Alpha_complex_3d.h

/*    This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
 *    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
 *    Author(s):       Vincent Rouvreau
 *
 *    Copyright (C) 2018 Inria
 *
 *    Modification(s):
 *      - 2019/08 Vincent Rouvreau: Fix issue #10 for CGAL and Eigen3
 *      - YYYY/MM Author: Description of the modification
 */

#ifndef ALPHA_COMPLEX_3D_H_
#define ALPHA_COMPLEX_3D_H_

#include <boost/version.hpp>
#include <boost/variant.hpp>

#include <gudhi/Debug_utils.h>
#include <gudhi/Alpha_complex_options.h>

#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
#include <CGAL/Exact_predicates_exact_constructions_kernel.h>
#include <CGAL/Delaunay_triangulation_3.h>
#include <CGAL/Periodic_3_Delaunay_triangulation_traits_3.h>
#include <CGAL/Periodic_3_Delaunay_triangulation_3.h>
#include <CGAL/Periodic_3_regular_triangulation_traits_3.h>
#include <CGAL/Periodic_3_regular_triangulation_3.h>
#include <CGAL/Regular_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/Object.h>
#include <CGAL/tuple.h>
#include <CGAL/iterator.h>
#include <CGAL/version.h>  // for CGAL_VERSION_NR

#include <Eigen/src/Core/util/Macros.h>  // for EIGEN_VERSION_AT_LEAST

#include <boost/container/static_vector.hpp>

#include <iostream>
#include <vector>
#include <unordered_map>
#include <stdexcept>
#include <cstddef>  // for std::size_t
#include <memory>       // for std::unique_ptr
#include <type_traits>  // for std::conditional and std::enable_if
#include <limits>  // for numeric_limits<>

// Make compilation fail - required for external projects - https://github.com/GUDHI/gudhi-devel/issues/10
#if CGAL_VERSION_NR < 1041101000
# error Alpha_complex_3d is only available for CGAL >= 4.11
#endif

#if !EIGEN_VERSION_AT_LEAST(3,1,0)
# error Alpha_complex_3d is only available for Eigen3 >= 3.1.0 installed with CGAL
#endif

namespace Gudhi {

namespace alpha_complex {

#ifdef GUDHI_CAN_USE_CXX11_THREAD_LOCAL
thread_local
#endif  // GUDHI_CAN_USE_CXX11_THREAD_LOCAL
    double RELATIVE_PRECISION_OF_TO_DOUBLE = 0.00001;

// Value_from_iterator returns the filtration value from an iterator on alpha shapes values
//
// FAST                         SAFE                         EXACT
// CGAL::to_double(*iterator)   CGAL::to_double(*iterator)   CGAL::to_double(iterator->exact())

template <complexity Complexity>
struct Value_from_iterator {
  template <typename Iterator>
  static double perform(Iterator it) {
    // Default behaviour
    return CGAL::to_double(*it);
  }
};

template <>
struct Value_from_iterator<complexity::EXACT> {
  template <typename Iterator>
  static double perform(Iterator it) {
    return CGAL::to_double(it->exact());
  }
};

template <complexity Complexity = complexity::SAFE, bool Weighted = false, bool Periodic = false>
class Alpha_complex_3d {
  // Epick = Exact_predicates_inexact_constructions_kernel
  // Epeck = Exact_predicates_exact_constructions_kernel
  // Exact_alpha_comparison_tag = exact version of CGAL Alpha_shape_3 and of its objects (Alpha_shape_vertex_base_3 and
  //                           Alpha_shape_cell_base_3). Not available if weighted or periodic.
  //                           Can be CGAL::Tag_false or CGAL::Tag_true. Default is False.
  //                           cf. https://doc.cgal.org/latest/Alpha_shapes_3/classCGAL_1_1Alpha__shape__3.html
  //
  // We could use Epick + CGAL::Tag_true for not weighted nor periodic, but during benchmark, we found a bug
  // https://github.com/CGAL/cgal/issues/3460
  // This is the reason we only use Epick + CGAL::Tag_false, or Epeck
  //
  // FAST                         SAFE                         EXACT
  // Epick + CGAL::Tag_false      Epeck                        Epeck
  using Predicates = typename std::conditional<(Complexity == complexity::FAST),
                                               CGAL::Exact_predicates_inexact_constructions_kernel,
                                               CGAL::Exact_predicates_exact_constructions_kernel>::type;

  // The other way to do a conditional type. Here there are 3 possibilities
  template <typename Predicates, bool Weighted_version, bool Periodic_version>
  struct Kernel_3 {};

  template <typename Predicates, bool Is_periodic>
  struct Kernel_3<Predicates, Is_periodic, false> {
    using Kernel = Predicates;
  };

  template <typename Predicates>
  struct Kernel_3<Predicates, false, true> {
    using Kernel = CGAL::Periodic_3_Delaunay_triangulation_traits_3<Predicates>;
  };
  template <typename Predicates>
  struct Kernel_3<Predicates, true, true> {
    using Kernel = CGAL::Periodic_3_regular_triangulation_traits_3<Predicates>;
  };

  using Kernel = typename Kernel_3<Predicates, Weighted, Periodic>::Kernel;

  using TdsVb = typename std::conditional<Periodic, CGAL::Periodic_3_triangulation_ds_vertex_base_3<>,
                                          CGAL::Triangulation_ds_vertex_base_3<>>::type;

  using Tvb = typename std::conditional<Weighted, CGAL::Regular_triangulation_vertex_base_3<Kernel, TdsVb>,
                                        CGAL::Triangulation_vertex_base_3<Kernel, TdsVb>>::type;

  using Vb = CGAL::Alpha_shape_vertex_base_3<Kernel, Tvb>;

  using TdsCb = typename std::conditional<Periodic, CGAL::Periodic_3_triangulation_ds_cell_base_3<>,
                                          CGAL::Triangulation_ds_cell_base_3<>>::type;

  using Tcb = typename std::conditional<Weighted, CGAL::Regular_triangulation_cell_base_3<Kernel, TdsCb>,
                                        CGAL::Triangulation_cell_base_3<Kernel, TdsCb>>::type;

  using Cb = CGAL::Alpha_shape_cell_base_3<Kernel, Tcb>;
  using Tds = CGAL::Triangulation_data_structure_3<Vb, Cb>;

  // The other way to do a conditional type. Here there 4 possibilities, cannot use std::conditional
  template <typename Kernel, typename Tds, bool Weighted_version, bool Periodic_version>
  struct Triangulation_3 {};

  template <typename Kernel, typename Tds>
  struct Triangulation_3<Kernel, Tds, false, false> {
    using Dt = CGAL::Delaunay_triangulation_3<Kernel, Tds>;
    using Weighted_point_3 = void;
  };
  template <typename Kernel, typename Tds>
  struct Triangulation_3<Kernel, Tds, true, false> {
    using Dt = CGAL::Regular_triangulation_3<Kernel, Tds>;
    using Weighted_point_3 = typename Dt::Weighted_point;
  };
  template <typename Kernel, typename Tds>
  struct Triangulation_3<Kernel, Tds, false, true> {
    using Dt = CGAL::Periodic_3_Delaunay_triangulation_3<Kernel, Tds>;
    using Weighted_point_3 = void;
  };
  template <typename Kernel, typename Tds>
  struct Triangulation_3<Kernel, Tds, true, true> {
    using Dt = CGAL::Periodic_3_regular_triangulation_3<Kernel, Tds>;
    using Weighted_point_3 = typename Dt::Weighted_point;
  };

  using Dt = typename Triangulation_3<Kernel, Tds, Weighted, Periodic>::Dt;

 public:
  using Alpha_shape_3 = CGAL::Alpha_shape_3<Dt>;

  using FT = typename Alpha_shape_3::FT;

  using Bare_point_3 = typename Kernel::Point_3;

  using Weighted_point_3 = typename Triangulation_3<Kernel, Tds, Weighted, Periodic>::Weighted_point_3;

  using Point_3 = typename Alpha_shape_3::Point;

 private:
  using Dispatch =
      CGAL::Dispatch_output_iterator<CGAL::cpp11::tuple<CGAL::Object, FT>,
                                     CGAL::cpp11::tuple<std::back_insert_iterator<std::vector<CGAL::Object>>,
                                                        std::back_insert_iterator<std::vector<FT>>>>;

  using Cell_handle = typename Alpha_shape_3::Cell_handle;
  using Facet = typename Alpha_shape_3::Facet;
  using Edge = typename Alpha_shape_3::Edge;
  using Alpha_vertex_handle = typename Alpha_shape_3::Vertex_handle;
  using Vertex_list = boost::container::static_vector<Alpha_vertex_handle, 4>;

 public:
  template <typename InputPointRange>
  Alpha_complex_3d(const InputPointRange& points) {
    static_assert(!Periodic, "This constructor is not available for periodic versions of Alpha_complex_3d");

    alpha_shape_3_ptr_ = std::unique_ptr<Alpha_shape_3>(
        new Alpha_shape_3(std::begin(points), std::end(points), 0, Alpha_shape_3::GENERAL));
  }

  template <typename InputPointRange, typename WeightRange>
  Alpha_complex_3d(const InputPointRange& points, WeightRange weights) {
    static_assert(Weighted, "This constructor is not available for non-weighted versions of Alpha_complex_3d");
    static_assert(!Periodic, "This constructor is not available for periodic versions of Alpha_complex_3d");
    GUDHI_CHECK((weights.size() == points.size()),
                std::invalid_argument("Points number in range different from weights range number"));

    std::vector<Weighted_point_3> weighted_points_3;

    std::size_t index = 0;
    weighted_points_3.reserve(points.size());
    while ((index < weights.size()) && (index < points.size())) {
      weighted_points_3.push_back(Weighted_point_3(points[index], weights[index]));
      index++;
    }

    alpha_shape_3_ptr_ = std::unique_ptr<Alpha_shape_3>(
        new Alpha_shape_3(std::begin(weighted_points_3), std::end(weighted_points_3), 0, Alpha_shape_3::GENERAL));
  }

  template <typename InputPointRange>
  Alpha_complex_3d(const InputPointRange& points, FT x_min, FT y_min,
                   FT z_min, FT x_max, FT y_max, FT z_max) {
    static_assert(Periodic, "This constructor is not available for non-periodic versions of Alpha_complex_3d");
    // Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it.
    GUDHI_CHECK(
        (x_max - x_min == y_max - y_min) && (x_max - x_min == z_max - z_min) && (z_max - z_min == y_max - y_min),
        std::invalid_argument("The size of the cuboid in every directions is not the same."));

    // Define the periodic cube
    Dt pdt(typename Kernel::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max));
    // Heuristic for inserting large point sets (if pts is reasonably large)
    pdt.insert(std::begin(points), std::end(points), true);
    // As pdt won't be modified anymore switch to 1-sheeted cover if possible
    if (!pdt.is_triangulation_in_1_sheet()) {
      throw std::invalid_argument("Unable to construct a triangulation within a single periodic domain.");
    }
    pdt.convert_to_1_sheeted_covering();

    // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode
    // Maybe need to set it to GENERAL mode
    alpha_shape_3_ptr_ = std::unique_ptr<Alpha_shape_3>(new Alpha_shape_3(pdt, 0, Alpha_shape_3::GENERAL));
  }

  template <typename InputPointRange, typename WeightRange>
  Alpha_complex_3d(const InputPointRange& points, WeightRange weights, FT x_min, FT y_min,
                   FT z_min, FT x_max, FT y_max, FT z_max) {
    static_assert(Weighted, "This constructor is not available for non-weighted versions of Alpha_complex_3d");
    static_assert(Periodic, "This constructor is not available for non-periodic versions of Alpha_complex_3d");
    GUDHI_CHECK((weights.size() == points.size()),
                std::invalid_argument("Points number in range different from weights range number"));
    // Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it.
    GUDHI_CHECK(
        (x_max - x_min == y_max - y_min) && (x_max - x_min == z_max - z_min) && (z_max - z_min == y_max - y_min),
        std::invalid_argument("The size of the cuboid in every directions is not the same."));

    std::vector<Weighted_point_3> weighted_points_3;

    std::size_t index = 0;
    weighted_points_3.reserve(points.size());

#ifdef GUDHI_DEBUG
    // Defined in GUDHI_DEBUG to avoid unused variable warning for GUDHI_CHECK
    FT maximal_possible_weight = 0.015625 * (x_max - x_min) * (x_max - x_min);
#endif

    while ((index < weights.size()) && (index < points.size())) {
      GUDHI_CHECK((weights[index] < maximal_possible_weight) && (weights[index] >= 0),
                  std::invalid_argument("Invalid weight at index " + std::to_string(index + 1) +
                                        ". Must be positive and less than maximal possible weight = 1/64*cuboid length "
                                        "squared, which is not an acceptable input."));
      weighted_points_3.push_back(Weighted_point_3(points[index], weights[index]));
      index++;
    }

    // Define the periodic cube
    Dt pdt(typename Kernel::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max));
    // Heuristic for inserting large point sets (if pts is reasonably large)
    pdt.insert(std::begin(weighted_points_3), std::end(weighted_points_3), true);
    // As pdt won't be modified anymore switch to 1-sheeted cover if possible
    if (!pdt.is_triangulation_in_1_sheet()) {
      throw std::invalid_argument("Unable to construct a triangulation within a single periodic domain.");
    }
    pdt.convert_to_1_sheeted_covering();

    // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode
    // Maybe need to set it to GENERAL mode
    alpha_shape_3_ptr_ = std::unique_ptr<Alpha_shape_3>(new Alpha_shape_3(pdt, 0, Alpha_shape_3::GENERAL));
  }

  template <typename SimplicialComplexForAlpha3d,
            typename Filtration_value = typename SimplicialComplexForAlpha3d::Filtration_value>
  bool create_complex(SimplicialComplexForAlpha3d& complex,
                      Filtration_value max_alpha_square = std::numeric_limits<Filtration_value>::infinity()) {
    if (complex.num_vertices() > 0) {
      std::cerr << "Alpha_complex_3d create_complex - complex is not empty\n";
      return false;  // ----- >>
    }

    using Complex_vertex_handle = typename SimplicialComplexForAlpha3d::Vertex_handle;
    using Simplex_tree_vector_vertex = std::vector<Complex_vertex_handle>;

#ifdef DEBUG_TRACES
    std::size_t count_vertices = 0;
    std::size_t count_edges = 0;
    std::size_t count_facets = 0;
    std::size_t count_cells = 0;
#endif  // DEBUG_TRACES
    std::vector<CGAL::Object> objects;
    std::vector<FT> alpha_values;

    Dispatch dispatcher = CGAL::dispatch_output<CGAL::Object, FT>(std::back_inserter(objects),
                                                                                std::back_inserter(alpha_values));

    alpha_shape_3_ptr_->filtration_with_alpha_values(dispatcher);
#ifdef DEBUG_TRACES
    std::cout << "filtration_with_alpha_values returns : " << objects.size() << " objects" << std::endl;
#endif  // DEBUG_TRACES

    using Alpha_value_iterator = typename std::vector<FT>::const_iterator;
    Alpha_value_iterator alpha_value_iterator = alpha_values.begin();
    for (auto object_iterator : objects) {
      Vertex_list vertex_list;

      // Retrieve Alpha shape vertex list from object
      if (const Cell_handle* cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
        for (auto i = 0; i < 4; i++) {
#ifdef DEBUG_TRACES
          std::cout << "from cell[" << i << "] - Point coordinates (" << (*cell)->vertex(i)->point() << ")"
                    << std::endl;
#endif  // DEBUG_TRACES
          vertex_list.push_back((*cell)->vertex(i));
        }
#ifdef DEBUG_TRACES
        count_cells++;
#endif  // DEBUG_TRACES
      } else if (const Facet* facet = CGAL::object_cast<Facet>(&object_iterator)) {
        for (auto i = 0; i < 4; i++) {
          if ((*facet).second != i) {
#ifdef DEBUG_TRACES
            std::cout << "from facet=[" << i << "] - Point coordinates (" << (*facet).first->vertex(i)->point() << ")"
                      << std::endl;
#endif  // DEBUG_TRACES
            vertex_list.push_back((*facet).first->vertex(i));
          }
        }
#ifdef DEBUG_TRACES
        count_facets++;
#endif  // DEBUG_TRACES
      } else if (const Edge* edge = CGAL::object_cast<Edge>(&object_iterator)) {
        for (auto i : {(*edge).second, (*edge).third}) {
#ifdef DEBUG_TRACES
          std::cout << "from edge[" << i << "] - Point coordinates (" << (*edge).first->vertex(i)->point() << ")"
                    << std::endl;
#endif  // DEBUG_TRACES
          vertex_list.push_back((*edge).first->vertex(i));
        }
#ifdef DEBUG_TRACES
        count_edges++;
#endif  // DEBUG_TRACES
      } else if (const Alpha_vertex_handle* vertex = CGAL::object_cast<Alpha_vertex_handle>(&object_iterator)) {
#ifdef DEBUG_TRACES
        count_vertices++;
        std::cout << "from vertex - Point coordinates (" << (*vertex)->point() << ")" << std::endl;
#endif  // DEBUG_TRACES
        vertex_list.push_back((*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) {
        auto 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
          Complex_vertex_handle vertex = map_cgal_simplex_tree.size();
#ifdef DEBUG_TRACES
          std::cout << "Point (" << the_alpha_shape_vertex->point() << ") not found - insert new vertex id " << 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
          Complex_vertex_handle vertex = the_map_iterator->second;
#ifdef DEBUG_TRACES
          std::cout << "Point (" << the_alpha_shape_vertex->point() << ") found as vertex id " << vertex << std::endl;
#endif  // DEBUG_TRACES
          the_simplex.push_back(vertex);
        }
      }
      // Construction of the simplex_tree
      Filtration_value filtr = Value_from_iterator<Complexity>::perform(alpha_value_iterator);

#ifdef DEBUG_TRACES
      std::cout << "filtration = " << filtr << std::endl;
#endif  // DEBUG_TRACES
      complex.insert_simplex(the_simplex, static_cast<Filtration_value>(filtr));
      GUDHI_CHECK(alpha_value_iterator != alpha_values.end(), "CGAL provided more simplices than values");
      ++alpha_value_iterator;
    }

#ifdef DEBUG_TRACES
    std::cout << "vertices \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;
#endif  // DEBUG_TRACES
    // --------------------------------------------------------------------------------------------
    // As Alpha value is an approximation, we have to make filtration non decreasing while increasing the dimension
    complex.make_filtration_non_decreasing();
    // Remove all simplices that have a filtration value greater than max_alpha_square
    complex.prune_above_filtration(max_alpha_square);
    // --------------------------------------------------------------------------------------------
    return true;
  }

  const Point_3& get_point(std::size_t vertex) {
    if (map_cgal_simplex_tree.size() != cgal_vertex_iterator_vector.size()) {
      cgal_vertex_iterator_vector.resize(map_cgal_simplex_tree.size());
      for (auto map_iterator : map_cgal_simplex_tree) {
        cgal_vertex_iterator_vector[map_iterator.second] = map_iterator.first;
      }

    }
    auto cgal_vertex_iterator = cgal_vertex_iterator_vector.at(vertex);
    return cgal_vertex_iterator->point();
  }

 private:
  // use of a unique_ptr on cgal Alpha_shape_3, as copy and default constructor is not available - no need to be freed
  std::unique_ptr<Alpha_shape_3> alpha_shape_3_ptr_;

  // Map type to switch from CGAL vertex iterator to simplex tree vertex handle.
  std::unordered_map<Alpha_vertex_handle, std::size_t> map_cgal_simplex_tree;
  // Vector type to switch from simplex tree vertex handle to CGAL vertex iterator.
  std::vector<Alpha_vertex_handle> cgal_vertex_iterator_vector;
};

}  // namespace alpha_complex

}  // namespace Gudhi

#endif  // ALPHA_COMPLEX_3D_H_