Fix documentation for CGAL version required by 3d version

Remove duplicated example (cf. the one in the Simplex tree)
Add the example for documentation


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@3713 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 204f77982c61bc30a6ad3218c82b98f8bb49d711

3 files changed, 9 insertions, 311 deletions

diff --git a/src/Alpha_complex/example/alpha_complex_3d_step_by_step.cpp b/src/Alpha_complex/example/alpha_complex_3d_step_by_step.cpp
deleted file mode 100644
index d76402e5..00000000
--- a/src/Alpha_complex/example/alpha_complex_3d_step_by_step.cpp
+++ /dev/null
@@ -1,309 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Vincent Rouvreau
- *
- *    Copyright (C) 2014 Inria
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <boost/version.hpp>
-#include <boost/program_options.hpp>
-#include <boost/variant.hpp>
-
-#if BOOST_VERSION >= 105400
-#include <boost/container/static_vector.hpp>
-#endif
-
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Points_3D_off_io.h>
-
-#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
-#include <CGAL/Delaunay_triangulation_3.h>
-#include <CGAL/Alpha_shape_3.h>
-#include <CGAL/Alpha_shape_cell_base_3.h>
-#include <CGAL/Alpha_shape_vertex_base_3.h>
-#include <CGAL/iterator.h>
-
-#include <fstream>
-#include <cmath>
-#include <string>
-#include <tuple>
-#include <map>
-#include <utility>
-#include <vector>
-#include <cstdlib>
-
-template <class Vertex_list, class Cell_handle>
-Vertex_list from_cell(const Cell_handle& ch) {
-  Vertex_list the_list;
-  for (auto i = 0; i < 4; i++) {
-#ifdef DEBUG_TRACES
-    std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl;
-#endif  // DEBUG_TRACES
-    the_list.push_back(ch->vertex(i));
-  }
-  return the_list;
-}
-
-template <class Vertex_list, class Facet>
-Vertex_list from_facet(const Facet& fct) {
-  Vertex_list the_list;
-  for (auto i = 0; i < 4; i++) {
-    if (fct.second != i) {
-#ifdef DEBUG_TRACES
-      std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl;
-#endif  // DEBUG_TRACES
-      the_list.push_back(fct.first->vertex(i));
-    }
-  }
-  return the_list;
-}
-
-template <class Vertex_list, class Edge_3>
-Vertex_list from_edge(const Edge_3& edg) {
-  Vertex_list the_list;
-  for (auto i : {edg.second, edg.third}) {
-#ifdef DEBUG_TRACES
-    std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl;
-#endif  // DEBUG_TRACES
-    the_list.push_back(edg.first->vertex(i));
-  }
-  return the_list;
-}
-
-template <class Vertex_list, class Vertex_handle>
-Vertex_list from_vertex(const Vertex_handle& vh) {
-  Vertex_list the_list;
-#ifdef DEBUG_TRACES
-  std::cout << "from vertex=" << vh->point() << std::endl;
-#endif  // DEBUG_TRACES
-  the_list.push_back(vh);
-  return the_list;
-}
-
-// Alpha_shape_3 templates type definitions
-using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel;
-using Vb = CGAL::Alpha_shape_vertex_base_3<Kernel>;
-using Fb = CGAL::Alpha_shape_cell_base_3<Kernel>;
-using Tds = CGAL::Triangulation_data_structure_3<Vb, Fb>;
-using Triangulation_3 = CGAL::Delaunay_triangulation_3<Kernel, Tds>;
-using Alpha_shape_3 = CGAL::Alpha_shape_3<Triangulation_3>;
-
-// From file type definition
-using Point_3 = Kernel::Point_3;
-
-// filtration with alpha values needed type definition
-using Alpha_value_type = Alpha_shape_3::FT;
-using Object = CGAL::Object;
-using Dispatch =
-    CGAL::Dispatch_output_iterator<CGAL::cpp11::tuple<Object, Alpha_value_type>,
-                                   CGAL::cpp11::tuple<std::back_insert_iterator<std::vector<Object> >,
-                                                      std::back_insert_iterator<std::vector<Alpha_value_type> > > >;
-using Cell_handle = Alpha_shape_3::Cell_handle;
-using Facet = Alpha_shape_3::Facet;
-using Edge_3 = Alpha_shape_3::Edge;
-using Vertex_handle = Alpha_shape_3::Vertex_handle;
-
-#if BOOST_VERSION >= 105400
-using Vertex_list = boost::container::static_vector<Alpha_shape_3::Vertex_handle, 4>;
-#else
-using Vertex_list = std::vector<Alpha_shape_3::Vertex_handle>;
-#endif
-
-// gudhi type definition
-using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
-using Filtration_value = ST::Filtration_value;
-using Simplex_tree_vertex = ST::Vertex_handle;
-using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
-using Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>;
-
-void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag);
-
-int main(int argc, char **argv) {
-  std::string off_file_points;
-  std::string output_file_diag;
-
-  program_options(argc, argv, off_file_points, output_file_diag);
-
-  // Read the OFF file (input file name given as parameter) and triangulate points
-  Gudhi::Points_3D_off_reader<Point_3> off_reader(off_file_points);
-  // Check the read operation was correct
-  if (!off_reader.is_valid()) {
-    std::cerr << "Unable to read file " << off_file_points << std::endl;
-    exit(-1);
-  }
-
-  // Retrieve the points
-  std::vector<Point_3> lp = off_reader.get_point_cloud();
-
-  // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode.
-  Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL);
-#ifdef DEBUG_TRACES
-  std::cout << "Alpha shape computed in GENERAL mode" << std::endl;
-#endif  // DEBUG_TRACES
-
-  // filtration with alpha values from alpha shape
-  std::vector<Object> the_objects;
-  std::vector<Alpha_value_type> the_alpha_values;
-
-  Dispatch disp = CGAL::dispatch_output<Object, Alpha_value_type>(std::back_inserter(the_objects),
-                                                                  std::back_inserter(the_alpha_values));
-
-  as.filtration_with_alpha_values(disp);
-#ifdef DEBUG_TRACES
-  std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl;
-#endif  // DEBUG_TRACES
-
-  Alpha_shape_3::size_type count_vertices = 0;
-  Alpha_shape_3::size_type count_edges = 0;
-  Alpha_shape_3::size_type count_facets = 0;
-  Alpha_shape_3::size_type count_cells = 0;
-
-  // Loop on objects vector
-  Vertex_list vertex_list;
-  ST simplex_tree;
-  Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
-  std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
-  for (auto object_iterator : the_objects) {
-    // Retrieve Alpha shape vertex list from object
-    if (const Cell_handle *cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
-      vertex_list = from_cell<Vertex_list, Cell_handle>(*cell);
-      count_cells++;
-    } else if (const Facet *facet = CGAL::object_cast<Facet>(&object_iterator)) {
-      vertex_list = from_facet<Vertex_list, Facet>(*facet);
-      count_facets++;
-    } else if (const Edge_3 *edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
-      vertex_list = from_edge<Vertex_list, Edge_3>(*edge);
-      count_edges++;
-    } else if (const Vertex_handle *vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
-      count_vertices++;
-      vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
-    }
-    // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
-    Simplex_tree_vector_vertex the_simplex;
-    for (auto the_alpha_shape_vertex : vertex_list) {
-      Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
-      if (the_map_iterator == map_cgal_simplex_tree.end()) {
-        // alpha shape not found
-        Simplex_tree_vertex vertex = map_cgal_simplex_tree.size();
-#ifdef DEBUG_TRACES
-        std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl;
-#endif  // DEBUG_TRACES
-        the_simplex.push_back(vertex);
-        map_cgal_simplex_tree.emplace(the_alpha_shape_vertex, vertex);
-      } else {
-        // alpha shape found
-        Simplex_tree_vertex vertex = the_map_iterator->second;
-#ifdef DEBUG_TRACES
-        std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
-#endif  // DEBUG_TRACES
-        the_simplex.push_back(vertex);
-      }
-    }
-    // Construction of the simplex_tree
-    Filtration_value filtr = /*std::sqrt*/ (*the_alpha_value_iterator);
-#ifdef DEBUG_TRACES
-    std::cout << "filtration = " << filtr << std::endl;
-#endif  // DEBUG_TRACES
-    simplex_tree.insert_simplex(the_simplex, filtr);
-    GUDHI_CHECK(the_alpha_value_iterator != the_alpha_values.end(), "CGAL provided more simplices than values");
-    ++the_alpha_value_iterator;
-  }
-
-#ifdef DEBUG_TRACES
-  std::cout << "vertices \t\t" << count_vertices << std::endl;
-  std::cout << "edges \t\t" << count_edges << std::endl;
-  std::cout << "facets \t\t" << count_facets << std::endl;
-  std::cout << "cells \t\t" << count_cells << std::endl;
-
-  std::cout << "Information of the Simplex Tree: " << std::endl;
-  std::cout << "  Number of vertices = " << simplex_tree.num_vertices() << " ";
-  std::cout << "  Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
-  std::cout << "  Dimension = " << simplex_tree.dimension() << " ";
-#endif  // DEBUG_TRACES
-
-#ifdef DEBUG_TRACES
-  std::cout << "Iterator on vertices: " << std::endl;
-  for (auto vertex : simplex_tree.complex_vertex_range()) {
-    std::cout << vertex << " ";
-  }
-#endif  // DEBUG_TRACES
-
-  // Sort the simplices in the order of the filtration
-  simplex_tree.initialize_filtration();
-
-  std::streambuf* streambufffer;
-  std::ofstream ouput_file_stream;
-  if (output_file_diag != std::string()) {
-    ouput_file_stream.open(output_file_diag);
-    streambufffer = ouput_file_stream.rdbuf();
-  } else {
-    streambufffer = std::cout.rdbuf();
-  }
-
-  std::ostream output_stream(streambufffer);
-
-  // ----------------------------------------------------------------------------
-  // Display information about the alpha complex
-  // ----------------------------------------------------------------------------
-  output_stream << "Alpha complex is of dimension " << simplex_tree.dimension() <<
-                " - " << simplex_tree.num_simplices() << " simplices - " <<
-                                                                         simplex_tree.num_vertices() << " vertices." << std::endl;
-
-  output_stream << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" <<
-                std::endl;
-  for (auto f_simplex : simplex_tree.filtration_simplex_range()) {
-    output_stream << "   ( ";
-    for (auto vertex : simplex_tree.simplex_vertex_range(f_simplex)) {
-      output_stream << vertex << " ";
-    }
-    output_stream << ") -> " << "[" << simplex_tree.filtration(f_simplex) << "] ";
-    output_stream << std::endl;
-  }
-
-  return 0;
-}
-
-void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag) {
-  namespace po = boost::program_options;
-  po::options_description hidden("Hidden options");
-  hidden.add_options()("input-file", po::value<std::string>(&off_file_points),
-                       "Name of file containing a point set. Format is one point per line:   X1 ... Xd ");
-
-  po::options_description visible("Allowed options", 100);
-  visible.add_options()("help,h", "produce help message")(
-      "output-file,o", po::value<std::string>(&output_file_diag)->default_value(std::string()),
-      "Name of file in which the persistence diagram is written. Default print in std::cout");
-
-  po::positional_options_description pos;
-  pos.add("input-file", 1);
-
-  po::options_description all;
-  all.add(visible).add(hidden);
-
-  po::variables_map vm;
-  po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm);
-  po::notify(vm);
-
-  if (vm.count("help") || !vm.count("input-file")) {
-    std::cout << std::endl;
-    std::cout << "Compute and displays the 3D Alpha complex defined on a set of input points.\n \n";
-    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
-    std::cout << visible << std::endl;
-    exit(-1);
-  }
-}
diff --git a/src/common/doc/examples.h b/src/common/doc/examples.h
index 7c2a8f69..c19b3444 100644
--- a/src/common/doc/examples.h
+++ b/src/common/doc/examples.h
@@ -53,6 +53,7 @@
  * @example Spatial_searching/example_spatial_searching.cpp
  * @example Alpha_complex/alpha_complex_3d_persistence.cpp
  * @example Alpha_complex/alpha_complex_persistence.cpp
+ * @example Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp
  * @example Bottleneck_distance/bottleneck_distance.cpp
  * @example Witness_complex/weak_witness_persistence.cpp
  * @example Witness_complex/strong_witness_persistence.cpp
diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h
index 8f91e9c1..d36a216f 100644
--- a/src/common/doc/installation.h
+++ b/src/common/doc/installation.h
@@ -56,8 +56,6 @@ make doxygen
  * 
  * The following examples/utilities require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms
  * Library</a> (CGAL \cite cgal:eb-15b) and will not be built if CGAL is not installed:
- * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html">
- * Alpha_complex/alpha_complex_3d_persistence.cpp</a>
  * \li <a href="_simplex_tree_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html">
  * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a>
  * 
@@ -113,6 +111,12 @@ make doxygen
  * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html">
  * Tangential_complex/example_with_perturb.cpp</a>
  *
+ * The following example requires CGAL version &ge; 4.11.0:
+ * \li <a href="_alpha_complex_2_weighted_alpha_complex_3d_from_points_8cpp-example.html">
+ * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp</a>
+ * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html">
+ * Alpha_complex/alpha_complex_3d_persistence.cpp</a>
+ *
  * \subsection eigen3 Eigen3
  * The \ref alpha_complex data structure and few examples requires
  * <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> is a C++ template library for linear algebra:
@@ -128,6 +132,8 @@ make doxygen
  * Alpha_complex/alpha_complex_persistence.cpp</a>
  * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html">
  * Alpha_complex/alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_alpha_complex_2_weighted_alpha_complex_3d_from_points_8cpp-example.html">
+ * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp</a>
  * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html">
  * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a>
  * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">