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plain_homology.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): Marc Glisse
*
* Copyright (C) 2015 Inria
*
* Modification(s):
* - YYYY/MM Author: Description of the modification
*/
#include <gudhi/Simplex_tree.h>
#include <gudhi/Persistent_cohomology.h>
#include <iostream>
#include <vector>
#include <cstdint> // for std::uint8_t
/* We could perfectly well use the default Simplex_tree<> (which uses
* Simplex_tree_options_default), the following simply demonstrates
* how to save on storage by not storing a filtration value. */
struct MyOptions : Gudhi::Simplex_tree_options_minimal {
// Implicitly use 0 as filtration value for all simplices - inherited from Simplex_tree_options_minimal
// static const bool store_filtration = false;
// However the persistence algorithm needs this
static const bool store_key = true;
// I have few vertices
typedef short Vertex_handle;
// Maximum number of simplices to compute persistence is 2^8 - 1 = 255. One is reserved for null_key
typedef std::uint8_t Simplex_key;
};
using ST = Gudhi::Simplex_tree<MyOptions>;
using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<ST, Field_Zp>;
int main() {
ST st;
/* Complex to build. */
/* 1 3 5 */
/* o---o---o */
/* / \ / */
/* o---o o */
/* 2 0 4 */
const short edge01[] = {0, 1};
const short edge02[] = {0, 2};
const short edge12[] = {1, 2};
const short edge03[] = {0, 3};
const short edge13[] = {1, 3};
const short edge35[] = {3, 5};
const short vertex4[] = {4};
st.insert_simplex_and_subfaces(edge01);
st.insert_simplex_and_subfaces(edge02);
st.insert_simplex_and_subfaces(edge12);
st.insert_simplex_and_subfaces(edge03);
st.insert_simplex(edge13);
st.insert_simplex_and_subfaces(edge35);
st.insert_simplex(vertex4);
// Class for homology computation
// By default, since the complex has dimension 1, only 0-dimensional homology would be computed.
// Here we also want persistent homology to be computed for the maximal dimension in the complex (persistence_dim_max = true)
Persistent_cohomology pcoh(st, true);
// Initialize the coefficient field Z/2Z for homology
pcoh.init_coefficients(2);
// Compute the persistence diagram of the complex
pcoh.compute_persistent_cohomology();
// Print the result. The format is, on each line: 2 dim 0 inf
// where 2 represents the field, dim the dimension of the feature.
// 2 0 0 inf
// 2 0 0 inf
// 2 1 0 inf
// 2 1 0 inf
// means that in Z/2Z-homology, the Betti numbers are b0=2 and b1=2.
pcoh.output_diagram();
// Print the Betti numbers are b0=2 and b1=2.
std::clog << std::endl;
std::clog << "The Betti numbers are : ";
for (int i = 0; i < 3; i++)
std::clog << "b" << i << " = " << pcoh.betti_number(i) << " ; ";
std::clog << std::endl;
}
Gudhi::Simplex_tree
Simplex Tree data structure for representing simplicial complexes.
Definition Simplex_tree.h:98
Gudhi::Simplex_tree::insert_simplex
std::pair< Simplex_handle, bool > insert_simplex(const InputVertexRange &simplex, Filtration_value filtration=0)
Insert a simplex, represented by a range of Vertex_handles, in the simplicial complex.
Definition Simplex_tree.h:1045
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
Gudhi::Simplex_tree_options_minimal
Definition simplex_tree_options.h:64