move everything about C3t3 to new package MDS_3

MDS_3/doc/MDS_3/MDS_3.txt

@@ -17,6 +17,22 @@ This package is devoted to the representation of 3-Dimensional Mesh Data Structu
 The domain to be meshed is a subset of 3D space, required to be bounded.
 
 
+//The template parameter `C3T3` is required to be a model of
+//the concept
+//`MeshComplex_3InTriangulation_3`, a data structure devised to
+//represent a three dimensional complex embedded in a 3D
+//triangulation. In both functions, an instance of type `C3T3` is used to maintain the current
+//approximating simplicial mesh
+//and to represent the final 3D mesh at the end
+//of the procedure.
+//
+//The embedding 3D triangulation is required to be the nested type
+//`CGAL::Mesh_triangulation_3::type`, provided by the class template
+//`CGAL::Mesh_triangulation_3`. The type for this triangulation is a
+//wrapper around the class `CGAL::Regular_triangulation_3` whose vertex and cell base classes
+//are respectively models of the concepts `MeshVertexBase_3` and
+//`MeshCellBase_3`.
+
 \subsection MDS_3ImplementationHistory Implementation History
 
 The code of the package `MDS_3` was initially part of the package `Mesh_3`.

MDS_3/include/CGAL/IO/File_binary_mesh_3.h

@@ -13,13 +13,13 @@
 #ifndef CGAL_IO_FILE_BINARY_MESH_3_H
 #define CGAL_IO_FILE_BINARY_MESH_3_H
 
-#include <CGAL/license/Triangulation_3.h>
+#include <CGAL/license/MDS_3.h>
 
 
 #include <iostream>
 #include <string>
 #include <limits>
-#include <CGAL/Mesh_3/io_signature.h>
+#include <CGAL/MDS_3/io_signature.h>
 
 namespace CGAL {
 

MDS_3/include/CGAL/MDS_3/Dump_c3t3.h

@@ -17,7 +17,7 @@
 
 #include <CGAL/disable_warnings.h>
 
-#include <CGAL/Mesh_3/io_signature.h>
+#include <CGAL/MDS_3/io_signature.h>
 #include <CGAL/MDS_3/Mesh_complex_3_in_triangulation_3_base.h>
 #include <CGAL/IO/File_medit.h>
 

MDS_3/include/CGAL/MDS_3/Mesh_complex_3_in_triangulation_3_base.h

@@ -24,12 +24,12 @@
 
 #include <CGAL/Mesh_3/config.h>
 
-#include <CGAL/Mesh_3/utilities.h>
+#include <CGAL/MDS_3/utilities.h>
 #include <CGAL/iterator.h>
 #include <CGAL/IO/File_medit.h>
 #include <CGAL/IO/File_maya.h>
 #include <CGAL/Bbox_3.h>
-#include <CGAL/Mesh_3/io_signature.h>
+#include <CGAL/MDS_3/io_signature.h>
 #include <CGAL/Union_find.h>
 #include <CGAL/Time_stamper.h>
 
@@ -70,7 +70,7 @@ namespace CGAL {
 #endif
 
 namespace CGAL {
-namespace Mesh_3 {
+namespace MDS_3 {
 
   namespace details {
 
@@ -110,7 +110,7 @@ namespace Mesh_3 {
 
     }; // end class template C3t3_helper_class
 
-  } // end namespace Mesh_3::details
+  } // end namespace MDS_3::details
 
 /**
  * @class Mesh_complex_3_in_triangulation_3_base
@@ -675,7 +675,7 @@ private:
   // Traversal
   //-------------------------------------------------------
 private:
-  typedef Mesh_3::internal::Iterator_not_in_complex<Self> Iterator_not_in_complex;
+  typedef MDS_3::internal::Iterator_not_in_complex<Self> Iterator_not_in_complex;
 
   class Facet_iterator_not_in_complex
   {
@@ -1136,7 +1136,7 @@ rescan_after_load_of_triangulation() {
   }
 }
 
-}  // end namespace Mesh_3
+}  // end namespace MDS_3
 }  // end namespace CGAL
 
 #include <CGAL/enable_warnings.h>

MDS_3/include/CGAL/MDS_3/utilities.h

@@ -14,10 +14,10 @@
 // File Description :
 //******************************************************************************
 
-#ifndef CGAL_MESH_3_UTILITIES_H
-#define CGAL_MESH_3_UTILITIES_H
+#ifndef CGAL_MDS_3_UTILITIES_H
+#define CGAL_MDS_3_UTILITIES_H
 
-#include <CGAL/license/Triangulation_3.h>
+#include <CGAL/license/MDS_3.h>
 
 #include <CGAL/Has_timestamp.h>
 #include <iterator>
@@ -25,7 +25,7 @@
 #include <sstream>
 
 namespace CGAL {
-namespace Mesh_3 {
+namespace MDS_3 {
 namespace internal {
 
 struct Debug_messages_tools {
@@ -115,7 +115,7 @@ public:
 
 
 } // end namespace internal
-} // end namespace Mesh_3
+} // end namespace MDS_3
 } //namespace CGAL
 
-#endif // CGAL_MESH_3_UTILITIES_H
+#endif // CGAL_MDS_3_UTILITIES_H

MDS_3/include/CGAL/Mesh_complex_3_in_triangulation_3.h

@@ -23,9 +23,9 @@
 #include <CGAL/MDS_3/Mesh_complex_3_in_triangulation_3_fwd.h>
 #include <CGAL/disable_warnings.h>
 #include <CGAL/iterator.h>
-#include <CGAL/Mesh_3/utilities.h>
+#include <CGAL/MDS_3/utilities.h>
 #include <CGAL/MDS_3/Mesh_complex_3_in_triangulation_3_base.h>
-#include <CGAL/internal/Mesh_3/Boundary_of_subdomain_of_complex_3_in_triangulation_3_to_off.h>
+#include <CGAL/internal/MDS_3/Boundary_of_subdomain_of_complex_3_in_triangulation_3_to_off.h>
 #include <CGAL/Time_stamper.h>
 
 #include <boost/bimap/bimap.hpp>
@@ -42,9 +42,9 @@ template <typename Tr,
           typename CornerIndex,
           typename CurveIndex>
 class Mesh_complex_3_in_triangulation_3 :
-  public Mesh_3::Mesh_complex_3_in_triangulation_3_base<
+  public MDS_3::Mesh_complex_3_in_triangulation_3_base<
     Tr, typename Tr::Concurrency_tag>
-  , public CGAL::Mesh_3::internal::Debug_messages_tools
+  , public CGAL::MDS_3::internal::Debug_messages_tools
 {
 public:
   typedef typename Tr::Concurrency_tag                   Concurrency_tag;
@@ -52,7 +52,7 @@ public:
 private:
   typedef Mesh_complex_3_in_triangulation_3<
     Tr,CornerIndex,CurveIndex>                                    Self;
-  typedef Mesh_3::Mesh_complex_3_in_triangulation_3_base<
+  typedef MDS_3::Mesh_complex_3_in_triangulation_3_base<
                                           Tr,Concurrency_tag>     Base;
 
 public:
@@ -454,7 +454,7 @@ private:
 
   // Iterator type to get the first element of pair
   typedef boost::transform_iterator <
-    Mesh_3::internal::First_of<typename Vertex_map_filter_iterator::value_type>,
+    MDS_3::internal::First_of<typename Vertex_map_filter_iterator::value_type>,
     Vertex_map_filter_iterator >                Vertex_map_iterator_first;
 
   // Iterator type to remove a level of referencing
@@ -775,7 +775,7 @@ operator<< (std::ostream& os,
   // TODO: implement edge saving
   typedef typename Mesh_complex_3_in_triangulation_3<Tr,CI_,CSI_>::Concurrency_tag Concurrency_tag;
   return os << static_cast<
-    const Mesh_3::Mesh_complex_3_in_triangulation_3_base<Tr, Concurrency_tag>&>(c3t3);
+    const MDS_3::Mesh_complex_3_in_triangulation_3_base<Tr, Concurrency_tag>&>(c3t3);
 }
 
 
@@ -787,7 +787,7 @@ operator>> (std::istream& is,
   // TODO: implement edge loading
   typedef typename Mesh_complex_3_in_triangulation_3<Tr,CI_,CSI_>::Concurrency_tag Concurrency_tag;
   is >> static_cast<
-    Mesh_3::Mesh_complex_3_in_triangulation_3_base<Tr, Concurrency_tag>&>(c3t3);
+    MDS_3::Mesh_complex_3_in_triangulation_3_base<Tr, Concurrency_tag>&>(c3t3);
   c3t3.rescan_after_load_of_triangulation();
   return is;
 }

MDS_3/include/CGAL/internal/MDS_3/Handle_IO_for_pair_of_int.h

@@ -18,7 +18,7 @@
 #include <CGAL/disable_warnings.h>
 
 #include <utility>
-#include <CGAL/Mesh_3/io_signature.h>
+#include <CGAL/MDS_3/io_signature.h>
 #include <ostream>
 #include <istream>
 #include <boost/variant.hpp>

MDS_3/test/MDS_3/CMakeLists.txt

@@ -0,0 +1,36 @@
+# Created by the script cgal_create_cmake_script
+# This is the CMake script for compiling a CGAL application.
+
+cmake_minimum_required(VERSION 3.1...3.15)
+project( MDS_3_Tests )
+
+if(POLICY CMP0074)
+  cmake_policy(SET CMP0074 NEW)
+endif()
+
+find_package(CGAL REQUIRED)
+
+# Use Eigen
+find_package(Eigen3 3.1.0 REQUIRED) #(3.1.0 or greater)
+include(CGAL_Eigen3_support)
+if (NOT TARGET CGAL::Eigen3_support)
+  message(STATUS "This project requires the Eigen library, and will not be compiled.")
+  return()
+endif()
+
+create_single_source_cgal_program( "test_c3t3.cpp" )
+create_single_source_cgal_program( "test_c3t3_io.cpp" )
+create_single_source_cgal_program( "test_c3t3_with_features.cpp" )
+create_single_source_cgal_program( "test_c3t3_into_facegraph.cpp" )
+create_single_source_cgal_program( "test_c3t3_extract_subdomains_boundaries.cpp" )
+
+foreach(target
+    test_c3t3
+    test_c3t3_io
+    test_c3t3_with_features
+    test_c3t3_into_facegraph
+    test_c3t3_extract_subdomains_boundaries)
+  if(TARGET ${target})
+    target_link_libraries(${target} PUBLIC CGAL::Eigen3_support)
+  endif()
+endforeach()

MDS_3/test/MDS_3/test_c3t3.cpp

@@ -37,9 +37,9 @@ struct Tester
 
   typedef typename CGAL::Mesh_triangulation_3<Mesh_domain>::type Tr;
   typedef CGAL::Mesh_complex_3_in_triangulation_3<Tr> C3t3;
-  typedef CGAL::Mesh_3::Mesh_complex_3_in_triangulation_3_base<Tr,
+  typedef CGAL::MDS_3::Mesh_complex_3_in_triangulation_3_base<Tr,
     CGAL::Sequential_tag> C3t3_base_sequential;
-  typedef CGAL::Mesh_3::Mesh_complex_3_in_triangulation_3_base<Tr,
+  typedef CGAL::MDS_3::Mesh_complex_3_in_triangulation_3_base<Tr,
     CGAL::Parallel_tag> C3t3_base_parallel;
 
   typedef typename Tr::Bare_point Bare_point;

MDS_3/test/MDS_3/test_c3t3_io.cpp

@@ -1,5 +1,5 @@
 #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
-#include <CGAL/Mesh_3/io_signature.h>
+#include <CGAL/MDS_3/io_signature.h>
 #include <CGAL/Mesh_triangulation_3.h>
 #include <CGAL/Mesh_complex_3_in_triangulation_3.h>
 #include <CGAL/IO/File_binary_mesh_3.h>

MDS_3/test/MDS_3/test_utilities.h

@@ -0,0 +1,51 @@
+// Copyright (c) 2009 INRIA Sophia-Antipolis (France).
+// All rights reserved.
+//
+// This file is part of CGAL (www.cgal.org).
+//
+// $URL$
+// $Id$
+// SPDX-License-Identifier: GPL-3.0-or-later OR LicenseRef-Commercial
+//
+//
+// Author(s)     : Stephane Tayeb
+//
+//******************************************************************************
+// File Description :
+//
+//******************************************************************************
+
+#ifndef CGAL_MESH_3_TEST_TEST_UTILITIES_H
+#define CGAL_MESH_3_TEST_TEST_UTILITIES_H
+
+#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
+#include <CGAL/Exact_predicates_exact_constructions_kernel.h>
+
+#include <CGAL/Mesh_triangulation_3.h>
+#include <CGAL/Mesh_complex_3_in_triangulation_3.h>
+
+#include <CGAL/disable_warnings.h>
+
+typedef CGAL::Exact_predicates_inexact_constructions_kernel K_e_i;
+typedef CGAL::Exact_predicates_exact_constructions_kernel K_e_e;
+
+namespace CGAL {
+namespace details {
+
+template<>
+struct Mesh_geom_traits_generator<K_e_e>
+{
+private:
+  typedef K_e_e Geom_traits;
+
+public:
+  typedef Geom_traits type;
+  typedef type Type;
+};  // end struct Mesh_geom_traits_generator<...>
+
+} // end namespace details
+} // end namespace CGAL
+
+#include <CGAL/enable_warnings.h>
+
+#endif // CGAL_MESH_3_TEST_TEST_UTILITIES_H

Mesh_3/doc/Mesh_3/PackageDescription.txt

@@ -57,8 +57,6 @@
 Here are the main concepts of this package:
 
 - `MeshTriangulationTraits_3`
-- `MeshComplex_3InTriangulation_3`
-- `MeshComplexWithFeatures_3InTriangulation_3`
 - `MeshDomain_3`
 - `MeshDomainWithFeatures_3`
 - `MeshCriteria_3`
@@ -80,7 +78,6 @@ related to the template parameters of some models of the main concepts:
 
 \cgalCRPSection{Classes}
 
-- `CGAL::Mesh_complex_3_in_triangulation_3<Tr,CornerIndex,CurveIndex>`
 - `CGAL::Mesh_triangulation_3<MD,Gt,Concurrency_tag,Vertex_base,Cell_base>`
 - `CGAL::Mesh_vertex_base_3<Gt,MD,Vb>`
 - `CGAL::Compact_mesh_cell_base_3<Gt,MD,Tds>`
@@ -114,7 +111,6 @@ and their associated classes:
 - `CGAL::perturb_mesh_3()`
 - `CGAL::lloyd_optimize_mesh_3()`
 - `CGAL::odt_optimize_mesh_3()`
-- `CGAL::facets_in_complex_3_to_triangle_mesh()`
 
 \cgalCRPSection{CGAL::parameters Functions}
 
@@ -137,8 +133,5 @@ and their associated classes:
 - `CGAL::Mesh_optimization_return_code`
 - `CGAL::Mesh_facet_topology`
 
-\cgalCRPSection{Input/Output Functions}
-- `CGAL::output_to_medit()`
-- `CGAL::output_to_vtu()`
 */
 

Mesh_3/doc/Mesh_3/dependencies

@@ -13,3 +13,5 @@ Polyhedron
 Miscellany
 Mesh_2
 Polygon_mesh_processing
+MDS_3
+

Mesh_3/include/CGAL/Compact_mesh_cell_base_3.h

@@ -28,7 +28,7 @@
 #include <CGAL/Has_timestamp.h>
 
 #include <CGAL/Regular_triangulation_cell_base_3.h>
-#include <CGAL/Mesh_3/io_signature.h>
+#include <CGAL/MDS_3/io_signature.h>
 
 #include <boost/type_traits/is_same.hpp>
 

Mesh_3/include/CGAL/Labeled_mesh_domain_3.h

@@ -33,7 +33,7 @@
 
 #include <functional>
 
-#include <CGAL/internal/Mesh_3/Handle_IO_for_pair_of_int.h>
+#include <CGAL/internal/MDS_3/Handle_IO_for_pair_of_int.h>
 #include <CGAL/internal/Mesh_3/indices_management.h>
 
 // support for `CGAL::Image_3`

Mesh_3/include/CGAL/Mesh_3/Mesh_surface_cell_base_3.h

@@ -24,7 +24,7 @@
 #include <CGAL/Mesh_3/config.h>
 
 #include <CGAL/Regular_triangulation_cell_base_3.h>
-#include <CGAL/Mesh_3/io_signature.h>
+#include <CGAL/MDS_3/io_signature.h>
 
 #ifdef CGAL_LINKED_WITH_TBB
 # include <atomic>

Mesh_3/include/CGAL/Mesh_3/Protect_edges_sizing_field.h

@@ -28,11 +28,11 @@
 #include <CGAL/disable_warnings.h>
 #include <CGAL/Mesh_3/config.h>
 
-#include <CGAL/Mesh_3/io_signature.h>
+#include <CGAL/MDS_3/io_signature.h>
 #ifdef CGAL_MESH_3_DUMP_FEATURES_PROTECTION_ITERATIONS
 #  include <CGAL/IO/File_binary_mesh_3.h>
 #endif
-#include <CGAL/Mesh_3/utilities.h>
+#include <CGAL/MDS_3/utilities.h>
 #include <CGAL/Mesh_3/Triangulation_helpers.h>
 #include <CGAL/iterator.h>
 #include <CGAL/Mesh_error_code.h>
@@ -108,7 +108,7 @@ void debug_dump_c3t3(const std::string filename, const C3t3& c3t3)
 
 template <typename C3T3, typename MeshDomain, typename SizingFunction>
 class Protect_edges_sizing_field
-  : public CGAL::Mesh_3::internal::Debug_messages_tools
+  : public CGAL::MDS_3::internal::Debug_messages_tools
 {
   typedef Protect_edges_sizing_field          Self;
 

Mesh_3/include/CGAL/Mesh_cell_base_3.h

@@ -27,7 +27,7 @@
 #include <CGAL/Regular_triangulation_cell_base_3.h>
 #include <CGAL/Regular_triangulation_cell_base_with_weighted_circumcenter_3.h>
 #include <CGAL/Mesh_3/Mesh_surface_cell_base_3.h>
-#include <CGAL/Mesh_3/io_signature.h>
+#include <CGAL/MDS_3/io_signature.h>
 #include <CGAL/tags.h>
 
 #include <boost/type_traits/is_convertible.hpp>

Mesh_3/include/CGAL/Mesh_triangulation_3.h

@@ -28,7 +28,7 @@
 
 #include <CGAL/Mesh_vertex_base_3.h>
 #include <CGAL/Compact_mesh_cell_base_3.h>
-#include <CGAL/Mesh_3/io_signature.h>
+#include <CGAL/MDS_3/io_signature.h>
 
 namespace CGAL {
 

Mesh_3/include/CGAL/Mesh_vertex_base_3.h

@@ -25,7 +25,7 @@
 
 #include <CGAL/Regular_triangulation_vertex_base_3.h>
 #include <CGAL/internal/Mesh_3/indices_management.h>
-#include <CGAL/Mesh_3/io_signature.h>
+#include <CGAL/MDS_3/io_signature.h>
 #include <CGAL/Has_timestamp.h>
 #include <CGAL/tags.h>
 

Mesh_3/include/CGAL/Polyhedral_mesh_domain_3.h

@@ -59,7 +59,7 @@
 
 // To handle I/O for Surface_patch_index if that is a pair of `int` (the
 // default)
-#include <CGAL/internal/Mesh_3/Handle_IO_for_pair_of_int.h>
+#include <CGAL/internal/MDS_3/Handle_IO_for_pair_of_int.h>
 
 #include <CGAL/internal/Mesh_3/indices_management.h>
 

Mesh_3/test/Mesh_3/CMakeLists.txt

@@ -29,16 +29,12 @@ if ( CGAL_FOUND )
   endif()
 
   create_single_source_cgal_program( "test_boost_has_xxx.cpp" )
-  create_single_source_cgal_program( "test_c3t3.cpp" )
   create_single_source_cgal_program( "test_mesh_capsule_var_distance_bound.cpp" )
   create_single_source_cgal_program( "test_implicit_multi_domain_to_labeling_function_wrapper.cpp" )
-  create_single_source_cgal_program( "test_c3t3_io.cpp" )
-  create_single_source_cgal_program( "test_c3t3_with_features.cpp" )
   create_single_source_cgal_program( "test_criteria.cpp" )
   create_single_source_cgal_program( "test_domain_with_polyline_features.cpp" )
   create_single_source_cgal_program( "test_labeled_mesh_domain_3.cpp" )
   create_single_source_cgal_program( "test_mesh_criteria_creation.cpp" )
-  create_single_source_cgal_program( "test_c3t3_into_facegraph.cpp" )
   create_single_source_cgal_program( "test_without_detect_features.cpp" )
   if(CGAL_ImageIO_USE_ZLIB)
     create_single_source_cgal_program( "test_meshing_3D_image.cpp" )
@@ -58,7 +54,6 @@ if ( CGAL_FOUND )
   create_single_source_cgal_program( "test_meshing_unit_tetrahedron.cpp" )
   create_single_source_cgal_program( "test_meshing_with_default_edge_size.cpp" )
   create_single_source_cgal_program( "test_meshing_determinism.cpp" )
-  create_single_source_cgal_program( "test_c3t3_extract_subdomains_boundaries.cpp" )
   create_single_source_cgal_program( "test_mesh_3_issue_1554.cpp" )
   create_single_source_cgal_program( "test_mesh_polyhedral_domain_with_features_deprecated.cpp" )
   create_single_source_cgal_program( "test_meshing_with_one_step.cpp" )
@@ -66,16 +61,12 @@ if ( CGAL_FOUND )
 
   foreach(target
       test_boost_has_xxx
-      test_c3t3
       test_mesh_capsule_var_distance_bound
       test_implicit_multi_domain_to_labeling_function_wrapper
-      test_c3t3_io
-      test_c3t3_with_features
       test_criteria
       test_domain_with_polyline_features
       test_labeled_mesh_domain_3
       test_mesh_criteria_creation
-      test_c3t3_into_facegraph
       test_without_detect_features
       test_meshing_3D_image
       test_meshing_3D_image_deprecated
@@ -91,7 +82,6 @@ if ( CGAL_FOUND )
       test_meshing_unit_tetrahedron
       test_meshing_with_default_edge_size
       test_meshing_determinism
-      test_c3t3_extract_subdomains_boundaries
       test_mesh_3_issue_1554
       test_mesh_polyhedral_domain_with_features_deprecated
       test_mesh_cell_base_3

Mesh_3/test/Mesh_3/test_meshing_polyhedron.cpp

@@ -15,7 +15,7 @@
 // File Description :
 //******************************************************************************
 
-#include <CGAL/Mesh_3/io_signature.h>
+#include <CGAL/MDS_3/io_signature.h>
 #include "test_meshing_utilities.h"
 #include <CGAL/Polyhedral_mesh_domain_3.h>
 #include <CGAL/IO/Polyhedron_iostream.h>