path: root/utilities/Alpha_complex/weighted_periodic_alpha_complex_3d_persistence.cpp

/*    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
 *                     Pawel Dlotko - 2017 - Swansea University, UK
 *
 *    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/variant.hpp>

#include <gudhi/Simplex_tree.h>
#include <gudhi/Persistent_cohomology.h>
#include <gudhi/Points_3D_off_io.h>

#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
#include <CGAL/Periodic_3_regular_triangulation_traits_3.h>
#include <CGAL/Periodic_3_regular_triangulation_3.h>
#include <CGAL/Alpha_shape_3.h>
#include <CGAL/iterator.h>

#include <fstream>
#include <cmath>
#include <string>
#include <tuple>
#include <map>
#include <utility>
#include <vector>
#include <cstdlib>

#include "alpha_complex_3d_helper.h"

// Traits
using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel;
using PK = CGAL::Periodic_3_regular_triangulation_traits_3<Kernel>;

// Vertex type
using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>;
using Vb = CGAL::Regular_triangulation_vertex_base_3<PK, DsVb>;
using AsVb = CGAL::Alpha_shape_vertex_base_3<PK, Vb>;
// Cell type
using DsCb = CGAL::Periodic_3_triangulation_ds_cell_base_3<>;
using Cb = CGAL::Regular_triangulation_cell_base_3<PK, DsCb>;
using AsCb = CGAL::Alpha_shape_cell_base_3<PK, Cb>;
using Tds = CGAL::Triangulation_data_structure_3<AsVb, AsCb>;
using P3RT3 = CGAL::Periodic_3_regular_triangulation_3<PK, Tds>;
using Alpha_shape_3 = CGAL::Alpha_shape_3<P3RT3>;

using Point_3 = P3RT3::Bare_point;
using Weighted_point_3 = P3RT3::Weighted_point;

// 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;
using Vertex_list = std::vector<Alpha_shape_3::Vertex_handle>;

// 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>;
using Persistent_cohomology =
    Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>;

void usage(const std::string& progName) {
  std::cerr << "Usage: " << progName << " path_to_the_OFF_file path_to_weight_file path_to_the_cuboid_file "
                                        "coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
  exit(-1);
}

int main(int argc, char* const argv[]) {
  // program args management
  if (argc != 6) {
    std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
    usage(argv[0]);
  }

  int coeff_field_characteristic = atoi(argv[4]);
  Filtration_value min_persistence = strtof(argv[5], nullptr);

  // Read points from file
  std::string offInputFile(argv[1]);
  // Read the OFF file (input file name given as parameter) and triangulate points
  Gudhi::Points_3D_off_reader<Point_3> off_reader(offInputFile);
  // Check the read operation was correct
  if (!off_reader.is_valid()) {
    std::cerr << "Unable to read file " << offInputFile << std::endl;
    usage(argv[0]);
  }

  // Retrieve the points
  std::vector<Point_3> lp = off_reader.get_point_cloud();

  // Read iso_cuboid_3 information from file
  std::ifstream iso_cuboid_str(argv[3]);
  double x_min, y_min, z_min, x_max, y_max, z_max;
  if (iso_cuboid_str.is_open()) {
    if (!(iso_cuboid_str >> x_min >> y_min >> z_min >> x_max >> y_max >> z_max)) {
      std::cerr << argv[3] << " - Bad file format." << std::endl;
      usage(argv[0]);
    }

  } else {
    std::cerr << "Unable to read file " << argv[3] << std::endl;
    usage(argv[0]);
  }
  // Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it.
  if ((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::cerr << "The size of the cuboid in every directions is not the same." << std::endl;
    exit(-1);
  }

  double maximal_possible_weight = 0.015625 * (x_max - x_min) * (x_max - x_min);

  // Read weights information from file
  std::ifstream weights_ifstr(argv[2]);
  std::vector<Weighted_point_3> wp;
  if (weights_ifstr.is_open()) {
    double weight = 0.0;
    std::size_t index = 0;
    wp.reserve(lp.size());
    // Attempt read the weight in a double format, return false if it fails
    while ((weights_ifstr >> weight) && (index < lp.size())) {
      if ((weight >= maximal_possible_weight) || (weight < 0)) {
        std::cerr << "At line " << (index + 1) << ", the weight (" << weight
                  << ") is negative or more than or equal to maximal possible weight (" << maximal_possible_weight
                  << ") = 1/64*cuboid length squared, which is not an acceptable input." << std::endl;
        exit(-1);
      }

      wp.push_back(Weighted_point_3(lp[index], weight));
      index++;
    }
    if (index != lp.size()) {
      std::cerr << "Bad number of weights in file " << argv[2] << std::endl;
      usage(argv[0]);
    }
  } else {
    std::cerr << "Unable to read file " << argv[2] << std::endl;
    usage(argv[0]);
  }

  // Define the periodic cube
  P3RT3 prt(PK::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)
  prt.insert(wp.begin(), wp.end(), true);
  // As prt won't be modified anymore switch to 1-sheeted cover if possible
  if (prt.is_triangulation_in_1_sheet()) {
    prt.convert_to_1_sheeted_covering();
  } else {
    std::cerr << "ERROR: we were not able to construct a triangulation within a single periodic domain." << std::endl;
    exit(-1);
  }
  std::cout << "Weighted Periodic Delaunay computed." << std::endl;

  // 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 as(prt, 0, Alpha_shape_3::GENERAL);

  // 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);
    if (the_alpha_value_iterator != the_alpha_values.end())
      ++the_alpha_value_iterator;
    else
      std::cout << "This shall not happen" << std::endl;
  }

#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::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl;
  // Compute the persistence diagram of the complex
  Persistent_cohomology pcoh(simplex_tree, true);
  // initializes the coefficient field for homology
  pcoh.init_coefficients(coeff_field_characteristic);

  pcoh.compute_persistent_cohomology(min_persistence);

  pcoh.output_diagram();

  return 0;
}