Persistent_cohomology/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
*
* 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 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 >;
void usage(char * const progName) {
std::cerr << "Usage: " << progName <<
" path_to_file_graph path_to_iso_cuboid_3_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 != 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_filtration(filtration_max);
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() << " ";
std::cout << " filtration = " << simplex_tree.filtration() << std::endl << std::endl;
#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;
}
GUDHI  Version 2.0.0  - C++ library for Topological Data Analysis (TDA) and Higher Dimensional Geometry Understanding. Generated on Wed Apr 19 2017 22:26:16 for GUDHI by doxygen 1.8.11