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-/* 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/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_Delaunay_triangulation_traits_3.h>
-#include <CGAL/Periodic_3_Delaunay_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 <list>
-#include <vector>
-#include <cstdlib>
-
-#include "alpha_complex_3d_helper.h"
-
-// Traits
-using K = CGAL::Exact_predicates_inexact_constructions_kernel;
-using PK = CGAL::Periodic_3_Delaunay_triangulation_traits_3<K>;
-// Vertex type
-using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>;
-using Vb = CGAL::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::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 P3DT3 = CGAL::Periodic_3_Delaunay_triangulation_3<PK, Tds>;
-using Alpha_shape_3 = CGAL::Alpha_shape_3<P3DT3>;
-using Point_3 = PK::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;
-using Vertex_list = std::list<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 Alpha_shape_simplex_tree_pair = std::pair<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(char * const progName) {
- std::cerr << "Usage:\n" << progName << " path_to_OFF_file path_to_iso_cuboid_3_file coeff_field_characteristic[" <<
- "integer > 0] min_persistence[float >= -1.0]\n" <<
- " path_to_OFF_file is the path to your points cloud in OFF format.\n" <<
- " path_to_iso_cuboid_3_file is the path to the iso cuboid file with the following format :\n" <<
- " x_min y_min z_min x_max y_max z_max\n" <<
- " In this example, the periodic cube will be " <<
- "{ x = [x_min,x_max]; y = [y_min,y_max]; z = [z_min,z_max] }.\n" <<
- " For more information, please refer to\n" <<
- " https://doc.cgal.org/latest/Kernel_23/classCGAL_1_1Iso__cuboid__3.html\n";
-
- exit(-1);
-}
-
-int main(int argc, char * const argv[]) {
- // program args management
- if (argc != 5) {
- std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
- usage(argv[0]);
- }
-
- int coeff_field_characteristic = atoi(argv[3]);
- Filtration_value min_persistence = strtof(argv[4], 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]);
- }
-
- // Read iso_cuboid_3 information from file
- std::ifstream iso_cuboid_str(argv[2]);
- double x_min, y_min, z_min, x_max, y_max, z_max;
- if (iso_cuboid_str.good()) {
- iso_cuboid_str >> x_min >> y_min >> z_min >> x_max >> y_max >> z_max;
- } else {
- std::cerr << "Unable to read file " << argv[2] << std::endl;
- usage(argv[0]);
- }
-
- // Retrieve the triangulation
- std::vector<Point_3> lp = off_reader.get_point_cloud();
-
- // Define the periodic cube
- P3DT3 pdt(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)
- pdt.insert(lp.begin(), lp.end(), true);
- // As pdt won't be modified anymore switch to 1-sheeted cover if possible
- if (pdt.is_triangulation_in_1_sheet()) pdt.convert_to_1_sheeted_covering();
- std::cout << "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(pdt, 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();
- int dim_max = 0;
- Filtration_value filtration_max = 0.0;
- 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++;
- if (dim_max < 3) {
- // Cell is of dim 3
- dim_max = 3;
- }
- } else if (const Facet * facet = CGAL::object_cast<Facet>(&object_iterator)) {
- vertex_list = from_facet<Vertex_list, Facet>(*facet);
- count_facets++;
- if (dim_max < 2) {
- // Facet is of dim 2
- dim_max = 2;
- }
- } else if (const Edge_3 * edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
- vertex_list = from_edge<Vertex_list, Edge_3>(*edge);
- count_edges++;
- if (dim_max < 1) {
- // Edge_3 is of dim 1
- dim_max = 1;
- }
- } else if (const Alpha_shape_3::Vertex_handle * vertex =
- CGAL::object_cast<Alpha_shape_3::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_tree;
- 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_tree.push_back(vertex);
- map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(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_tree.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
- if (filtr > filtration_max) {
- filtration_max = filtr;
- }
- simplex_tree.insert_simplex(the_simplex_tree, filtr);
- if (the_alpha_value_iterator != the_alpha_values.end())
- ++the_alpha_value_iterator;
- else
- std::cout << "This shall not happen" << std::endl;
- }
- simplex_tree.set_dimension(dim_max);
-
-#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;
-}