Merge remote-tracking branch 'origin/master' into insert

1 files changed, 42 insertions, 8 deletions

diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 9a4f2c34..6eafacb3 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -1063,8 +1063,8 @@ class Simplex_tree {
    *
    * Inserts all vertices and edges given by a OneSkeletonGraph.
    * OneSkeletonGraph must be a model of
-   * <a href="http://www.boost.org/doc/libs/1_65_1/libs/graph/doc/EdgeListGraph.html">boost::EdgeListGraph</a>
-   * and <a href="http://www.boost.org/doc/libs/1_65_1/libs/graph/doc/PropertyGraph.html">boost::PropertyGraph</a>.
+   * <a href="http://www.boost.org/doc/libs/1_76_0/libs/graph/doc/VertexAndEdgeListGraph.html">boost::VertexAndEdgeListGraph</a>
+   * and <a href="http://www.boost.org/doc/libs/1_76_0/libs/graph/doc/PropertyGraph.html">boost::PropertyGraph</a>.
    *
    * The vertex filtration value is accessible through the property tag
    * vertex_filtration_t.
@@ -1084,7 +1084,10 @@ class Simplex_tree {
     // the simplex tree must be empty
     assert(num_simplices() == 0);
 
-    if (boost::num_vertices(skel_graph) == 0) {
+    // is there a better way to let the compiler know that we don't mean Simplex_tree::num_vertices?
+    using boost::num_vertices;
+
+    if (num_vertices(skel_graph) == 0) {
       return;
     }
     if (num_edges(skel_graph) == 0) {
@@ -1093,18 +1096,18 @@ class Simplex_tree {
       dimension_ = 1;
     }
 
-    root_.members_.reserve(boost::num_vertices(skel_graph));
+    root_.members_.reserve(num_vertices(skel_graph));
 
     typename boost::graph_traits<OneSkeletonGraph>::vertex_iterator v_it,
         v_it_end;
-    for (std::tie(v_it, v_it_end) = boost::vertices(skel_graph); v_it != v_it_end;
+    for (std::tie(v_it, v_it_end) = vertices(skel_graph); v_it != v_it_end;
          ++v_it) {
       root_.members_.emplace_hint(
                                   root_.members_.end(), *v_it,
-                                  Node(&root_, boost::get(vertex_filtration_t(), skel_graph, *v_it)));
+                                  Node(&root_, get(vertex_filtration_t(), skel_graph, *v_it)));
     }
     std::pair<typename boost::graph_traits<OneSkeletonGraph>::edge_iterator,
-              typename boost::graph_traits<OneSkeletonGraph>::edge_iterator> boost_edges = boost::edges(skel_graph);
+              typename boost::graph_traits<OneSkeletonGraph>::edge_iterator> boost_edges = 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++) {
@@ -1126,7 +1129,7 @@ class Simplex_tree {
       }
 
       sh->second.children()->members().emplace(v,
-          Node(sh->second.children(), boost::get(edge_filtration_t(), skel_graph, edge)));
+          Node(sh->second.children(), get(edge_filtration_t(), skel_graph, edge)));
     }
   }
 
@@ -1670,6 +1673,37 @@ class Simplex_tree {
     return sh; // None of its faces has the same filtration.
   }
 
+ public:
+  /** \brief This function resets the filtration value of all the simplices of dimension at least min_dim. Resets all
+   * the Simplex_tree when `min_dim = 0`.
+   * `reset_filtration` may break the filtration property with `min_dim > 0`, and it is the user's responsibility to
+   * make it a valid filtration (using a large enough `filt_value`, or calling `make_filtration_non_decreasing`
+   * afterwards for instance).
+   * @param[in] filt_value The new filtration value.
+   * @param[in] min_dim The minimal dimension. Default value is 0.
+   */
+  void reset_filtration(Filtration_value filt_value, int min_dim = 0) {
+    rec_reset_filtration(&root_, filt_value, min_dim);
+    clear_filtration(); // Drop the cache.
+  }
+
+ private:
+  /** \brief Recursively resets filtration value when minimal depth <= 0.
+   * @param[in] sib Siblings to be parsed.
+   * @param[in] filt_value The new filtration value.
+   * @param[in] min_depth The minimal depth.
+   */
+  void rec_reset_filtration(Siblings * sib, Filtration_value filt_value, int min_depth) {
+    for (auto sh = sib->members().begin(); sh != sib->members().end(); ++sh) {
+      if (min_depth <= 0) {
+        sh->second.assign_filtration(filt_value);
+      }
+      if (has_children(sh)) {
+        rec_reset_filtration(sh->second.children(), filt_value, min_depth - 1);
+      }
+    }
+  }
+
  private:
   Vertex_handle null_vertex_;
   /** \brief Total number of simplices in the complex, without the empty simplex.*/