Alpha_complex/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/program_options.hpp>
#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/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>
#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::vector<Alpha_shape_3::Vertex_handle>;
// gudhi type definition
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 &cuboid_file,
std::string &output_file_diag, int &coeff_field_characteristic, Filtration_value &min_persistence);
int main(int argc, char **argv) {
std::string off_file_points;
std::string cuboid_file;
std::string output_file_diag;
int coeff_field_characteristic;
Filtration_value min_persistence;
program_options(argc, argv, off_file_points, cuboid_file, output_file_diag, coeff_field_characteristic,
min_persistence);
// 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 OFF file " << off_file_points << std::endl;
exit(-1);
}
// Read iso_cuboid_3 information from file
std::ifstream iso_cuboid_str(cuboid_file);
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 " << cuboid_file << std::endl;
exit(-1);
}
// 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);
}
// Retrieve the points
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();
} else {
std::cerr << "ERROR: we were not able to construct a triangulation within a single periodic domain." << std::endl;
exit(-1);
}
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();
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);
// Output the diagram in filediag
if (output_file_diag.empty()) {
pcoh.output_diagram();
} else {
std::cout << "Result in file: " << output_file_diag << std::endl;
std::ofstream out(output_file_diag);
pcoh.output_diagram(out);
out.close();
}
return 0;
}
void program_options(int argc, char *argv[], std::string &off_file_points, std::string &cuboid_file,
std::string &output_file_diag, int &coeff_field_characteristic,
Filtration_value &min_persistence) {
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 ")(
"cuboid-file", po::value<std::string>(&cuboid_file),
"Name of file describing the periodic domain. Format is: min_hx min_hy min_hz\nmax_hx max_hy max_hz");
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")(
"field-charac,p", po::value<int>(&coeff_field_characteristic)->default_value(11),
"Characteristic p of the coefficient field Z/pZ for computing homology.")(
"min-persistence,m", po::value<Filtration_value>(&min_persistence),
"Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length "
"intervals");
po::positional_options_description pos;
pos.add("input-file", 1);
pos.add("cuboid-file", 2);
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") || !vm.count("cuboid-file")) {
std::cout << std::endl;
std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
std::cout << "of a periodic 3D Alpha complex defined on a set of input points.\n \n";
std::cout << "The output diagram contains one bar per line, written with the convention: \n";
std::cout << " p dim b d \n";
std::cout << "where dim is the dimension of the homological feature,\n";
std::cout << "b and d are respectively the birth and death of the feature and \n";
std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
std::cout << "Usage: " << argv[0] << " [options] input-file cuboid-file" << std::endl << std::endl;
std::cout << visible << std::endl;
exit(-1);
}
}
GUDHI  Version 2.3.0  - C++ library for Topological Data Analysis (TDA) and Higher Dimensional Geometry Understanding.  - Copyright : GPL v3 Generated on Tue Sep 4 2018 14:32:59 for GUDHI by Doxygen 1.8.13