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Diffstat (limited to 'src/GudhUI/utils/Persistence_compute.h')
-rw-r--r-- | src/GudhUI/utils/Persistence_compute.h | 106 |
1 files changed, 106 insertions, 0 deletions
diff --git a/src/GudhUI/utils/Persistence_compute.h b/src/GudhUI/utils/Persistence_compute.h new file mode 100644 index 00000000..f7974287 --- /dev/null +++ b/src/GudhUI/utils/Persistence_compute.h @@ -0,0 +1,106 @@ +/* + * Persistence_compute.h + * Created on: Jan 26, 2015 + * This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): David Salinas + * + * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + * + */ + + +#ifndef PERSISTENCE_COMPUTE_H_ +#define PERSISTENCE_COMPUTE_H_ + + +#include "gudhi/graph_simplicial_complex.h" +#include "gudhi/Simplex_tree.h" +#include "gudhi/distance_functions.h" +#include "gudhi/Persistent_cohomology.h" +#include "gudhi/Persistent_cohomology/Multi_field.h" + + +struct Persistence_params{ + int p; + double threshold; + int max_dim; + double min_pers; + + Persistence_params(int p_,double th_,int max_dim_=10,double min_pers_=0) + :p(p_),threshold(th_),max_dim(max_dim_),min_pers(min_pers_){} +}; + + +/** + * Show persistence into output stream + */ +template<typename SkBlComplex> class Persistence_compute{ +private: + SkBlComplex& complex_; + std::ostream& stream_; +public: + typedef typename SkBlComplex::Vertex_handle Vertex_handle; + typedef typename SkBlComplex::Edge_handle Edge_handle; + + /** + * @brief Compute persistence + * parameters : + * unsigned dim_max + * double threshold + * int p for Z_p + */ + Persistence_compute(SkBlComplex& complex,std::ostream& stream,const Persistence_params& params): +// +// double threshold = 0.5,unsigned dim_max = 8): + complex_(complex),stream_(stream){ + + //for now everything is copied, todo boost adapt iterators to points of SkBlComplex instead of copying to an intial vector + typedef std::vector<double> Point_t; + std::vector< Point_t > points; + points.reserve(complex.num_vertices()); + for(auto v : complex.vertex_range()){ + const auto & pt = complex.point(v); + Point_t pt_to_add(pt.cartesian_begin(),pt.cartesian_end()); + points.emplace_back(std::move(pt_to_add)); + } + + + Graph_t prox_graph = compute_proximity_graph( points, params.threshold, euclidean_distance<Point_t> ); + Gudhi::Simplex_tree<> st; + st.insert_graph(prox_graph); + st.expansion( params.max_dim ); + + Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::Simplex_tree<>,Gudhi::persistent_cohomology::Field_Zp > pcoh (st); + pcoh.init_coefficients( params.p ); //initilizes the coefficient field for homology + pcoh.compute_persistent_cohomology( INFINITY ); //put params.min_persistence + stream_<<"persistence: \n"; + pcoh.output_diagram(stream_); + } + +private: + + +}; + + + + + + +#endif /* PERSISTENCE_COMPUTE_H_ */ |