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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/program_options.hpp>
#include <boost/variant.hpp>
#include <gudhi/Alpha_complex_3d.h>
#include <gudhi/Alpha_complex_3d_options.h>
#include <gudhi/Simplex_tree.h>
#include <gudhi/Persistent_cohomology.h>
#include <gudhi/Points_3D_off_io.h>
#include <fstream>
#include <cmath>
#include <string>
#include <tuple>
#include <map>
#include <utility>
#include <vector>
#include <cstdlib>
#include "alpha_complex_3d_helper.h"
// gudhi type definition
using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::Weighted_alpha_shapes_3d>;
using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
using Filtration_value = Simplex_tree::Filtration_value;
using Persistent_cohomology =
Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Gudhi::persistent_cohomology::Field_Zp>;
void program_options(int argc, char *argv[], std::string &off_file_points, std::string &weight_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 weight_file;
std::string output_file_diag;
int coeff_field_characteristic;
Filtration_value min_persistence;
program_options(argc, argv, off_file_points, weight_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<Alpha_complex_3d::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 weights information from file
std::ifstream weights_ifstr(weight_file);
std::vector<double> weights;
if (weights_ifstr.good()) {
double weight = 0.0;
// Attempt read the weight in a double format, return false if it fails
while (weights_ifstr >> weight) {
weights.push_back(weight);
}
} else {
std::cerr << "Unable to read weights file " << weight_file << std::endl;
exit(-1);
}
Alpha_complex_3d alpha_complex(off_reader.get_point_cloud(), weights);
Simplex_tree simplex_tree;
alpha_complex.create_complex(simplex_tree);
// 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 &weight_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 ")(
"weight-file", po::value<std::string>(&weight_file),
"Name of file containing a point weights. Format is one weigt per line: W1\n...\nWn ");
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("weight-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("weight-file")) {
std::cout << std::endl;
std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
std::cout << "of a weighted 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 weight-file" << std::endl << std::endl;
std::cout << visible << std::endl;
std::abort();
}
}
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