension);
         boost::add_vertex(one_skeleton_OFF);
         vertices.push_back(boost::add_vertex(one_skeleton));
+        std::vector<int> dummy; dummy.clear(); cover.push_back(dummy);
         i++;
       }
     }
@@ -430,17 +435,29 @@ class Cover_complex {
 
     if (distances.size() == 0) compute_pairwise_distances(distance);
 
-    // #pragma omp parallel for
-    for (int i = 0; i < N; i++) {
-      SampleWithoutReplacement(n, m, samples);
-      double hausdorff_dist = 0;
-      for (int j = 0; j < n; j++) {
-        double mj = distances[j][samples[0]];
-        for (int k = 1; k < m; k++) mj = std::min(mj, distances[j][samples[k]]);
-        hausdorff_dist = std::max(hausdorff_dist, mj);
+    #ifdef GUDHI_USE_TBB
+      tbb::parallel_for(0, N, [&](int i){
+        SampleWithoutReplacement(n, m, samples);
+        double hausdorff_dist = 0;
+        for (int j = 0; j < n; j++) {
+          double mj = distances[j][samples[0]];
+          for (int k = 1; k < m; k++) mj = std::min(mj, distances[j][samples[k]]);
+          hausdorff_dist = std::max(hausdorff_dist, mj);
+        }
+        delta += hausdorff_dist / N;
+      });
+    #else
+      for (int i = 0; i < N; i++) {
+        SampleWithoutReplacement(n, m, samples);
+        double hausdorff_dist = 0;
+        for (int j = 0; j < n; j++) {
+          double mj = distances[j][samples[0]];
+          for (int k = 1; k < m; k++) mj = std::min(mj, distances[j][samples[k]]);
+          hausdorff_dist = std::max(hausdorff_dist, mj);
+        }
+        delta += hausdorff_dist / N;
       }
-      delta += hausdorff_dist / N;
-    }
+    #endif
 
     if (verbose) std::cout << "delta = " << delta << std::endl;
     set_graph_from_rips(delta, distance);
@@ -465,7 +482,7 @@ class Cover_complex {
     while (std::getline(input, line)) {
       std::stringstream stream(line);
       stream >> f;
-      func.emplace(i, f);
+      func.push_back(f);
       i++;
     }
     functional_cover = true;
@@ -479,7 +496,7 @@ class Cover_complex {
            *
            */
   void set_function_from_coordinate(int k) {
-    for (int i = 0; i < n; i++) func.emplace(i, point_cloud[i][k]);
+    for (int i = 0; i < n; i++) func.push_back(point_cloud[i][k]);
     functional_cover = true;
     cover_name = "coordinate " + std::to_string(k);
   }
@@ -492,7 +509,7 @@ class Cover_complex {
            */
   template <class InputRange>
   void set_function_from_range(InputRange const& function) {
-    for (int i = 0; i < n; i++) func.emplace(i, function[i]);
+    for (int i = 0; i < n; i++) func.push_back(function[i]);
     functional_cover = true;
   }
 
@@ -710,37 +727,69 @@ class Cover_complex {
       funcstd[i] = 0.5 * (u + v);
     }
 
-    if (verbose) std::cout << "Computing connected components..." << std::endl;
-    // #pragma omp parallel for
-    for (int i = 0; i < res; i++) {
-      // Compute connected components
-      Graph G = one_skeleton.create_subgraph();
-      int num = preimages[i].size();
-      std::vector<int> component(num);
-      for (int j = 0; j < num; j++) boost::add_vertex(index[vertices[preimages[i][j]]], G);
-      boost::connected_components(G, &component[0]);
-      int max = 0;
-
-      // For each point in preimage
-      for (int j = 0; j < num; j++) {
-        // Update number of components in preimage
-        if (component[j] > max) max = component[j];
-
-        // Identify component with Cantor polynomial N^2 -> N
-        int identifier = (std::pow(i + component[j], 2) + 3 * i + component[j]) / 2;
-
-        // Update covers
-        cover[preimages[i][j]].push_back(identifier);
-        cover_back[identifier].push_back(preimages[i][j]);
-        cover_fct[identifier] = i;
-        cover_std[identifier] = funcstd[i];
-        cover_color[identifier].second += func_color[preimages[i][j]];
-        cover_color[identifier].first += 1;
-      }
+    #ifdef GUDHI_USE_TBB
+      if (verbose) std::cout << "Computing connected components (parallelized)..." << std::endl;
+      tbb::parallel_for(0, res, [&](int i){
+        // Compute connected components
+        Graph G = one_skeleton.create_subgraph();
+        int num = preimages[i].size();
+        std::vector<int> component(num);
+        for (int j = 0; j < num; j++) boost::add_vertex(index[vertices[preimages[i][j]]], G);
+        boost::connected_components(G, &component[0]);
+        int max = 0;
+
+        // For each point in preimage
+        for (int j = 0; j < num; j++) {
+          // Update number of components in preimage
+          if (component[j] > max) max = component[j];
+
+          // Identify component with Cantor polynomial N^2 -> N
+          int identifier = ((i + component[j])*(i + component[j]) + 3 * i + component[j]) / 2;
+
+          // Update covers
+          cover[preimages[i][j]].push_back(identifier);
+          cover_back[identifier].push_back(preimages[i][j]);
+          cover_fct[identifier] = i;
+          cover_std[identifier] = funcstd[i];
+          cover_color[identifier].second += func_color[preimages[i][j]];
+          cover_color[identifier].first += 1;
+        }
 
-      // Maximal dimension is total number of connected components
-      id += max + 1;
-    }
+        // Maximal dimension is total number of connected components
+        id += max + 1;
+      });
+    #else
+      if (verbose) std::cout << "Computing connected components..." << std::endl;
+      for (int i = 0; i < res; i++) {
+        // Compute connected components
+        Graph G = one_skeleton.create_subgraph();
+        int num = preimages[i].size();
+        std::vector<int> component(num);
+        for (int j = 0; j < num; j++) boost::add_vertex(index[vertices[preimages[i][j]]], G);
+        boost::connected_components(G, &component[0]);
+        int max = 0;
+
+        // For each point in preimage
+        for (int j = 0; j < num; j++) {
+          // Update number of components in preimage
+          if (component[j] > max) max = component[j];
+
+          // Identify component with Cantor polynomial N^2 -> N
+          int identifier = (std::pow(i + component[j], 2) + 3 * i + component[j]) / 2;
+
+          // Update covers
+          cover[preimages[i][j]].push_back(identifier);
+          cover_back[identifier].push_back(preimages[i][j]);
+          cover_fct[identifier] = i;
+          cover_std[identifier] = funcstd[i];
+          cover_color[identifier].second += func_color[preimages[i][j]];
+          cover_color[identifier].first += 1;
+        }
+
+        // Maximal dimension is total number of connected components
+        id += max + 1;
+      }
+    #endif
 
     maximal_dim = id - 1;
     for (std::map<int, std::pair<int, double> >::iterator iit = cover_color.begin(); iit != cover_color.end(); iit++)
@@ -803,24 +852,46 @@ class Cover_complex {
     for (int j = 0; j < n; j++) mindist[j] = std::numeric_limits<double>::max();
 
     // Compute the geodesic distances to subsamples with Dijkstra
-    // #pragma omp parallel for
-    for (int i = 0; i < m; i++) {
-      if (verbose) std::cout << "Computing geodesic distances to seed " << i << "..." << std::endl;
-      int seed = voronoi_subsamples[i];
-      std::vector<double> dmap(n);
-      boost::dijkstra_shortest_paths(
-          one_skeleton, vertices[seed],
-          boost::weight_map(weight).distance_map(boost::make_iterator_property_map(dmap.begin(), index)));
-
-      for (int j = 0; j < n; j++)
-        if (mindist[j] > dmap[j]) {
-          mindist[j] = dmap[j];
-          if (cover[j].size() == 0)
-            cover[j].push_back(i);
-          else
-            cover[j][0] = i;
-        }
-    }
+    #ifdef GUDHI_USE_TBB
+      if (verbose) std::cout << "Computing geodesic distances (parallelized)..." << std::endl;
+      tbb::mutex coverMutex; tbb::mutex mindistMutex;
+      tbb::parallel_for(0, m, [&](int i){
+        int seed = voronoi_subsamples[i];
+        std::vector<double> dmap(n);
+        boost::dijkstra_shortest_paths(
+            one_skeleton, vertices[seed],
+            boost::weight_map(weight).distance_map(boost::make_iterator_property_map(dmap.begin(), index)));
+
+        coverMutex.lock(); mindistMutex.lock();
+        for (int j = 0; j < n; j++)
+          if (mindist[j] > dmap[j]) {
+            mindist[j] = dmap[j];
+            if (cover[j].size() == 0)
+              cover[j].push_back(i);
+            else
+              cover[j][0] = i;
+          }
+        coverMutex.unlock(); mindistMutex.unlock();
+      });
+    #else
+      for (int i = 0; i < m; i++) {
+        if (verbose) std::cout << "Computing geodesic distances to seed " << i << "..." << std::endl;
+        int seed = voronoi_subsamples[i];
+        std::vector<double> dmap(n);
+        boost::dijkstra_shortest_paths(
+            one_skeleton, vertices[seed],
+            boost::weight_map(weight).distance_map(boost::make_iterator_property_map(dmap.begin(), index)));
+
+        for (int j = 0; j < n; j++)
+          if (mindist[j] > dmap[j]) {
+            mindist[j] = dmap[j];
+            if (cover[j].size() == 0)
+              cover[j].push_back(i);
+            else
+              cover[j][0] = i;
+          }
+      }
+    #endif
 
     for (int i = 0; i < n; i++) {
       cover_back[cover[i][0]].push_back(i);
@@ -860,7 +931,7 @@ class Cover_complex {
     while (std::getline(input, line)) {
       std::stringstream stream(line);
       stream >> f;
-      func_color.emplace(i, f);
+      func_color.push_back(f);
       i++;
     }
     color_name = color_file_name;
@@ -873,7 +944,7 @@ class Cover_complex {
            *
            */
   void set_color_from_coordinate(int k = 0) {
-    for (int i = 0; i < n; i++) func_color[i] = point_cloud[i][k];
+    for (int i = 0; i < n; i++) func_color.push_back(point_cloud[i][k]);
     color_name = "coordinate ";
     color_name.append(std::to_string(k));
   }
@@ -885,7 +956,7 @@ class Cover_complex {
    *
    */
   void set_color_from_vector(std::vector<double> color) {
-    for (unsigned int i = 0; i < color.size(); i++) func_color[i] = color[i];
+    for (unsigned int i = 0; i < color.size(); i++) func_color.push_back(color[i]);
   }
 
  public:  // Create a .dot file that can be compiled with neato to produce a .pdf file.
@@ -1039,45 +1110,29 @@ class Cover_complex {
       minf = std::min(minf, it->second);
     }
 
+    // Build filtration
     for (auto const& simplex : simplices) {
-      // Add a simplex and a cone on it
-      std::vector<int> splx = simplex;
-      splx.push_back(-2);
-      st.insert_simplex_and_subfaces(splx);
+      std::vector<int> splx = simplex; splx.push_back(-2);
+      st.insert_simplex_and_subfaces(splx, -3);
     }
 
-    // Build filtration
-    for (auto simplex : st.complex_simplex_range()) {
-      double filta = std::numeric_limits<double>::lowest();
-      double filts = filta;
-      bool ascending = true;
-      for (auto vertex : st.simplex_vertex_range(simplex)) {
-        if (vertex == -2) {
-          ascending = false;
-          continue;
-        }
-        filta = std::max(-2 + (cover_std[vertex] - minf) / (maxf - minf), filta);
-        filts = std::max(2 - (cover_std[vertex] - minf) / (maxf - minf), filts);
-      }
-      if (ascending)
-        st.assign_filtration(simplex, filta);
-      else
-        st.assign_filtration(simplex, filts);
+    for (std::map<int, double>::iterator it = cover_std.begin(); it != cover_std.end(); it++) {
+      int vertex = it->first; float val = it->second;
+      int vert[] = {vertex}; int edge[] = {vertex, -2};
+      st.assign_filtration(st.find(vert), -2 + (val - minf)/(maxf - minf));
+      st.assign_filtration(st.find(edge),  2 - (val - minf)/(maxf - minf));
     }
-    int magic[] = {-2};
-    st.assign_filtration(st.find(magic), -3);
+    st.make_filtration_non_decreasing();
 
     // Compute PD
-    st.initialize_filtration();
-    Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Gudhi::persistent_cohomology::Field_Zp> pcoh(st);
-    pcoh.init_coefficients(2);
+    Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Gudhi::persistent_cohomology::Field_Zp> pcoh(st); pcoh.init_coefficients(2);
     pcoh.compute_persistent_cohomology();
 
     // Output PD
     int max_dim = st.dimension();
     for (int i = 0; i < max_dim; i++) {
       std::vector<std::pair<double, double> > bars = pcoh.intervals_in_dimension(i);
-      int num_bars = bars.size();
+      int num_bars = bars.size(); if(i == 0)  num_bars -= 1;
       if(verbose)  std::cout << num_bars << " interval(s) in dimension " << i << ":" << std::endl;
       for (int j = 0; j < num_bars; j++) {
         double birth = bars[j].first;
@@ -1206,8 +1261,7 @@ class Cover_complex {
     }
 
     if (type == "Nerve") {
-      for(auto& simplex : cover)
-        simplices.push_back(simplex.second);
+      for(int i = 0; i < n; i++)  simplices.push_back(cover[i]);
       std::sort(simplices.begin(), simplices.end());
       std::vector<std::vector<int> >::iterator it = std::unique(simplices.begin(), simplices.end());
       simplices.resize(std::distance(simplices.begin(), it));
diff --git a/src/Nerve_GIC/test/test_GIC.cpp b/src/Nerve_GIC/test/test_GIC.cpp
index d633753c..e3067d35 100644
--- a/src/Nerve_GIC/test/test_GIC.cpp
+++ b/src/Nerve_GIC/test/test_GIC.cpp
@@ -39,6 +39,7 @@ BOOST_AUTO_TEST_CASE(check_nerve) {
   N.set_type("Nerve");
   std::string cloud_file_name("data/cloud");
   N.read_point_cloud(cloud_file_name);
+  N.set_color_from_coordinate();
   std::string graph_file_name("data/graph");
   N.set_graph_from_file(graph_file_name);
   std::string cover_file_name("data/cover");
@@ -58,6 +59,7 @@ BOOST_AUTO_TEST_CASE(check_GIC) {
   GIC.set_type("GIC");
   std::string cloud_file_name("data/cloud");
   GIC.read_point_cloud(cloud_file_name);
+  GIC.set_color_from_coordinate();
   std::string graph_file_name("data/graph");
   GIC.set_graph_from_file(graph_file_name);
   std::string cover_file_name("data/cover");
@@ -77,6 +79,7 @@ BOOST_AUTO_TEST_CASE(check_voronoiGIC) {
   GIC.set_type("GIC");
   std::string cloud_file_name("data/cloud");
   GIC.read_point_cloud(cloud_file_name);
+  GIC.set_color_from_coordinate();
   std::string graph_file_name("data/graph");
   GIC.set_graph_from_file(graph_file_name);
   GIC.set_cover_from_Voronoi(Gudhi::Euclidean_distance(), 2);
diff --git a/src/Nerve_GIC/utilities/covercomplex.md b/src/Nerve_GIC/utilities/covercomplex.md
index f33cb2e0..6d16d16f 100644
--- a/src/Nerve_GIC/utilities/covercomplex.md
+++ b/src/Nerve_GIC/utilities/covercomplex.md
@@ -1,3 +1,13 @@
+---
+layout: page
+title: "Cover complex"
+meta_title: "Cover complex"
+teaser: ""
+permalink: /covercomplex/
+---
+{::comment}
+Leave the lines above as it is required by the web site generator 'Jekyll'
+{:/comment}
 
 
 # Cover complex #
diff --git a/src/Persistent_cohomology/concept/FilteredComplex.h b/src/Persistent_cohomology/concept/FilteredComplex.h
index c19698df..d6b662e9 100644
--- a/src/Persistent_cohomology/concept/FilteredComplex.h
+++ b/src/Persistent_cohomology/concept/FilteredComplex.h
@@ -31,7 +31,7 @@ struct FilteredComplex
   typedef unspecified      Simplex_handle;
 /** \brief Key associated to each simplex. 
   *
-  * Must be a signed integer type. */
+  * Must be an integer type. */
   typedef unspecified      Simplex_key;
 /** \brief Type for the value of the filtration function.
   *
@@ -67,8 +67,8 @@ struct FilteredComplex
   Simplex_key              key      ( Simplex_handle sh );
 /** \brief Returns the simplex that has index idx in the filtration.
  *
- * This is never called on null_key(). */
-  Simplex_handle           simplex  ( Simplex_key idx );
+ * This is only called on valid indices. */
+  Simplex_handle           simplex  ( size_t idx );
 /** \brief Assign a key to a simplex. */
   void                     assign_key(Simplex_handle sh, Simplex_key key);
  
diff --git a/src/Rips_complex/utilities/ripscomplex.md b/src/Rips_complex/utilities/ripscomplex.md
index 857e6293..d4dbc36e 100644
--- a/src/Rips_complex/utilities/ripscomplex.md
+++ b/src/Rips_complex/utilities/ripscomplex.md
@@ -1,3 +1,13 @@
+---
+layout: page
+title: "Rips complex"
+meta_title: "Rips complex"
+teaser: ""
+permalink: /ripscomplex/
+---
+{::comment}
+Leave the lines above as it is required by the web site generator 'Jekyll'
+{:/comment}
 
 
 # Rips complex #
diff --git a/src/Witness_complex/utilities/witnesscomplex.md b/src/Witness_complex/utilities/witnesscomplex.md
index 2341759b..3be9bc55 100644
--- a/src/Witness_complex/utilities/witnesscomplex.md
+++ b/src/Witness_complex/utilities/witnesscomplex.md
@@ -1,3 +1,13 @@
+---

+layout: page

+title: "Witness complex"

+meta_title: "Witness complex"

+teaser: ""

+permalink: /witnesscomplex/

+---

+{::comment}

+Leave the lines above as it is required by the web site generator 'Jekyll'

+{:/comment}

 

 

 # Witness complex #

diff --git a/src/common/doc/header.html b/src/common/doc/header.html
index d69b28fa..2f54e68d 100644
--- a/src/common/doc/header.html
+++ b/src/common/doc/header.html
@@ -9,7 +9,7 @@
 <!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME-->
 <!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME-->
 <!-- GUDHI website css for header BEGIN -->
-<link rel="stylesheet" type="text/css" href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/gudhi-doc-2.0.0/assets/css/styles_feeling_responsive.css" />
+<link rel="stylesheet" type="text/css" href="http://gudhi.gforge.inria.fr/assets/css/styles_feeling_responsive.css" />
 <!-- GUDHI website css for header END -->
 <link href="$relpath^tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="$relpath^jquery.js"></script>
diff --git a/src/common/doc/offline_header.html b/src/common/doc/offline_header.html
new file mode 100644
index 00000000..6a02a895
--- /dev/null
+++ b/src/common/doc/offline_header.html
@@ -0,0 +1,41 @@
+<!-- HTML header for doxygen 1.8.6-->
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!-- GUDHI website : class="no-js" lang="en" is necessary -->
+<html xmlns="http://www.w3.org/1999/xhtml" class="no-js" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen $doxygenversion"/>
+<!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME-->
+<!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME-->
+<!-- GUDHI website css for header END -->
+<link href="$relpath^tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="$relpath^jquery.js"></script>
+<script type="text/javascript" src="$relpath^dynsections.js"></script>
+$treeview
+$search
+$mathjax
+<link href="$relpath^$stylesheet" rel="stylesheet" type="text/css" />
+$extrastylesheet
+</head>
+<body>
+
+
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+
+<!--BEGIN TITLEAREA-->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 30px;">
+  <!--BEGIN DISABLE_INDEX-->
+   <!--BEGIN SEARCHENGINE-->
+   <td>$searchbox</td>
+   <!--END SEARCHENGINE-->
+  <!--END DISABLE_INDEX-->
+ </tr>
+ </tbody>
+</table>
+</div>
+<!--END TITLEAREA-->
+<!-- end header part -->
diff --git a/src/common/example/CMakeLists.txt b/src/common/example/CMakeLists.txt
index afe865d4..1273c699 100644
--- a/src/common/example/CMakeLists.txt
+++ b/src/common/example/CMakeLists.txt
@@ -3,11 +3,20 @@ 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/src/common/example/example_CGAL_3D_points_off_reader.cpp b/src/common/example/example_CGAL_3D_points_off_reader.cpp
index 665b7a29..4658d8d5 100644
--- a/src/common/example/example_CGAL_3D_points_off_reader.cpp
+++ b/src/common/example/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/src/common/example/example_CGAL_points_off_reader.cpp b/src/common/example/example_CGAL_points_off_reader.cpp
index 8c6a6b54..f45683a5 100644
--- a/src/common/example/example_CGAL_points_off_reader.cpp
+++ b/src/common/example/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/src/common/example/example_vector_double_points_off_reader.cpp b/src/common/example/example_vector_double_points_off_reader.cpp
index 8aecb26e..5093da85 100644
--- a/src/common/example/example_vector_double_points_off_reader.cpp
+++ b/src/common/example/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/src/common/example/cgaloffreader_result.txt b/src/common/example/vectordoubleoffreader_result.txt
index 1deb8dbd..1deb8dbd 100644
--- a/src/common/example/cgaloffreader_result.txt
+++ b/src/common/example/vectordoubleoffreader_result.txt
diff --git a/src/common/include/gudhi/Off_reader.h b/src/common/include/gudhi/Off_reader.h
index 4fcd2af2..32320e4d 100644
--- a/src/common/include/gudhi/Off_reader.h
+++ b/src/common/include/gudhi/Off_reader.h
@@ -105,25 +105,26 @@ class Off_reader {
     bool is_off_file = (line.find("OFF") != std::string::npos);
     bool is_noff_file = (line.find("nOFF") != std::string::npos);
 
+
+
     if (!is_off_file && !is_noff_file) {
       std::cerr << line << std::endl;
       std::cerr << "missing off header\n";
       return false;
     }
 
+    if (is_noff_file) {
+      // Should be on a separate line, but we accept it on the same line as the number of vertices
+      stream_ >> off_info_.dim;
+    } else {
+      off_info_.dim = 3;
+    }
+
     if (!goto_next_uncomment_line(line)) return false;
     std::istringstream iss(line);
-    if ((is_off_file) && (!is_noff_file)) {
-      off_info_.dim = 3;
-      if (!(iss >> off_info_.num_vertices >> off_info_.num_faces >> off_info_.num_edges)) {
-        std::cerr << "incorrect number of vertices/faces/edges\n";
-        return false;
-      }
-    } else {
-      if (!(iss >> off_info_.dim >> off_info_.num_vertices >> off_info_.num_faces >> off_info_.num_edges)) {
+    if (!(iss >> off_info_.num_vertices >> off_info_.num_faces >> off_info_.num_edges)) {
       std::cerr << "incorrect number of vertices/faces/edges\n";
       return false;
-      }
     }
     off_visitor.init(off_info_.dim, off_info_.num_vertices, off_info_.num_faces, off_info_.num_edges);
 
@@ -131,10 +132,12 @@ class Off_reader {
   }
 
   bool goto_next_uncomment_line(std::string& uncomment_line) {
-    uncomment_line.clear();
-    do
-      std::getline(stream_, uncomment_line); while (uncomment_line[0] == '%');
-    return (uncomment_line.size() > 0 && uncomment_line[0] != '%');
+    do {
+      // skip whitespace, including empty lines
+      if (!std::ifstream::sentry(stream_)) return false;
+      std::getline(stream_, uncomment_line);
+    } while (uncomment_line[0] == '#');
+    return (bool)stream_;
   }
 
   template<typename OffVisitor>
diff --git a/src/common/include/gudhi/Points_off_io.h b/src/common/include/gudhi/Points_off_io.h
index 29af8a8a..08f324c6 100644
--- a/src/common/include/gudhi/Points_off_io.h
+++ b/src/common/include/gudhi/Points_off_io.h
@@ -126,9 +126,9 @@ class Points_off_visitor_reader {
  * \code $> ./vector_double_off_reader ../../data/points/alphacomplexdoc.off
  * \endcode
  *
- * the program output is:
+ * the program outputs a file ../../data/points/alphacomplexdoc.off.txt:
  * 
- * \include common/cgaloffreader_result.txt
+ * \include common/vectordoubleoffreader_result.txt
  */
 template<typename Point_d>
 class Points_off_reader {
diff --git a/src/common/utilities/pointsetgenerator.md b/src/common/utilities/pointsetgenerator.md
index 284715d4..3b23e668 100644
--- a/src/common/utilities/pointsetgenerator.md
+++ b/src/common/utilities/pointsetgenerator.md
@@ -1,6 +1,16 @@
-
-
-# common #
+---
+layout: page
+title: "OFF point set generator"
+meta_title: "OFF point set generator"
+teaser: ""
+permalink: /pointsetgenerator/
+---
+{::comment}
+Leave the lines above as it is required by the web site generator 'Jekyll'
+{:/comment}
+
+
+# Miscellaneous #
 
 ## off_file_from_shape_generator ##
 
diff --git a/src/cython/example/bottleneck_basic_example.py b/src/cython/example/bottleneck_basic_example.py
index 31cecb29..a7fa01c1 100755
--- a/src/cython/example/bottleneck_basic_example.py
+++ b/src/cython/example/bottleneck_basic_example.py
@@ -28,8 +28,6 @@ __author__ = "Francois Godi, Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 INRIA"
 __license__ = "GPL v3"
 
-import gudhi
-
 diag1 = [[2.7, 3.7],[9.6, 14.],[34.2, 34.974], [3.,float('Inf')]]
 
 diag2 = [[2.8, 4.45],[9.5, 14.1],[3.2,float('Inf')]]