adjacency lists can be directed, undirected or bidirectional for Simplex tree insert_graph method

Use of directed adjacency lists to fasten computation and use less memory


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/adjacency_list_direction_improvement@4061 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 839fabc15398ce590d09806bd783cd656029f3c1

6 files changed, 47 insertions, 27 deletions

diff --git a/src/Rips_complex/include/gudhi/Rips_complex.h b/src/Rips_complex/include/gudhi/Rips_complex.h
index f0fe57f4..e902e52c 100644
--- a/src/Rips_complex/include/gudhi/Rips_complex.h
+++ b/src/Rips_complex/include/gudhi/Rips_complex.h
@@ -59,7 +59,7 @@ class Rips_complex {
   /**
    * \brief Type of the one skeleton graph stored inside the Rips complex structure.
    */
-  typedef typename boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS
+  typedef typename boost::adjacency_list < boost::vecS, boost::vecS, boost::directedS
   , boost::property < vertex_filtration_t, Filtration_value >
   , boost::property < edge_filtration_t, Filtration_value >> OneSkeletonGraph;
 
diff --git a/src/Rips_complex/include/gudhi/Sparse_rips_complex.h b/src/Rips_complex/include/gudhi/Sparse_rips_complex.h
index 4dcc08ed..00da148f 100644
--- a/src/Rips_complex/include/gudhi/Sparse_rips_complex.h
+++ b/src/Rips_complex/include/gudhi/Sparse_rips_complex.h
@@ -55,7 +55,7 @@ template <typename Filtration_value>
 class Sparse_rips_complex {
  private:
   // TODO(MG): use a different graph where we know we can safely insert in parallel.
-  typedef typename boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS,
+  typedef typename boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS,
                                          boost::property<vertex_filtration_t, Filtration_value>,
                                          boost::property<edge_filtration_t, Filtration_value>>
       Graph;
diff --git a/src/Simplex_tree/example/cech_complex_cgal_mini_sphere_3d.cpp b/src/Simplex_tree/example/cech_complex_cgal_mini_sphere_3d.cpp
index 34092ef6..6bab8adb 100644
--- a/src/Simplex_tree/example/cech_complex_cgal_mini_sphere_3d.cpp
+++ b/src/Simplex_tree/example/cech_complex_cgal_mini_sphere_3d.cpp
@@ -50,7 +50,7 @@ using Vertex_handle = Simplex_tree::Vertex_handle;
 using Simplex_handle = Simplex_tree::Simplex_handle;
 using Filtration_value = Simplex_tree::Filtration_value;
 using Siblings = Simplex_tree::Siblings;
-using Graph_t = boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS,
+using Graph_t = boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS,
                                       boost::property<Gudhi::vertex_filtration_t, Filtration_value>,
                                       boost::property<Gudhi::edge_filtration_t, Filtration_value> >;
 using Edge_t = std::pair<Vertex_handle, Vertex_handle>;
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 78697ea2..4b18651c 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -1049,7 +1049,8 @@ class Simplex_tree {
    * boost::graph_traits<OneSkeletonGraph>::vertex_descriptor
    *                                    must be Vertex_handle.
    * boost::graph_traits<OneSkeletonGraph>::directed_category
-   *                                    must be undirected_tag.
+   *                                    can be directed_tag (the fastest, the least RAM use), undirected_tag or even
+   *                                    bidirected_tag.
    *
    * If an edge appears with multiplicity, the function will arbitrarily pick
    * one representative to read the filtration value.  */
@@ -1077,12 +1078,14 @@ class Simplex_tree {
                                   root_.members_.end(), *v_it,
                                   Node(&root_, boost::get(vertex_filtration_t(), skel_graph, *v_it)));
     }
-    typename boost::graph_traits<OneSkeletonGraph>::edge_iterator e_it,
-        e_it_end;
-    for (std::tie(e_it, e_it_end) = boost::edges(skel_graph); e_it != e_it_end;
-         ++e_it) {
-      auto u = source(*e_it, skel_graph);
-      auto v = target(*e_it, skel_graph);
+    std::pair<typename boost::graph_traits<OneSkeletonGraph>::edge_iterator,
+              typename boost::graph_traits<OneSkeletonGraph>::edge_iterator> boost_edges = boost::edges(skel_graph);
+    // boost_edges.first is the equivalent to boost_edges.begin()
+    // boost_edges.second is the equivalent to boost_edges.end()
+    for (; boost_edges.first != boost_edges.second; boost_edges.first++) {
+      auto edge = *(boost_edges.first);
+      auto u = source(edge, skel_graph);
+      auto v = target(edge, skel_graph);
       if (u == v) throw "Self-loops are not simplicial";
       // We cannot skip edges with the wrong orientation and expect them to
       // come a second time with the right orientation, that does not always
@@ -1098,7 +1101,7 @@ class Simplex_tree {
       }
 
       sh->second.children()->members().emplace(v,
-          Node(sh->second.children(), boost::get(edge_filtration_t(), skel_graph, *e_it)));
+          Node(sh->second.children(), boost::get(edge_filtration_t(), skel_graph, edge)));
     }
   }
 
diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
index f63ea080..0ae073ca 100644
--- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp
+++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
@@ -864,34 +864,51 @@ BOOST_AUTO_TEST_CASE(make_filtration_non_decreasing) {
   
 }
 
-BOOST_AUTO_TEST_CASE(insert_graph) {
+
+typedef boost::mpl::list<boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS,
+                                               boost::property<vertex_filtration_t, double>,
+                                               boost::property<edge_filtration_t, double>>,
+                         boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS,
+                                               boost::property<vertex_filtration_t, double>,
+                                               boost::property<edge_filtration_t, double>>,
+                         boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS,
+                                               boost::property<vertex_filtration_t, double>,
+                                               boost::property<edge_filtration_t, double>>> list_of_graph_variants;
+
+BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insert_graph, Graph, list_of_graph_variants) {
   std::cout << "********************************************************************" << std::endl;
   std::cout << "INSERT GRAPH" << std::endl;
-  typedef typename boost::adjacency_list<boost::vecS, boost::vecS,
-          boost::undirectedS,
-          boost::property<vertex_filtration_t, double>,
-          boost::property<edge_filtration_t, double>> Graph;
+
   Graph g(3);
   // filtration value 0 everywhere
   put(Gudhi::vertex_filtration_t(), g, 0, 0);
   put(Gudhi::vertex_filtration_t(), g, 1, 0);
   put(Gudhi::vertex_filtration_t(), g, 2, 0);
   // vertices don't always occur in sorted order
-  add_edge(0, 1, 0, g);
-  add_edge(2, 1, 0, g);
-  add_edge(2, 0, 0, g);
+  add_edge(0, 1, 1.1, g);
+  add_edge(2, 0, 2.2, g);
+  add_edge(2, 1, 3.3, g);
 
-  typedef Simplex_tree<> typeST;
-  typeST st1;
+  Simplex_tree<> st1;
   st1.insert_graph(g);
   BOOST_CHECK(st1.num_simplices() == 6);
 
   // edges can have multiplicity in the graph unless we replace the first vecS with (hash_)setS
-  add_edge(1, 0, 0, g);
-  add_edge(1, 2, 0, g);
-  add_edge(0, 2, 0, g);
-  add_edge(0, 2, 0, g);
-  typeST st2;
+  add_edge(1, 0, 1.1, g);
+  add_edge(1, 2, 3.3, g);
+  add_edge(0, 2, 2.2, g);
+  add_edge(0, 1, 1.1, g);
+  add_edge(2, 1, 3.3, g);
+  add_edge(2, 0, 2.2, g);
+  Simplex_tree<> st2;
   st2.insert_graph(g);
   BOOST_CHECK(st2.num_simplices() == 6);
+
+  std::cout << "st1 is" << std::endl;
+  std::cout << st1 << std::endl;
+
+  std::cout << "st2 is" << std::endl;
+  std::cout << st2 << std::endl;
+
+  BOOST_CHECK(st1 == st2);
 }
diff --git a/src/common/include/gudhi/graph_simplicial_complex.h b/src/common/include/gudhi/graph_simplicial_complex.h
index 49fe56cc..0d81ca71 100644
--- a/src/common/include/gudhi/graph_simplicial_complex.h
+++ b/src/common/include/gudhi/graph_simplicial_complex.h
@@ -49,7 +49,7 @@ struct vertex_filtration_t {
  *
  */
 template <typename SimplicialComplexForProximityGraph>
-using Proximity_graph = typename boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS
+using Proximity_graph = typename boost::adjacency_list < boost::vecS, boost::vecS, boost::directedS
 , boost::property < vertex_filtration_t, typename SimplicialComplexForProximityGraph::Filtration_value >
 , boost::property < edge_filtration_t, typename SimplicialComplexForProximityGraph::Filtration_value >>;