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periodic_cubical_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): Pawel Dlotko
*
* Copyright (C) 2015 Inria
*
* Modification(s):
* - YYYY/MM Author: Description of the modification
*/
#include <gudhi/reader_utils.h>
#include <gudhi/Bitmap_cubical_complex.h>
#include <gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h>
#include <gudhi/Persistent_cohomology.h>
// standard stuff
#include <iostream>
#include <sstream>
#include <vector>
#include <string>
int main(int argc, char** argv) {
std::clog
<< "This program computes persistent homology, by using "
<< "Bitmap_cubical_complex_periodic_boundary_conditions class, of cubical complexes provided in text files in "
<< "Perseus style (the only numbered in the first line is a dimension D of a bitmap. In the lines I between 2 "
<< "and D+1 there are numbers of top dimensional cells in the direction I. Let N denote product of the numbers "
<< "in the lines between 2 and D. In the lines D+2 to D+2+N there are filtrations of top dimensional cells. We "
<< "assume that the cells are in the lexicographical order. See CubicalOneSphere.txt or CubicalTwoSphere.txt for"
<< " example.\n"
<< std::endl;
if (argc != 2) {
std::cerr << "Wrong number of parameters. Please provide the name of a file with a Perseus style bitmap at "
<< "the input. The program will now terminate.\n";
return 1;
}
typedef Gudhi::cubical_complex::Bitmap_cubical_complex_periodic_boundary_conditions_base<double> Bitmap_base;
typedef Gudhi::cubical_complex::Bitmap_cubical_complex<Bitmap_base> Bitmap_cubical_complex;
Bitmap_cubical_complex b(argv[1]);
typedef Gudhi::persistent_cohomology::Field_Zp Field_Zp;
typedef Gudhi::persistent_cohomology::Persistent_cohomology<Bitmap_cubical_complex, Field_Zp> Persistent_cohomology;
// Compute the persistence diagram of the complex
Persistent_cohomology pcoh(b, true);
int p = 11;
double min_persistence = 0;
pcoh.init_coefficients(p); // initializes the coefficient field for homology
pcoh.compute_persistent_cohomology(min_persistence);
std::string output_file_name(argv[1]);
output_file_name += "_persistence";
std::size_t last_in_path = output_file_name.find_last_of("/\\");
if (last_in_path != std::string::npos) {
output_file_name = output_file_name.substr(last_in_path + 1);
}
std::ofstream out(output_file_name.c_str());
pcoh.output_diagram(out);
out.close();
std::clog << "Result in file: " << output_file_name << "\n";
return 0;
}
Gudhi::cubical_complex::Bitmap_cubical_complex_periodic_boundary_conditions_base
Cubical complex with periodic boundary conditions represented as a bitmap.
Definition Bitmap_cubical_complex_periodic_boundary_conditions_base.h:41
Gudhi::cubical_complex::Bitmap_cubical_complex
Cubical complex represented as a bitmap.
Definition Bitmap_cubical_complex.h:49
Gudhi::persistent_cohomology::Field_Zp
Structure representing the coefficient field .
Definition Field_Zp.h:27
Gudhi::persistent_cohomology::Persistent_cohomology
Computes the persistent cohomology of a filtered complex.
Definition Persistent_cohomology.h:54
Gudhi::persistent_cohomology::Persistent_cohomology::output_diagram
void output_diagram(std::ostream &ostream=std::cout)
Output the persistence diagram in ostream.
Definition Persistent_cohomology.h:562
Gudhi::persistent_cohomology::Persistent_cohomology::compute_persistent_cohomology
void compute_persistent_cohomology(Filtration_value min_interval_length=0)
Compute the persistent homology of the filtered simplicial complex.
Definition Persistent_cohomology.h:168
Gudhi::persistent_cohomology::Persistent_cohomology::init_coefficients
void init_coefficients(int charac)
Initializes the coefficient field.
Definition Persistent_cohomology.h:152
reader_utils.h
This file includes common file reader for GUDHI.