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alpha_complex_3d_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) 2014 Inria
*
* Modification(s):
* - YYYY/MM Author: Description of the modification
*/
#include <boost/program_options.hpp>
#include <boost/variant.hpp>
#include <gudhi/Alpha_complex_3d.h>
#include <gudhi/Simplex_tree.h>
#include <gudhi/Persistent_cohomology.h>
#include <gudhi/Points_3D_off_io.h>
#include <fstream>
#include <string>
#include <vector>
#include <limits> // for numeric_limits<>
// gudhi type definition
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, bool &exact, bool &safe,
std::string &weight_file, std::string &cuboid_file, std::string &output_file_diag,
Filtration_value &alpha_square_max_value, int &coeff_field_characteristic,
Filtration_value &min_persistence);
bool 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 {
return false;
}
return true;
}
bool read_cuboid_file(const std::string &cuboid_file, double &x_min, double &y_min, double &z_min, double &x_max,
double &y_max, double &z_max) {
// Read weights information from file
std::ifstream iso_cuboid_str(cuboid_file);
if (iso_cuboid_str.is_open()) {
if (!(iso_cuboid_str >> x_min >> y_min >> z_min >> x_max >> y_max >> z_max)) {
return false;
}
} else {
return false;
}
return true;
}
template <typename AlphaComplex3d>
std::vector<typename AlphaComplex3d::Bare_point_3> read_off(const std::string &off_file_points) {
// Read the OFF file (input file name given as parameter) and triangulate points
Gudhi::Points_3D_off_reader<typename AlphaComplex3d::Bare_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);
}
return off_reader.get_point_cloud();
}
int main(int argc, char **argv) {
std::string off_file_points;
std::string weight_file;
std::string cuboid_file;
std::string output_file_diag;
Filtration_value alpha_square_max_value = 0.;
int coeff_field_characteristic = 0;
Filtration_value min_persistence = 0.;
bool exact_version = false;
bool fast_version = false;
bool weighted_version = false;
bool periodic_version = false;
program_options(argc, argv, off_file_points, exact_version, fast_version, weight_file, cuboid_file, output_file_diag,
alpha_square_max_value, coeff_field_characteristic, min_persistence);
std::vector<double> weights;
if (weight_file != std::string()) {
if (!read_weight_file(weight_file, weights)) {
std::cerr << "Unable to read weights file " << weight_file << std::endl;
exit(-1);
}
weighted_version = true;
}
double x_min = 0., y_min = 0., z_min = 0., x_max = 0., y_max = 0., z_max = 0.;
std::ifstream iso_cuboid_str(argv[3]);
if (cuboid_file != std::string()) {
if (!read_cuboid_file(cuboid_file, x_min, y_min, z_min, x_max, y_max, z_max)) {
std::cerr << "Unable to read cuboid file " << cuboid_file << std::endl;
exit(-1);
}
periodic_version = true;
}
Gudhi::alpha_complex::complexity complexity = Gudhi::alpha_complex::complexity::SAFE;
if (exact_version) {
if (fast_version) {
std::cerr << "You cannot set the exact and the fast version." << std::endl;
exit(-1);
}
complexity = Gudhi::alpha_complex::complexity::EXACT;
}
if (fast_version) {
complexity = Gudhi::alpha_complex::complexity::FAST;
}
Simplex_tree simplex_tree;
switch (complexity) {
case Gudhi::alpha_complex::complexity::FAST:
if (weighted_version) {
if (periodic_version) {
using Alpha_complex_3d =
Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::FAST, true, true>;
auto points = read_off<Alpha_complex_3d>(off_file_points);
Alpha_complex_3d alpha_complex(points, weights, x_min, y_min, z_min, x_max, y_max, z_max);
alpha_complex.create_complex(simplex_tree, alpha_square_max_value);
} else {
using Alpha_complex_3d =
Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::FAST, true, false>;
auto points = read_off<Alpha_complex_3d>(off_file_points);
Alpha_complex_3d alpha_complex(points, weights);
alpha_complex.create_complex(simplex_tree, alpha_square_max_value);
}
} else {
if (periodic_version) {
using Alpha_complex_3d =
Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::FAST, false, true>;
auto points = read_off<Alpha_complex_3d>(off_file_points);
Alpha_complex_3d alpha_complex(points, x_min, y_min, z_min, x_max, y_max, z_max);
alpha_complex.create_complex(simplex_tree, alpha_square_max_value);
} else {
using Alpha_complex_3d =
Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::FAST, false, false>;
auto points = read_off<Alpha_complex_3d>(off_file_points);
Alpha_complex_3d alpha_complex(points);
alpha_complex.create_complex(simplex_tree, alpha_square_max_value);
}
}
break;
case Gudhi::alpha_complex::complexity::EXACT:
if (weighted_version) {
if (periodic_version) {
using Alpha_complex_3d =
Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::EXACT, true, true>;
auto points = read_off<Alpha_complex_3d>(off_file_points);
Alpha_complex_3d alpha_complex(points, weights, x_min, y_min, z_min, x_max, y_max, z_max);
alpha_complex.create_complex(simplex_tree, alpha_square_max_value);
} else {
using Alpha_complex_3d =
Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::EXACT, true, false>;
auto points = read_off<Alpha_complex_3d>(off_file_points);
Alpha_complex_3d alpha_complex(points, weights);
alpha_complex.create_complex(simplex_tree, alpha_square_max_value);
}
} else {
if (periodic_version) {
using Alpha_complex_3d =
Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::EXACT, false, true>;
auto points = read_off<Alpha_complex_3d>(off_file_points);
Alpha_complex_3d alpha_complex(points, x_min, y_min, z_min, x_max, y_max, z_max);
alpha_complex.create_complex(simplex_tree, alpha_square_max_value);
} else {
using Alpha_complex_3d =
Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::EXACT, false, false>;
auto points = read_off<Alpha_complex_3d>(off_file_points);
Alpha_complex_3d alpha_complex(points);
alpha_complex.create_complex(simplex_tree, alpha_square_max_value);
}
}
break;
case Gudhi::alpha_complex::complexity::SAFE:
if (weighted_version) {
if (periodic_version) {
using Alpha_complex_3d =
Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::SAFE, true, true>;
auto points = read_off<Alpha_complex_3d>(off_file_points);
Alpha_complex_3d alpha_complex(points, weights, x_min, y_min, z_min, x_max, y_max, z_max);
alpha_complex.create_complex(simplex_tree, alpha_square_max_value);
} else {
using Alpha_complex_3d =
Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::SAFE, true, false>;
auto points = read_off<Alpha_complex_3d>(off_file_points);
Alpha_complex_3d alpha_complex(points, weights);
alpha_complex.create_complex(simplex_tree, alpha_square_max_value);
}
} else {
if (periodic_version) {
using Alpha_complex_3d =
Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::SAFE, false, true>;
auto points = read_off<Alpha_complex_3d>(off_file_points);
Alpha_complex_3d alpha_complex(points, x_min, y_min, z_min, x_max, y_max, z_max);
alpha_complex.create_complex(simplex_tree, alpha_square_max_value);
} else {
using Alpha_complex_3d =
Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::SAFE, false, false>;
auto points = read_off<Alpha_complex_3d>(off_file_points);
Alpha_complex_3d alpha_complex(points);
alpha_complex.create_complex(simplex_tree, alpha_square_max_value);
}
}
break;
default:
std::cerr << "Unknown complexity value " << std::endl;
exit(-1);
break;
}
std::clog << "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::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,
std::string &weight_file, std::string &cuboid_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);
visible.add_options()("help,h", "produce help message")(
"exact,e", po::bool_switch(&exact),
"To activate exact version of Alpha complex 3d (default is false, not available if fast is set)")(
"fast,f", po::bool_switch(&fast),
"To activate fast version of Alpha complex 3d (default is false, not available if exact is set)")(
"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 ")(
"cuboid-file,c", po::value<std::string>(&cuboid_file),
"Name of file describing the periodic domain. Format is:\n min_hx min_hy min_hz\n max_hx max_hy max_hz")(
"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") || !vm.count("weight-file")) {
std::clog << std::endl;
std::clog << "Compute the persistent homology with coefficient field Z/pZ \n";
std::clog << "of a 3D Alpha complex defined on a set of input points.\n";
std::clog << "Different versions of 3D 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 << "3D Alpha complex can be, or not, weighted (requires a file containing weights values)\n";
std::clog << "and/or periodic (requires a file describing the periodic domain).\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.\n\n";
std::clog << "Usage: " << argv[0] << " [options] input-file weight-file\n\n";
std::clog << visible << std::endl;
exit(-1);
}
}
Gudhi::Points_3D_off_reader
Definition Points_3D_off_io.h:140
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::alpha_complex::Alpha_complex_3d
Alpha complex data structure for 3d specific case.
Definition Alpha_complex_3d.h:118
Gudhi::persistent_cohomology::Persistent_cohomology
Computes the persistent cohomology of a filtered complex.
Definition Persistent_cohomology.h:54
Gudhi::alpha_complex::complexity
complexity
Alpha complex complexity template parameter possible values.
Definition Alpha_complex_options.h:23
Gudhi::alpha_complex::complexity::SAFE
@ SAFE
Safe version.
Definition Alpha_complex_options.h:25
Gudhi::alpha_complex::complexity::EXACT
@ EXACT
Exact version.
Definition Alpha_complex_options.h:26
Gudhi::alpha_complex::complexity::FAST
@ FAST
Fast version.
Definition Alpha_complex_options.h:24