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alpha_complex_persistence.cpp
/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
* See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
* Author(s): Vincent Rouvreau
*
* Copyright (C) 2016 Inria
*
* Modification(s):
* - 2024/10 Vincent Rouvreau: Add square root filtration values interface
* - YYYY/MM Author: Description of the modification
*/
#include <boost/program_options.hpp>
#include <CGAL/Epick_d.h>
#include <CGAL/Epeck_d.h>
#include <gudhi/Alpha_complex.h>
#include <gudhi/Persistent_cohomology.h>
// to construct a simplex_tree from alpha complex
#include <gudhi/Simplex_tree.h>
#include <gudhi/Points_off_io.h>
#include <iostream>
#include <string>
#include <limits> // for numeric_limits
#include <vector>
#include <fstream>
using Simplex_tree = Gudhi::Simplex_tree<>;
using Filtration_value = Simplex_tree::Filtration_value;
void program_options(int argc, char *argv[], std::string &off_file_points, bool &exact, bool &fast,
bool& output_squared_values, std::string &weight_file, std::string &output_file_diag,
Filtration_value &alpha_square_max_value, int &coeff_field_characteristic,
Filtration_value &min_persistence);
template<class Point_d>
std::vector<Point_d> read_off(const std::string &off_file_points) {
Gudhi::Points_off_reader<Point_d> off_reader(off_file_points);
if (!off_reader.is_valid()) {
std::cerr << "Alpha_complex - Unable to read file " << off_file_points << "\n";
exit(-1); // ----- >>
}
return off_reader.get_point_cloud();
}
std::vector<double> read_weight_file(const std::string &weight_file) {
std::vector<double> weights;
// Read weights information from file
std::ifstream weights_ifstr(weight_file);
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);
}
return weights;
}
template<class Kernel>
Simplex_tree create_simplex_tree(const std::string &off_file_points, const std::string &weight_file,
bool exact_version, Filtration_value alpha_square_max_value,
bool output_squared_values) {
Simplex_tree stree;
auto points = read_off<typename Kernel::Point_d>(off_file_points);
bool complex_creation = false;
if (weight_file != std::string()) {
std::vector<double> weights = read_weight_file(weight_file);
if (points.size() != weights.size()) {
std::cerr << "Alpha_complex - Inconsistency between number of points (" << points.size()
<< ") and number of weights (" << weights.size() << ")" << "\n";
exit(-1); // ----- >>
}
// Init of an alpha complex from an OFF file
Gudhi::alpha_complex::Alpha_complex<Kernel, true> alpha_complex_from_file(points, weights);
if (!output_squared_values)
std::clog << "WARNING: Weighted Alpha complex only accept to output squared values.\n";
complex_creation = alpha_complex_from_file.template create_complex<true>(stree, alpha_square_max_value,
exact_version);
} else {
// Init of an alpha complex from an OFF file
Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(points);
if (output_squared_values)
complex_creation = alpha_complex_from_file.template create_complex<true>(stree, alpha_square_max_value,
exact_version);
else
complex_creation = alpha_complex_from_file.template create_complex<false>(stree, alpha_square_max_value,
exact_version);
}
if (!complex_creation) {
std::cerr << "Alpha complex simplicial complex creation failed." << std::endl;
exit(-1);
}
return stree;
}
int main(int argc, char **argv) {
std::string weight_file;
std::string off_file_points;
std::string output_file_diag;
bool exact_version = false;
bool fast_version = false;
bool output_squared_values;
Filtration_value alpha_square_max_value;
int coeff_field_characteristic;
Filtration_value min_persistence;
program_options(argc, argv, off_file_points, exact_version, fast_version, output_squared_values, weight_file,
output_file_diag, alpha_square_max_value, coeff_field_characteristic, min_persistence);
if ((exact_version) && (fast_version)) {
std::cerr << "Exact and fast version cannot be set together." << std::endl;
exit(-1);
}
Simplex_tree stree;
if (fast_version) {
// WARNING : CGAL::Epick_d is fast but not safe (unlike CGAL::Epeck_d)
// (i.e. when the points are on a grid)
using Fast_kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
stree = create_simplex_tree<Fast_kernel>(off_file_points, weight_file, exact_version, alpha_square_max_value,
output_squared_values);
} else {
using Kernel = CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>;
stree = create_simplex_tree<Kernel>(off_file_points, weight_file, exact_version, alpha_square_max_value,
output_squared_values);
}
// ----------------------------------------------------------------------------
// Display information about the alpha complex
// ----------------------------------------------------------------------------
std::clog << "Simplicial complex is of dimension " << stree.dimension() << " - " << stree.num_simplices()
<< " simplices - " << stree.num_vertices() << " vertices." << std::endl;
std::clog << "Simplex_tree dim: " << stree.dimension() << std::endl;
// Compute the persistence diagram of the complex
Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Gudhi::persistent_cohomology::Field_Zp> pcoh(
stree);
// 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::clog << "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, bool &exact, bool &fast,
bool& output_squared_values, std::string &weight_file, std::string &output_file_diag,
Filtration_value &alpha_square_max_value, 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 ");
po::options_description visible("Allowed options", 100);
std::string str_output_squared_values;
visible.add_options()("help,h", "produce help message")(
"exact,e", po::bool_switch(&exact),
"To activate exact version of Alpha complex (default is false, not available if fast is set)")(
"fast,f", po::bool_switch(&fast),
"To activate fast version of Alpha complex (default is false, not available if exact is set)")(
"squared-filtrations,s", po::value<std::string>(&str_output_squared_values)->default_value(std::string("on")),
"To activate square filtration computations (default is 'on', can be 'off')")(
"weight-file,w", po::value<std::string>(&weight_file)->default_value(std::string()),
"Name of file containing a point weights. Format is one weight per line:\n W1\n ...\n Wn ")(
"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 standard output")(
"max-alpha-square-value,r", po::value<Filtration_value>(&alpha_square_max_value)
->default_value(std::numeric_limits<Filtration_value>::infinity()),
"Maximal alpha square value for the Alpha complex construction.")(
"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);
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::clog << std::endl;
std::clog << "Compute the persistent homology with coefficient field Z/pZ \n";
std::clog << "of an Alpha complex defined on a set of input points.\n \n";
std::clog << "Different versions of Alpha complex computation are available:\n";
std::clog << " * fast: right combinatorics, values can be arbitrarily bad\n";
std::clog << " * safe (default): values can have a relative error at most 1e-5\n";
std::clog << " * exact: true values rounded to double.\n\n";
std::clog << "Default Alpha complex filtrations computation are square of the circumradius of the simplex.\n";
std::clog << "If you are interested in the circumradius of the simplex as filtration values, pass the ";
std::clog << "'--squared-filtrations off' (or '-s off') option.\n";
std::clog << "Alpha complex can be, or not, weighted (requires a file containing weights values).\n\n";
std::clog << "Weighted Alpha complex can have negative filtration values, this is the reason why '-s off' or "; std::clog << "'--square-root-filtrations off' is ignored in this case (filtration values would be Nan in this ";
std::clog << "case).\n\n";
std::clog << "The output diagram contains one bar per line, written with the convention: \n";
std::clog << " p dim b d \n";
std::clog << "where dim is the dimension of the homological feature,\n";
std::clog << "b and d are respectively the birth and death of the feature and \n";
std::clog << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
std::clog << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
std::clog << visible << std::endl;
exit(-1);
}
// To lower case
std::transform(str_output_squared_values.begin(), str_output_squared_values.end(), str_output_squared_values.begin(),
[](unsigned char c){ return std::tolower(c); });
if (str_output_squared_values == "on")
output_squared_values = true;
else if (str_output_squared_values == "off")
output_squared_values = false;
else {
std::clog << "'--squared-filtrations' (or '-s') option cannot be set with '" << str_output_squared_values;
std::clog << "'. Only 'on' or 'off' are accepted.";
exit(-1);
}
}
Gudhi::Points_off_reader
OFF file reader implementation in order to read points from an OFF file.
Definition Points_off_io.h:122
Gudhi::Simplex_tree
Simplex Tree data structure for representing simplicial complexes.
Definition Simplex_tree.h:98
Gudhi::Simplex_tree< Gudhi::Simplex_tree_options_fast_persistence >::Filtration_value
Options::Filtration_value Filtration_value
Definition Simplex_tree.h:105
Gudhi::Simplex_tree::num_vertices
size_t num_vertices() const
Returns the number of vertices in the complex.
Definition Simplex_tree.h:778
Gudhi::Simplex_tree::num_simplices
size_t num_simplices() const
Returns the number of simplices in the simplex_tree.
Definition Simplex_tree.h:791
Gudhi::alpha_complex::Alpha_complex
Alpha complex data structure.
Definition Alpha_complex.h:103
Gudhi::persistent_cohomology::Persistent_cohomology
Computes the persistent cohomology of a filtered complex.
Definition Persistent_cohomology.h:54