Persistent_cohomology/rips_persistence_via_boundary_matrix.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): Clément Maria, Marc Glisse
*
* 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 <gudhi/Simplex_tree.h>
#include <gudhi/Persistent_cohomology.h>
#include <gudhi/Rips_complex.h>
#include <gudhi/Hasse_complex.h>
#include <gudhi/Points_off_io.h>
#include <boost/program_options.hpp>
#ifdef GUDHI_USE_TBB
#include <tbb/task_scheduler_init.h>
#endif
#include <string>
#include <vector>
// //
// WARNING: persistence computation itself is not parallel, //
// and this uses more memory than rips_persistence. //
// //
// Types definition
using Simplex_tree = Gudhi::Simplex_tree<>;
using Filtration_value = Simplex_tree::Filtration_value;
using Point = std::vector<double>;
using Points_off_reader = Gudhi::Points_off_reader<Point>;
void program_options(int argc, char * argv[]
, std::string & off_file_points
, std::string & filediag
, Filtration_value & threshold
, int & dim_max
, int & p
, Filtration_value & min_persistence);
int main(int argc, char * argv[]) {
std::string off_file_points;
std::string filediag;
Filtration_value threshold;
int dim_max;
int p;
Filtration_value min_persistence;
program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence);
Points_off_reader off_reader(off_file_points);
Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance());
// Construct the Rips complex in a Simplex Tree
Simplex_tree& st = *new Simplex_tree;
rips_complex_from_file.create_complex(st, dim_max);
std::cout << "The complex contains " << st.num_simplices() << " simplices \n";
std::cout << " and has dimension " << st.dimension() << " \n";
#ifdef GUDHI_USE_TBB
// Unnecessary, but clarifies which operations are parallel.
tbb::task_scheduler_init ts;
#endif
// Sort the simplices in the order of the filtration
st.initialize_filtration();
int count = 0;
for (auto sh : st.filtration_simplex_range())
st.assign_key(sh, count++);
// Convert to a more convenient representation.
Gudhi::Hasse_complex<> hcpx(st);
#ifdef GUDHI_USE_TBB
ts.terminate();
#endif
// Free some space.
delete &st;
// Compute the persistence diagram of the complex
// initializes the coefficient field for homology
pcoh.init_coefficients(p);
pcoh.compute_persistent_cohomology(min_persistence);
// Output the diagram in filediag
if (filediag.empty()) {
pcoh.output_diagram();
} else {
std::ofstream out(filediag);
pcoh.output_diagram(out);
out.close();
}
}
void program_options(int argc, char * argv[]
, std::string & off_file_points
, std::string & filediag
, Filtration_value & threshold
, int & dim_max
, int & p
, 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 ");
po::options_description visible("Allowed options", 100);
visible.add_options()
("help,h", "produce help message")
("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
"Name of file in which the persistence diagram is written. Default print in std::cout")
("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(0),
"Maximal length of an edge for the Rips complex construction.")
("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
"Maximal dimension of the Rips complex we want to compute.")
("field-charac,p", po::value<int>(&p)->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);
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")) {
std::cout << std::endl;
std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
std::cout << "of a Rips 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" << std::endl << std::endl;
std::cout << visible << std::endl;
std::abort();
}
}
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