Merge master and resolve commits

6 files changed, 112 insertions, 93 deletions

diff --git a/src/Simplex_tree/doc/Intro_simplex_tree.h b/src/Simplex_tree/doc/Intro_simplex_tree.h
index 800879fe..ef8dec91 100644
--- a/src/Simplex_tree/doc/Intro_simplex_tree.h
+++ b/src/Simplex_tree/doc/Intro_simplex_tree.h
@@ -39,10 +39,10 @@ namespace Gudhi {
  * \subsubsection filteredcomplexessimplextreeexamples Examples
  * 
  * Here is a list of simplex tree examples :
- * \li <a href="_simplex_tree_2simple_simplex_tree_8cpp-example.html">
+ * \li <a href="simple_simplex_tree_8cpp-example.html">
  * Simplex_tree/simple_simplex_tree.cpp</a> - Simple simplex tree construction and basic function use.
  *
- * \li <a href="_simplex_tree_2simplex_tree_from_cliques_of_graph_8cpp-example.html">
+ * \li <a href="simplex_tree_from_cliques_of_graph_8cpp-example.html">
  * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp</a> - Simplex tree construction from cliques of graph read in
  * a file.
  * 
@@ -54,11 +54,11 @@ Expand the simplex tree in 3.8e-05 s.
 Information of the Simplex Tree: 
 Number of vertices = 10   Number of simplices = 98 \endcode
  * 
- * \li <a href="_simplex_tree_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html">
+ * \li <a href="example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html">
  * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a> - Simplex tree is computed and displayed
  * from a 3D alpha complex (Requires CGAL, GMP and GMPXX to be installed).
  * 
- * \li <a href="_simplex_tree_2graph_expansion_with_blocker_8cpp-example.html">
+ * \li <a href="graph_expansion_with_blocker_8cpp-example.html">
  * Simplex_tree/graph_expansion_with_blocker.cpp</a> - Simple simplex tree construction from a one-skeleton graph with
  * a simple blocker expansion method.
  *
diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt
index a0aabee2..81d352fc 100644
--- a/src/Simplex_tree/example/CMakeLists.txt
+++ b/src/Simplex_tree/example/CMakeLists.txt
@@ -29,18 +29,20 @@ if(GMP_FOUND AND NOT CGAL_VERSION VERSION_LESS 4.11.0)
     target_link_libraries(Simplex_tree_example_alpha_shapes_3_from_off ${TBB_LIBRARIES})
   endif()
   add_test(NAME Simplex_tree_example_alpha_shapes_3_from_off COMMAND $<TARGET_FILE:Simplex_tree_example_alpha_shapes_3_from_off>
-      "${CMAKE_SOURCE_DIR}/data/points/bunny_5000.off")
+      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off")
 
 endif()
 
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
-  add_executable ( Simplex_tree_example_cech_complex_cgal_mini_sphere_3d cech_complex_cgal_mini_sphere_3d.cpp )
-  target_link_libraries(Simplex_tree_example_cech_complex_cgal_mini_sphere_3d Boost::program_options ${CGAL_LIBRARY})
-  if (TBB_FOUND)
-    target_link_libraries(Simplex_tree_example_cech_complex_cgal_mini_sphere_3d ${TBB_LIBRARIES})
+  if(TARGET Boost::program_options)
+    add_executable ( Simplex_tree_example_cech_complex_cgal_mini_sphere_3d cech_complex_cgal_mini_sphere_3d.cpp )
+    target_link_libraries(Simplex_tree_example_cech_complex_cgal_mini_sphere_3d Boost::program_options ${CGAL_LIBRARY})
+    if (TBB_FOUND)
+      target_link_libraries(Simplex_tree_example_cech_complex_cgal_mini_sphere_3d ${TBB_LIBRARIES})
+    endif()
+    add_test(NAME Simplex_tree_example_cech_complex_cgal_mini_sphere_3d COMMAND $<TARGET_FILE:Simplex_tree_example_cech_complex_cgal_mini_sphere_3d>
+        "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" -r 0.3 -d 3)
   endif()
-  add_test(NAME Simplex_tree_example_cech_complex_cgal_mini_sphere_3d COMMAND $<TARGET_FILE:Simplex_tree_example_cech_complex_cgal_mini_sphere_3d>
-      "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" -r 0.3 -d 3)
 endif ()
 
 add_executable ( Simplex_tree_example_graph_expansion_with_blocker graph_expansion_with_blocker.cpp )
diff --git a/src/Simplex_tree/example/README b/src/Simplex_tree/example/README
deleted file mode 100644
index a9498173..00000000
--- a/src/Simplex_tree/example/README
+++ /dev/null
@@ -1,73 +0,0 @@
-To build the example, run in a Terminal:
-
-cd /path-to-gudhi/
-cmake .
-cd /path-to-example/
-make
-
-
-Example of use :
-
-*** Simple simplex tree construction
-
-./Simplex_tree_example_simple_simplex_tree
-
-********************************************************************
-EXAMPLE OF SIMPLE INSERTION
-   * INSERT 0
-   + 0 INSERTED
-   * INSERT 1
-   + 1 INSERTED
-   * INSERT (0,1)
-   + (0,1) INSERTED
-   * INSERT 2
-   + 2 INSERTED
-   * INSERT (2,0)
-   + (2,0) INSERTED
-   * INSERT (2,1)
-   + (2,1) INSERTED
-   * INSERT (2,1,0)
-   + (2,1,0) INSERTED
-   * INSERT 3
-   + 3 INSERTED
-   * INSERT (3,0)
-   + (3,0) INSERTED
-   * INSERT 0 (already inserted)
-   - 0 NOT INSERTED
-   * INSERT (2,1,0) (already inserted)
-   - (2,1,0) NOT INSERTED
-********************************************************************
-* The complex contains 9 simplices
-   - dimension 2   - filtration 0.4
-* Iterator on Simplices in the filtration, with [filtration value]:
-   [0.1] 0 
-   [0.1] 1 
-   [0.1] 2 
-   [0.1] 3 
-   [0.2] 1 0 
-   [0.2] 2 0 
-   [0.2] 2 1 
-   [0.2] 3 0 
-   [0.3] 2 1 0 
-
-*** Simplex tree construction with Z/2Z coefficients on weighted graph Klein bottle file:
-
-./Simplex_tree_example_from_cliques_of_graph ../../../data/points/Klein_bottle_complex.txt 2
-Insert the 1-skeleton in the simplex tree in 0 s. 
-Expand the simplex tree in 0 s. 
-Information of the Simplex Tree: 
-  Number of vertices = 10   Number of simplices = 82
-
-with Z/3Z coefficients:
-
-./Simplex_tree_example_from_cliques_of_graph ../../../data/points/Klein_bottle_complex.txt 3
-
-Insert the 1-skeleton in the simplex tree in 0 s.
-Expand the simplex tree in 0 s.
-Information of the Simplex Tree:
-  Number of vertices = 10   Number of simplices = 106
-
-*** Simplex_tree computed and displayed from a 3D alpha complex:
-    [ Requires CGAL, GMP and GMPXX to be installed]
-
-./Simplex_tree_example_alpha_shapes_3_from_off ../../../data/points/bunny_5000
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 889dbd00..85790baf 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -1060,8 +1060,8 @@ 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.
@@ -1081,7 +1081,10 @@ 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) {
@@ -1090,18 +1093,18 @@ 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++) {
@@ -1123,7 +1126,7 @@ 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)));
     }
   }
 
@@ -1667,6 +1670,37 @@ 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.*/
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h
index 9007b6bd..e5522cc7 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h
@@ -14,7 +14,6 @@
 #include <gudhi/Debug_utils.h>
 
 #include <boost/iterator/iterator_facade.hpp>
-#include <boost/version.hpp>
 #include <boost/container/static_vector.hpp>
 
 #include <vector>
@@ -85,6 +84,12 @@ class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade<
   typedef typename SimplexTree::Vertex_handle Vertex_handle;
   typedef typename SimplexTree::Siblings Siblings;
 
+  // For cython purpose only. The object it initializes should be overwritten ASAP and never used before it is overwritten.
+  Simplex_tree_boundary_simplex_iterator()
+      : sib_(nullptr),
+        st_(nullptr)  {
+  }
+
 // any end() iterator
   explicit Simplex_tree_boundary_simplex_iterator(SimplexTree * st)
       : last_(st->null_vertex()),
diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
index 9b5fa8fe..bdd41d34 100644
--- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp
+++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
@@ -940,3 +940,54 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(generators, typeST, list_of_tested_variants) {
     BOOST_CHECK(st.edge_with_same_filtration(st.find({1,5}))==st.find({1,5}));
   }
 }
+
+BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_reset_filtration, typeST, list_of_tested_variants) {
+  std::clog << "********************************************************************" << std::endl;
+  std::clog << "TEST RESET FILTRATION" << std::endl;
+  typeST st;
+
+  st.insert_simplex_and_subfaces({2, 1, 0}, 3.);
+  st.insert_simplex_and_subfaces({3, 0}, 2.);
+  st.insert_simplex_and_subfaces({3, 4, 5}, 3.);
+  st.insert_simplex_and_subfaces({0, 1, 6, 7}, 4.);
+
+  /* Inserted simplex:        */
+  /*    1   6                 */
+  /*    o---o                 */
+  /*   /X\7/                  */
+  /*  o---o---o---o           */
+  /*  2   0   3\X/4           */
+  /*            o             */
+  /*            5             */
+
+  for (auto f_simplex : st.skeleton_simplex_range(3)) {
+    std::clog << "vertex = (";
+    for (auto vertex : st.simplex_vertex_range(f_simplex)) {
+      std::clog << vertex << ",";
+    }
+    std::clog << ") - filtration = " << st.filtration(f_simplex);
+    std::clog << " - dimension = " << st.dimension(f_simplex) << std::endl;
+    // Guaranteed by construction
+    BOOST_CHECK(st.filtration(f_simplex) >= 2.);
+  }
+
+  // dimension until 5 even if simplex tree is of dimension 3 to test the limits
+  for(int dimension = 5; dimension >= 0; dimension --) {
+    std::clog << "### reset_filtration - dimension = " << dimension << "\n";
+    st.reset_filtration(0., dimension);
+    for (auto f_simplex : st.skeleton_simplex_range(3)) {
+      std::clog << "vertex = (";
+      for (auto vertex : st.simplex_vertex_range(f_simplex)) {
+        std::clog << vertex << ",";
+      }
+      std::clog << ") - filtration = " << st.filtration(f_simplex);
+      std::clog << " - dimension = " << st.dimension(f_simplex) << std::endl;
+      if (st.dimension(f_simplex) < dimension)
+        BOOST_CHECK(st.filtration(f_simplex) >= 2.);
+      else
+        BOOST_CHECK(st.filtration(f_simplex) == 0.);
+    }
+  }
+
+}
+