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persistence_from_simple_simplex_tree.cpp

# Subsampling

/* 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 <gudhi/graph_simplicial_complex.h>
#include <gudhi/Simplex_tree.h>
#include <gudhi/Persistent_cohomology.h>
#include <iostream>
#include <ctime>
#include <utility>
#include <vector>
// Types definition
using Simplex_tree = Gudhi::Simplex_tree<>;
using Filtration_value = Simplex_tree::Filtration_value;
using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp >;
using typeVectorVertex = std::vector< Simplex_tree::Vertex_handle >;
void usage(char * const progName) {
std::cerr << "Usage: " << progName << " coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
exit(-1);
}
int main(int argc, char * const argv[]) {
// program args management
if (argc != 3) {
std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
usage(argv[0]);
}
int coeff_field_characteristic = 0;
int returnedScanValue = sscanf(argv[1], "%d", &coeff_field_characteristic);
if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) {
std::cerr << "Error: " << argv[1] << " is not correct\n";
usage(argv[0]);
}
Filtration_value min_persistence = 0.0;
returnedScanValue = sscanf(argv[2], "%lf", &min_persistence);
if ((returnedScanValue == EOF) || (min_persistence < -1.0)) {
std::cerr << "Error: " << argv[2] << " is not correct\n";
usage(argv[0]);
}
// TEST OF INSERTION
std::clog << "********************************************************************" << std::endl;
std::clog << "TEST OF INSERTION" << std::endl;
Simplex_tree st;
// ++ FIRST
std::clog << " - INSERT (0,1,2)" << std::endl;
typeVectorVertex SimplexVector = {0, 1, 2};
st.insert_simplex_and_subfaces(SimplexVector, 0.3);
// ++ SECOND
std::clog << " - INSERT 3" << std::endl;
SimplexVector = {3};
st.insert_simplex_and_subfaces(SimplexVector, 0.1);
// ++ THIRD
std::clog << " - INSERT (0,3)" << std::endl;
SimplexVector = {0, 3};
st.insert_simplex_and_subfaces(SimplexVector, 0.2);
// ++ FOURTH
std::clog << " - INSERT (0,1) (already inserted)" << std::endl;
SimplexVector = {0, 1};
st.insert_simplex_and_subfaces(SimplexVector, 0.2);
// ++ FIFTH
std::clog << " - INSERT (3,4,5)" << std::endl;
SimplexVector = {3, 4, 5};
st.insert_simplex_and_subfaces(SimplexVector, 0.3);
// ++ SIXTH
std::clog << " - INSERT (0,1,6,7)" << std::endl;
SimplexVector = {0, 1, 6, 7};
st.insert_simplex_and_subfaces(SimplexVector, 0.4);
// ++ SEVENTH
std::clog << " - INSERT (4,5,8,9)" << std::endl;
SimplexVector = {4, 5, 8, 9};
st.insert_simplex_and_subfaces(SimplexVector, 0.4);
// ++ EIGHTH
std::clog << " - INSERT (9,10,11)" << std::endl;
SimplexVector = {9, 10, 11};
st.insert_simplex_and_subfaces(SimplexVector, 0.3);
// ++ NINTH
std::clog << " - INSERT (2,10,12)" << std::endl;
SimplexVector = {2, 10, 12};
st.insert_simplex_and_subfaces(SimplexVector, 0.3);
// ++ TENTH
std::clog << " - INSERT (11,6)" << std::endl;
SimplexVector = {6, 11};
st.insert_simplex_and_subfaces(SimplexVector, 0.2);
// ++ ELEVENTH
std::clog << " - INSERT (13,14,15)" << std::endl;
SimplexVector = {13, 14, 15};
st.insert_simplex_and_subfaces(SimplexVector, 0.25);
/* Inserted simplex: */
/* 1 6 */
/* o---o */
/* /X\7/ 4 2 */
/* o---o---o---o o */
/* 2 0 3\X/8\ 10 /X\ */
/* o---o---o---o */
/* 5 9\X/ 12 */
/* o---o */
/* 11 6 */
/* In other words: */
/* A facet [2,1,0] */
/* An edge [0,3] */
/* A facet [3,4,5] */
/* A cell [0,1,6,7] */
/* A cell [4,5,8,9] */
/* A facet [9,10,11] */
/* An edge [11,6] */
/* An edge [10,12,2] */
std::clog << "The complex contains " << st.num_simplices() << " simplices - " << st.num_vertices() << " vertices "
<< std::endl;
std::clog << " - dimension " << st.dimension() << std::endl;
std::clog << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:"
<< std::endl;
std::clog << "**************************************************************" << std::endl;
std::clog << "strict graph G { " << std::endl;
for (auto f_simplex : st.filtration_simplex_range()) {
std::clog << " " << "[" << st.filtration(f_simplex) << "] ";
for (auto vertex : st.simplex_vertex_range(f_simplex)) {
std::clog << static_cast<int>(vertex) << " -- ";
}
std::clog << ";" << std::endl;
}
std::clog << "}" << std::endl;
std::clog << "**************************************************************" << std::endl;
// Compute the persistence diagram of the complex
Persistent_cohomology pcoh(st);
// initializes the coefficient field for homology
pcoh.init_coefficients(coeff_field_characteristic);
pcoh.compute_persistent_cohomology(min_persistence);
// Output the diagram in filediag
pcoh.output_diagram();
return 0;
}
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::simplex_vertex_range
Simplex_vertex_range simplex_vertex_range(Simplex_handle sh) const
Returns a range over the vertices of a simplex.
Definition Simplex_tree.h:369
Gudhi::Simplex_tree::filtration
static Filtration_value filtration(Simplex_handle sh)
Returns the filtration value of a simplex.
Definition Simplex_tree.h:727
Gudhi::Simplex_tree::filtration_simplex_range
Filtration_simplex_range const & filtration_simplex_range(Indexing_tag=Indexing_tag()) const
Returns a range over the simplices of the simplicial complex, in the order of the filtration.
Definition Simplex_tree.h:358
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::Simplex_tree::insert_simplex_and_subfaces
std::pair< Simplex_handle, bool > insert_simplex_and_subfaces(const InputVertexRange &Nsimplex, Filtration_value filtration=0)
Insert a N-simplex and all his subfaces, from a N-simplex represented by a range of Vertex_handles,...
Definition Simplex_tree.h:1074
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
graph_simplicial_complex.h
Graph simplicial complex methods.