Introduce remove_all_elements(Graph)

Alpha_wrap_3/include/CGAL/Alpha_wrap_3/internal/Alpha_wrap_3.h

@@ -657,7 +657,7 @@ class Alpha_wrap_3
  std::cout << "> Extract possibly non-manifold wrap... ()" << std::endl;
 #endif
 
- clear(output_mesh);
+ remove_all_elements(output_mesh);
 
  CGAL_assertion_code(for(auto cit=m_dt.finite_cells_begin(), cend=m_dt.finite_cells_end(); cit!=cend; ++cit))
  CGAL_assertion(cit->tds_data().is_clear());
@@ -745,7 +745,7 @@ class Alpha_wrap_3
  CGAL_assertion_code(for(Vertex_handle v : m_dt.finite_vertex_handles()))
  CGAL_assertion(!is_non_manifold(v));
 
- clear(output_mesh);
+ remove_all_elements(output_mesh);
 
  // boundary faces to polygon soup
  std::vector<Point_3> points;

BGL/doc/BGL/PackageDescription.txt

@@ -679,6 +679,7 @@ user might encounter.
 - `CGAL::make_grid()`
 
 - `CGAL::clear()`
+- `CGAL::remove_all_elements()`
 - `CGAL::copy_face_graph()`
 
 - `CGAL::set_triangulation_ids()`

BGL/include/CGAL/boost/graph/IO/STL.h

@@ -172,7 +172,7 @@ bool read_STL(const std::string& fname,
  {
  return true;
  }
- g.clear();
+ clear(g);
  }
  std::ifstream is(fname);
  CGAL::IO::set_mode(is, CGAL::IO::ASCII);

BGL/include/CGAL/boost/graph/IO/polygon_mesh_io.h

@@ -45,25 +45,25 @@ bool read_polygon_mesh(std::istream& is,
  ok = read_OFF(is, g, np, false);
  if(ok)
  return true;
- g.clear();
+ clear(g);
  is.clear();//reset the error state
  is.seekg (0, is.beg);
  ok = read_OBJ(is, g, np, false);
  if(ok)
  return true;
- g.clear();
+ clear(g);
  is.clear();
  is.seekg (0, is.beg);
  ok = read_PLY(is, g, np, false);
  if(ok)
  return true;
- g.clear();
+ clear(g);
  is.clear();
  is.seekg (0, is.beg);
  ok = read_STL(is, g, np, false);
  if(ok)
  return true;
- g.clear();
+ clear(g);
  is.clear();
  is.seekg (0, is.beg);
  ok = read_GOCAD(is, g, np, false);

BGL/include/CGAL/boost/graph/helpers.h

@@ -837,25 +837,6 @@ bool is_hexahedron(typename boost::graph_traits<FaceGraph>::halfedge_descriptor
 
 namespace internal {
 
-template<typename FaceGraph>
-inline
-std::enable_if_t<Has_member_clear<FaceGraph>::value, void>
-clear_impl(FaceGraph& g)
-{ g.clear(); }
-
-template<typename FaceGraph>
-inline
-std::enable_if_t<!Has_member_clear<FaceGraph>::value, void>
-clear_impl(FaceGraph& g)
-{
- while(boost::begin(edges(g))!=boost::end(edges(g)))
- remove_edge(*boost::begin(edges(g)), g);
- while(boost::begin(faces(g))!=boost::end(faces(g)))
- remove_face(*boost::begin(faces(g)), g);
- while(boost::begin(vertices(g))!=boost::end(vertices(g)))
- remove_vertex(*boost::begin(vertices(g)), g);
-}
-
 template <class FaceGraph>
 void swap_vertices(typename boost::graph_traits<FaceGraph>::vertex_descriptor& p,
  typename boost::graph_traits<FaceGraph>::vertex_descriptor& q,
@@ -960,24 +941,83 @@ void swap_edges(const typename boost::graph_traits<FaceGraph>::halfedge_descript
  * \ingroup PkgBGLHelperFct
  *
  * removes all vertices, faces and halfedges from a graph. Calls
- * `remove_edge()`, `remove_vertex()`, and `remove_face()` for each
- * edge, vertex or face.
+ * \link MutableHalfedgeGraph `remove_vertex()`\endlink,
+ * \link MutableHalfedgeGraph `remove_edge()`\endlink, and
+ * \link MutableFaceGraph `remove_face()`\endlink, for each vertex, edge, and face.
+ *
+ * @warning This function does not perform anything more than what is advertised above. It is
+ * up to the user to e.g. clean garbage or remove internal property maps (if relevant, and desired).
+ *
+ * @tparam FaceGraph model of `MutableHalfedgeGraph` and `MutableFaceGraph`
+ *
+ * @param g the graph whose elements will be removed
+ *
+ * @sa `CGAL::clear()`
+ **/
+template<typename FaceGraph>
+void remove_all_elements(FaceGraph& g)
+{
+ while(std::begin(edges(g)) != std::end(edges(g)))
+ remove_edge(*std::begin(edges(g)), g);
+ while(std::begin(faces(g)) != std::end(faces(g)))
+ remove_face(*std::begin(faces(g)), g);
+ while(std::begin(vertices(g)) != std::end(vertices(g)))
+ remove_vertex(*std::begin(vertices(g)), g);
+
+ CGAL_postcondition(std::distance(std::cbegin(vertices(g)), std::cend(vertices(g))) == 0);
+ CGAL_postcondition(std::distance(std::cbegin(edges(g)), std::cend(edges(g))) == 0);
+ CGAL_postcondition(std::distance(std::cbegin(faces(g)), std::cend(faces(g))) == 0);
+}
+
+namespace internal {
+
+template<typename FaceGraph>
+inline
+std::enable_if_t<Has_member_clear<FaceGraph>::value, void>
+clear_impl(FaceGraph& g)
+{
+ g.clear();
+}
+
+template<typename FaceGraph>
+inline
+std::enable_if_t<!Has_member_clear<FaceGraph>::value, void>
+clear_impl(FaceGraph& g)
+{
+ remove_all_elements(g);
+}
+
+} // namespace internal
+
+/**
+ * \ingroup PkgBGLHelperFct
+ *
+ * removes all vertices, faces and halfedges from a graph. Calls
+ * \link MutableHalfedgeGraph `remove_vertex()`\endlink,
+ * \link MutableHalfedgeGraph `remove_edge()`\endlink, and
+ * \link MutableFaceGraph `remove_face()`\endlink, for each vertex, edge, and face.
  *
  * If the graph has a member function `clear()`, it will be called
  * instead.
  *
+ * @warning If it exists, the `clear()` function of a graph might do more than
+ * simply remove elements. For example, `CGAL::Surface_mesh::clear()` collects garbage
+ * and removes *all* property maps added by a call to `CGAL::Surface_mesh::add_property_map()` for all simplex types.
+ *
  * @tparam FaceGraph model of `MutableHalfedgeGraph` and `MutableFaceGraph`
  *
  * @param g the graph to clear
  *
+ * @sa `CGAL::remove_all_elements()`
  **/
 template<typename FaceGraph>
 void clear(FaceGraph& g)
 {
  internal::clear_impl(g);
- CGAL_postcondition(std::distance(boost::begin(edges(g)),boost::end(edges(g))) == 0);
- CGAL_postcondition(std::distance(boost::begin(vertices(g)),boost::end(vertices(g))) == 0);
- CGAL_postcondition(std::distance(boost::begin(faces(g)),boost::end(faces(g))) == 0);
+
+ CGAL_postcondition(std::distance(std::cbegin(vertices(g)), std::cend(vertices(g))) == 0);
+ CGAL_postcondition(std::distance(std::cbegin(edges(g)), std::cend(edges(g))) == 0);
+ CGAL_postcondition(std::distance(std::cbegin(faces(g)), std::cend(faces(g))) == 0);
 }
 
 /**

BGL/test/BGL/test_Face_filtered_graph.cpp

@@ -489,7 +489,7 @@ void test_invalid_selections()
  assert(pinched_fg.is_selection_valid());
 
  // this creates a non-manifold vertex (multiple umbrellas)
- clear(mesh);
+ CGAL::clear(mesh);
  read_a_mesh(mesh, "data/genus3.off");
  assert(is_valid_polygon_mesh(mesh));
 

BGL/test/BGL/test_bgl_read_write.cpp

@@ -122,7 +122,7 @@ void test_bgl_OFF(const std::string filename)
  assert(ok);
  assert(num_vertices(fg) != 0 && num_faces(fg) != 0);
  is.close();
- fg.clear();
+ CGAL::clear(fg);
 
  is.open(filename, std::ios::binary);
  ok = CGAL::IO::read_OFF(is, fg);
@@ -286,7 +286,7 @@ void test_bgl_OFF(const std::string filename)
 
  for(auto f : faces(fg))
  assert(get(fcm2, f) != CGAL::IO::Color());
- fg.clear();
+ CGAL::clear(fg);
  is.close();
 
  is.open("data/full.off");
@@ -478,7 +478,7 @@ void test_bgl_PLY(const std::string filename,
  assert(filename != CGAL::data_file_path("meshes/colored_tetra.ply") || (num_vertices(fg) == 4 && num_faces(fg) == 4));
  if(!binary)
  {
- fg.clear();
+ CGAL::clear(fg);
  is.open(filename, std::ios::binary);
  bool ok = CGAL::IO::read_PLY(is, fg, CGAL::parameters::use_binary_mode(false));
  is.close();
@@ -711,7 +711,6 @@ void test_bgl_GOCAD(const char* filename)
  assert(num_vertices(fg) != 0 && num_faces(fg) != 0);
 
  is.seekg(0);
- fg.clear();
  CGAL::clear(fg);
  std::pair<std::string, std::string> name_and_color;
  ok = CGAL::IO::read_GOCAD(is, name_and_color, fg);

Polygon_mesh_processing/examples/Polygon_mesh_processing/cc_compatible_orientations.cpp

@@ -43,7 +43,7 @@ void create_mesh_with_cc_to_orient(Mesh& mesh)
  }
 
  // load the soup into the mesh;
- mesh.clear();
+ CGAL::clear(mesh);
  PMP::polygon_soup_to_polygon_mesh(points, triangles, mesh);
 }
 

Polygon_mesh_processing/include/CGAL/Polygon_mesh_processing/clip.h

@@ -738,7 +738,7 @@ bool clip(TriangleMesh& tm,
  case ON_NEGATIVE_SIDE:
  return true; // nothing to clip, the full mesh is on the negative side
  case ON_POSITIVE_SIDE:
- clear(tm); // clear the mesh that is fully on the positive side
+ remove_all_elements(tm); // clear the mesh that is fully on the positive side
  return true;
  default:
  break;

Polygon_mesh_processing/include/CGAL/Polygon_mesh_processing/connected_components.h

@@ -423,7 +423,7 @@ std::size_t keep_largest_connected_components(PolygonMesh& pmesh,
 
  if(nb_components_to_keep == 0)
  {
- CGAL::clear(pmesh);
+ remove_all_elements(pmesh);
  return num;
  }
 

Polygon_mesh_processing/include/CGAL/Polygon_mesh_processing/corefinement.h

@@ -266,11 +266,11 @@ corefine_and_compute_boolean_operations(
 
  if (output[Corefinement::TM1_MINUS_TM2] != boost::none)
  if (&tm1 == *output[Corefinement::TM1_MINUS_TM2])
- clear(tm1);
+ remove_all_elements(tm1);
 
  if (output[Corefinement::TM2_MINUS_TM1] != boost::none)
  if (&tm1 == *output[Corefinement::TM2_MINUS_TM1])
- clear(tm1);
+ remove_all_elements(tm1);
 
  return CGAL::make_array(true, true, true, true);
  }
@@ -282,7 +282,7 @@ corefine_and_compute_boolean_operations(
  {
  for (int i=0; i<4; ++i)
  if (output[i] != boost::none)
- clear(*(*output[i]));
+ remove_all_elements(*(*output[i]));
  return CGAL::make_array(true, true, true, true);
  }
  // tm2 is not empty
@@ -293,9 +293,9 @@ corefine_and_compute_boolean_operations(
  parameters::vertex_point_map(vpm2),
  parameters::vertex_point_map(*std::get<Corefinement::UNION>(vpm_out_tuple)));
  if (output[Corefinement::INTERSECTION] != boost::none)
- clear(*(*output[Corefinement::INTERSECTION]));
+ remove_all_elements(*(*output[Corefinement::INTERSECTION]));
  if (output[Corefinement::TM1_MINUS_TM2] != boost::none)
- clear(*(*output[Corefinement::TM1_MINUS_TM2]));
+ remove_all_elements(*(*output[Corefinement::TM1_MINUS_TM2]));
  if (output[Corefinement::TM2_MINUS_TM1] != boost::none)
  if (&tm2 != *output[Corefinement::TM2_MINUS_TM1])
  copy_face_graph(tm2,
@@ -315,9 +315,9 @@ corefine_and_compute_boolean_operations(
  parameters::vertex_point_map(vpm1),
  parameters::vertex_point_map(*std::get<Corefinement::UNION>(vpm_out_tuple)));
  if (output[Corefinement::INTERSECTION] != boost::none)
- clear(*(*output[Corefinement::INTERSECTION]));
+ remove_all_elements(*(*output[Corefinement::INTERSECTION]));
  if (output[Corefinement::TM2_MINUS_TM1] != boost::none)
- clear(*(*output[Corefinement::TM2_MINUS_TM1]));
+ remove_all_elements(*(*output[Corefinement::TM2_MINUS_TM1]));
  if (output[Corefinement::TM1_MINUS_TM2] != boost::none)
  if (&tm1 != *output[Corefinement::TM1_MINUS_TM2])
  copy_face_graph(tm1,

Polygon_mesh_processing/include/CGAL/Polygon_mesh_processing/remesh_planar_patches.h

@@ -1265,8 +1265,7 @@ bool decimate_meshes_with_common_interfaces_impl(TriangleMeshRange& meshes,
  }
  CGAL_assertion(is_polygon_soup_a_polygon_mesh(all_faces[mesh_id]));
 
- //clear(tm);
- tm.clear_without_removing_property_maps();
+ remove_all_elements(tm);
  polygon_soup_to_polygon_mesh(all_corners[mesh_id], all_faces[mesh_id],
  tm, parameters::default_values(), parameters::vertex_point_map(vpms[mesh_id]));
  }

Polygon_mesh_processing/include/CGAL/Polygon_mesh_processing/repair_degeneracies.h

@@ -1934,7 +1934,7 @@ bool remove_degenerate_faces(const FaceRange& face_range,
 
  if(degenerate_face_set.size() == faces_size)
  {
- clear(tmesh);
+ remove_all_elements(tmesh);
  return true;
  }
 

Polygon_mesh_processing/test/Polygon_mesh_processing/data_degeneracies/all_degen.off

@@ -0,0 +1,16 @@
+OFF
+7 7 0
+0 0 0
+1 1 0
+1 1 0
+2 2 0
+1 1 0
+2 2 0
+0.5 1 0
+3 0 2 1
+3 0 3 2
+3 4 3 5
+3 1 4 5
+3 1 2 6
+3 6 2 4
+3 6 4 1

Polygon_mesh_processing/test/Polygon_mesh_processing/test_pmp_repair_degeneracies.cpp

@@ -287,6 +287,11 @@ void test()
  0, 1, // expected number of degenerate edges/faces in the selection
  0, 0); // expected number of degenerate edges/faces in the mesh after partial removal
 
+ remove_degeneracies<K, Mesh>("data_degeneracies/all_degen.off",
+ std::initializer_list<std::size_t>({0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13}), // edge selection
+ std::initializer_list<std::size_t>({0, 1, 2, 3, 4, 5, 6}), // face selection
+ 4, 7, 4, 7, 0, 0);
+
  remove_degeneracies<K, Mesh>("data_degeneracies/degtri_four.off",
  std::initializer_list<std::size_t>({1}),
  std::initializer_list<std::size_t>({3}),