Merge upstream and resolve conflict

6 files changed, 69 insertions, 51 deletions

diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h
index 6931420a..60da7169 100644
--- a/src/Alpha_complex/doc/Intro_alpha_complex.h
+++ b/src/Alpha_complex/doc/Intro_alpha_complex.h
@@ -31,8 +31,8 @@ namespace alpha_complex {
  * circumsphere is empty (the simplex is then said to be Gabriel), and as the minimum of the filtration
  * values of the codimension 1 cofaces that make it not Gabriel otherwise.
  *
- * All simplices that have a filtration value strictly greater than a given alpha squared value are not inserted into
- * the complex.
+ * All simplices that have a filtration value \f$ > \alpha^2 \f$ are removed from the Delaunay complex
+ * when creating the simplicial complex if it is specified.
  *
  * \image html "alpha_complex_representation.png" "Alpha-complex representation"
  *
@@ -46,8 +46,8 @@ namespace alpha_complex {
  * \cite cgal:s-gkd-19b from CGAL as template parameter.
  *
  * \remark
- * - When the simplicial complex is constructed with an infinite value of alpha, the complex is a Delaunay
- * complex with filtration values. The Delaunay complex without filtartion values is also available by passing
+ * - When the simplicial complex is constructed with an infinite value of \f$ \alpha^2 \f$, the complex is a Delaunay
+ * complex with special filtration values. The Delaunay complex without filtration values is also available by passing
  * `default_filtration_value=true` to `Alpha_complex::create_complex`.
  * - For people only interested in the topology of the \ref alpha_complex (for instance persistence),
  * \ref alpha_complex is equivalent to the \ref cech_complex and much smaller if you do not bound the radii.
@@ -136,13 +136,13 @@ namespace alpha_complex {
  *
  * \subsubsection nondecreasing Non decreasing filtration values
  *
- * As the squared radii computed by CGAL are an approximation, it might happen that these alpha squared values do not
- * quite define a proper filtration (i.e. non-decreasing with respect to inclusion).
+ * As the squared radii computed by CGAL are an approximation, it might happen that these \f$ \alpha^2 \f$ values do
+ * not quite define a proper filtration (i.e. non-decreasing with respect to inclusion).
  * We fix that up by calling `SimplicialComplexForAlpha::make_filtration_non_decreasing()`.
  *
  * \subsubsection pruneabove Prune above given filtration value
  *
- * The simplex tree is pruned from the given maximum alpha squared value (cf.
+ * The simplex tree is pruned from the given maximum \f$ \alpha^2 \f$ value (cf.
  * `SimplicialComplexForAlpha::prune_above_filtration()`).
  * In the following example, the value is given by the user as argument of the program.
  *
diff --git a/src/Alpha_complex/doc/alpha_complex_representation.ipe b/src/Alpha_complex/doc/alpha_complex_representation.ipe
index e8096b93..40ff1d0f 100644
--- a/src/Alpha_complex/doc/alpha_complex_representation.ipe
+++ b/src/Alpha_complex/doc/alpha_complex_representation.ipe
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <!DOCTYPE ipe SYSTEM "ipe.dtd">
-<ipe version="70107" creator="Ipe 7.1.10">
-<info created="D:20150603143945" modified="D:20160404172133"/>
+<ipe version="70206" creator="Ipe 7.2.7">
+<info created="D:20150603143945" modified="D:20200110100102"/>
 <ipestyle name="basic">
 <symbol name="arrow/arc(spx)">
 <path stroke="sym-stroke" fill="sym-stroke" pen="sym-pen">
@@ -305,7 +305,7 @@ h
 108.275 743.531 m
 166.45 743.531 l
 </path>
-<text matrix="1 0 0 1 142.618 -109.867" transformations="translations" pos="127.397 746.763" stroke="darkgray" type="label" width="6.41" height="4.289" depth="0" valign="baseline">$\alpha$</text>
+<text matrix="1 0 0 1 126.618 -109.867" transformations="translations" pos="127.397 746.763" stroke="darkgray" type="label" width="45.707" height="9.041" depth="1.32" valign="baseline" style="math">\alpha = \sqrt{32.0}</text>
 <use matrix="1 0 0 1 -209.478 12.0238" name="mark/fdisk(sfx)" pos="300 720" size="normal" stroke="black" fill="white"/>
 <use matrix="1 0 0 1 -210.178 22.1775" name="mark/fdisk(sfx)" pos="280 660" size="normal" stroke="black" fill="white"/>
 <use matrix="1 0 0 1 -210.178 22.1775" name="mark/fdisk(sfx)" pos="370 690" size="normal" stroke="black" fill="white"/>
diff --git a/src/Alpha_complex/doc/alpha_complex_representation.png b/src/Alpha_complex/doc/alpha_complex_representation.png
index 7b81cd69..5ebb1e75 100644
--- a/src/Alpha_complex/doc/alpha_complex_representation.png
+++ b/src/Alpha_complex/doc/alpha_complex_representation.png
diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h
index 13fcae99..4c61ba73 100644
--- a/src/Alpha_complex/include/gudhi/Alpha_complex.h
+++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h
@@ -121,8 +121,8 @@ class Alpha_complex {
   // size_type type from CGAL.
   typedef typename Delaunay_triangulation::size_type size_type;
 
-  // Map type to switch from simplex tree vertex handle to CGAL vertex iterator.
-  typedef typename std::map< std::size_t, CGAL_vertex_iterator > Vector_vertex_iterator;
+  // Structure to switch from simplex tree vertex handle to CGAL vertex iterator.
+  typedef typename std::vector< CGAL_vertex_iterator > Vector_vertex_iterator;
 
  private:
   /** \brief Vertex iterator vector to switch from simplex tree vertex handle to CGAL vertex iterator.
@@ -191,14 +191,6 @@ class Alpha_complex {
     return vertex_handle_to_iterator_.at(vertex)->point();
   }
 
-  /** \brief number_of_vertices returns the number of vertices (same as the number of points).
-   *
-   * @return The number of vertices.
-   */
-  std::size_t number_of_vertices() const {
-    return vertex_handle_to_iterator_.size();
-  }
-
  private:
   template<typename InputPointRange >
   void init_from_range(const InputPointRange& points) {
@@ -238,14 +230,16 @@ class Alpha_complex {
         hint = pos->full_cell();
       }
       // --------------------------------------------------------------------------------------------
-      // double map to retrieve simplex tree vertex handles from CGAL vertex iterator and vice versa
+      // structure to retrieve CGAL points from vertex handle - one vertex handle per point.
+      // Needs to be constructed before as vertex handles arrives in no particular order.
+      vertex_handle_to_iterator_.resize(point_cloud.size());
       // Loop on triangulation vertices list
       for (CGAL_vertex_iterator vit = triangulation_->vertices_begin(); vit != triangulation_->vertices_end(); ++vit) {
         if (!triangulation_->is_infinite(*vit)) {
 #ifdef DEBUG_TRACES
           std::cout << "Vertex insertion - " << vit->data() << " -> " << vit->point() << std::endl;
 #endif  // DEBUG_TRACES
-          vertex_handle_to_iterator_.emplace(vit->data(), vit);
+          vertex_handle_to_iterator_[vit->data()] = vit;
         }
       }
       // --------------------------------------------------------------------------------------------
diff --git a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
index 40b3fe09..27b671dd 100644
--- a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
+++ b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
@@ -53,20 +53,12 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_from_OFF_file, TestedKernel, list_of
 
   Gudhi::alpha_complex::Alpha_complex<TestedKernel> alpha_complex_from_file(off_file_name);
 
-  std::cout << "alpha_complex_from_points.number_of_vertices()=" << alpha_complex_from_file.number_of_vertices()
-      << std::endl;
-  BOOST_CHECK(alpha_complex_from_file.number_of_vertices() == 7);
-
   Gudhi::Simplex_tree<> simplex_tree_60;
   BOOST_CHECK(alpha_complex_from_file.create_complex(simplex_tree_60, max_alpha_square_value));
 
   std::cout << "simplex_tree_60.dimension()=" << simplex_tree_60.dimension() << std::endl;
   BOOST_CHECK(simplex_tree_60.dimension() == 2);
 
-  std::cout << "alpha_complex_from_points.number_of_vertices()=" << alpha_complex_from_file.number_of_vertices()
-      << std::endl;
-  BOOST_CHECK(alpha_complex_from_file.number_of_vertices() == 7);
-
   std::cout << "simplex_tree_60.num_vertices()=" << simplex_tree_60.num_vertices() << std::endl;
   BOOST_CHECK(simplex_tree_60.num_vertices() == 7);
 
@@ -128,10 +120,6 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) {
   Gudhi::Simplex_tree<> simplex_tree;
   BOOST_CHECK(alpha_complex_from_points.create_complex(simplex_tree));
   
-  std::cout << "alpha_complex_from_points.number_of_vertices()=" << alpha_complex_from_points.number_of_vertices()
-      << std::endl;
-  BOOST_CHECK(alpha_complex_from_points.number_of_vertices() == points.size());
-
   // Another way to check num_simplices
   std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl;
   int num_simplices = 0;
@@ -151,7 +139,7 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) {
   std::cout << "simplex_tree.dimension()=" << simplex_tree.dimension() << std::endl;
   BOOST_CHECK(simplex_tree.dimension() == 3);
   std::cout << "simplex_tree.num_vertices()=" << simplex_tree.num_vertices() << std::endl;
-  BOOST_CHECK(simplex_tree.num_vertices() == 4);
+  BOOST_CHECK(simplex_tree.num_vertices() == points.size());
 
   for (auto f_simplex : simplex_tree.filtration_simplex_range()) {
     switch (simplex_tree.dimension(f_simplex)) {
@@ -261,10 +249,6 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_from_empty_points, TestedKernel, lis
   Gudhi::Simplex_tree<> simplex_tree;
   BOOST_CHECK(!alpha_complex_from_points.create_complex(simplex_tree));
   
-  std::cout << "alpha_complex_from_points.number_of_vertices()=" << alpha_complex_from_points.number_of_vertices()
-      << std::endl;
-  BOOST_CHECK(alpha_complex_from_points.number_of_vertices() == points.size());
-
   std::cout << "simplex_tree.num_simplices()=" << simplex_tree.num_simplices() << std::endl;
   BOOST_CHECK(simplex_tree.num_simplices() == 0);
 
@@ -272,5 +256,45 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_from_empty_points, TestedKernel, lis
   BOOST_CHECK(simplex_tree.dimension() == -1);
   
   std::cout << "simplex_tree.num_vertices()=" << simplex_tree.num_vertices() << std::endl;
-  BOOST_CHECK(simplex_tree.num_vertices() == 0);
+  BOOST_CHECK(simplex_tree.num_vertices() == points.size());
+}
+
+using Inexact_kernel_2 = CGAL::Epick_d< CGAL::Dimension_tag<2> >;
+using Exact_kernel_2 = CGAL::Epeck_d< CGAL::Dimension_tag<2> >;
+using list_of_kernel_2_variants = boost::mpl::list<Inexact_kernel_2, Exact_kernel_2>;
+
+BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_with_duplicated_points, TestedKernel, list_of_kernel_2_variants) {
+  std::cout << "========== Alpha_complex_with_duplicated_points ==========" << std::endl;
+
+  using Point = typename TestedKernel::Point_d;
+  using Vector_of_points = std::vector<Point>;
+
+  // ----------------------------------------------------------------------------
+  // Init of a list of points
+  // ----------------------------------------------------------------------------
+  Vector_of_points points;
+  points.push_back(Point(1.0, 1.0));
+  points.push_back(Point(7.0, 0.0));
+  points.push_back(Point(4.0, 6.0));
+  points.push_back(Point(9.0, 6.0));
+  points.push_back(Point(0.0, 14.0));
+  points.push_back(Point(2.0, 19.0));
+  points.push_back(Point(9.0, 17.0));
+  // duplicated points
+  points.push_back(Point(1.0, 1.0));
+  points.push_back(Point(7.0, 0.0));
+
+  // ----------------------------------------------------------------------------
+  // Init of an alpha complex from the list of points
+  // ----------------------------------------------------------------------------
+  std::cout << "Init" << std::endl;
+  Gudhi::alpha_complex::Alpha_complex<TestedKernel> alpha_complex_from_points(points);
+
+  Gudhi::Simplex_tree<> simplex_tree;
+  std::cout << "create_complex" << std::endl;
+  BOOST_CHECK(alpha_complex_from_points.create_complex(simplex_tree));
+  
+  std::cout << "simplex_tree.num_vertices()=" << simplex_tree.num_vertices()
+      << std::endl;
+  BOOST_CHECK(simplex_tree.num_vertices() < points.size());
 }
diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt
index ad5b6314..0476c6d4 100644
--- a/src/Alpha_complex/test/CMakeLists.txt
+++ b/src/Alpha_complex/test/CMakeLists.txt
@@ -1,27 +1,27 @@
 project(Alpha_complex_tests)
 
-include(GUDHI_test_coverage)
+include(GUDHI_boost_test)
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
 
   # Do not forget to copy test files in current binary dir
   file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
   add_executable ( Alpha_complex_test_unit Alpha_complex_unit_test.cpp )
-  target_link_libraries(Alpha_complex_test_unit ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  target_link_libraries(Alpha_complex_test_unit ${CGAL_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(Alpha_complex_test_unit ${TBB_LIBRARIES})
   endif()
 
-  gudhi_add_coverage_test(Alpha_complex_test_unit)
+  gudhi_add_boost_test(Alpha_complex_test_unit)
 
   add_executable ( Alpha_complex_3d_test_unit Alpha_complex_3d_unit_test.cpp )
-  target_link_libraries(Alpha_complex_3d_test_unit ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  target_link_libraries(Alpha_complex_3d_test_unit ${CGAL_LIBRARY})
   add_executable ( Weighted_alpha_complex_3d_test_unit Weighted_alpha_complex_3d_unit_test.cpp )
-  target_link_libraries(Weighted_alpha_complex_3d_test_unit ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  target_link_libraries(Weighted_alpha_complex_3d_test_unit ${CGAL_LIBRARY})
   add_executable ( Periodic_alpha_complex_3d_test_unit Periodic_alpha_complex_3d_unit_test.cpp )
-  target_link_libraries(Periodic_alpha_complex_3d_test_unit ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  target_link_libraries(Periodic_alpha_complex_3d_test_unit ${CGAL_LIBRARY})
   add_executable ( Weighted_periodic_alpha_complex_3d_test_unit Weighted_periodic_alpha_complex_3d_unit_test.cpp )
-  target_link_libraries(Weighted_periodic_alpha_complex_3d_test_unit ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  target_link_libraries(Weighted_periodic_alpha_complex_3d_test_unit ${CGAL_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(Alpha_complex_3d_test_unit ${TBB_LIBRARIES})
     target_link_libraries(Weighted_alpha_complex_3d_test_unit ${TBB_LIBRARIES})
@@ -29,9 +29,9 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
     target_link_libraries(Weighted_periodic_alpha_complex_3d_test_unit ${TBB_LIBRARIES})
   endif()
 
-  gudhi_add_coverage_test(Alpha_complex_3d_test_unit)
-  gudhi_add_coverage_test(Weighted_alpha_complex_3d_test_unit)
-  gudhi_add_coverage_test(Periodic_alpha_complex_3d_test_unit)
-  gudhi_add_coverage_test(Weighted_periodic_alpha_complex_3d_test_unit)
+  gudhi_add_boost_test(Alpha_complex_3d_test_unit)
+  gudhi_add_boost_test(Weighted_alpha_complex_3d_test_unit)
+  gudhi_add_boost_test(Periodic_alpha_complex_3d_test_unit)
+  gudhi_add_boost_test(Weighted_periodic_alpha_complex_3d_test_unit)
 
 endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)