diff options
Diffstat (limited to 'trunk/src/Hasse_complex/include/gudhi/Hasse_complex.h')
-rw-r--r-- | trunk/src/Hasse_complex/include/gudhi/Hasse_complex.h | 248 |
1 files changed, 248 insertions, 0 deletions
diff --git a/trunk/src/Hasse_complex/include/gudhi/Hasse_complex.h b/trunk/src/Hasse_complex/include/gudhi/Hasse_complex.h new file mode 100644 index 00000000..e67f7609 --- /dev/null +++ b/trunk/src/Hasse_complex/include/gudhi/Hasse_complex.h @@ -0,0 +1,248 @@ +/* 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): Clément Maria + * + * 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 HASSE_COMPLEX_H_ +#define HASSE_COMPLEX_H_ + +#include <gudhi/allocator.h> + +#include <boost/iterator/counting_iterator.hpp> + +#include <algorithm> +#include <utility> // for pair +#include <vector> +#include <limits> // for infinity value + +#ifdef GUDHI_USE_TBB +#include <tbb/parallel_for.h> +#endif + +namespace Gudhi { + +template < class HasseCpx > +struct Hasse_simplex { + // Complex_ds must verify that cpx->key(sh) is the order of sh in the filtration + + template< class Complex_ds > + Hasse_simplex(Complex_ds & cpx + , typename Complex_ds::Simplex_handle sh) + : filtration_(cpx.filtration(sh)) + , boundary_() { + boundary_.reserve(cpx.dimension(sh) + 1); + for (auto b_sh : cpx.boundary_simplex_range(sh)) { + boundary_.push_back(cpx.key(b_sh)); + } + } + + Hasse_simplex(typename HasseCpx::Simplex_key key + , typename HasseCpx::Filtration_value fil + , std::vector<typename HasseCpx::Simplex_handle> const& boundary) + : key_(key) + , filtration_(fil) + , boundary_(boundary) { } + + typename HasseCpx::Simplex_key key_; + typename HasseCpx::Filtration_value filtration_; + std::vector<typename HasseCpx::Simplex_handle> boundary_; +}; + +/** \private + * \brief Data structure representing a Hasse diagram, i.e. + * a complex where all codimension 1 incidence + * relations are explicitly encoded. + * + * \implements FilteredComplex + * \ingroup simplex_tree + */ +template < typename FiltrationValue = double +, typename SimplexKey = int +, typename VertexHandle = int +> +class Hasse_complex { + public: + typedef Hasse_simplex<Hasse_complex> Hasse_simp; + typedef FiltrationValue Filtration_value; + typedef SimplexKey Simplex_key; + typedef int Simplex_handle; // index in vector complex_ + + typedef boost::counting_iterator< Simplex_handle > Filtration_simplex_iterator; + typedef boost::iterator_range<Filtration_simplex_iterator> Filtration_simplex_range; + + typedef typename std::vector< Simplex_handle >::iterator Boundary_simplex_iterator; + typedef boost::iterator_range<Boundary_simplex_iterator> Boundary_simplex_range; + + typedef typename std::vector< Simplex_handle >::iterator Skeleton_simplex_iterator; + typedef boost::iterator_range< Skeleton_simplex_iterator > Skeleton_simplex_range; + + /* only dimension 0 skeleton_simplex_range(...) */ + Skeleton_simplex_range skeleton_simplex_range(int dim = 0) { + if (dim != 0) { + std::cerr << "Dimension must be 0 \n"; + } + return Skeleton_simplex_range(vertices_.begin(), vertices_.end()); + } + + template < class Complex_ds > + Hasse_complex(Complex_ds & cpx) + : complex_(cpx.num_simplices()) + , vertices_() + , num_vertices_() + , dim_max_(cpx.dimension()) { + int size = complex_.size(); +#ifdef GUDHI_USE_TBB + tbb::parallel_for(0, size, [&](int idx){new (&complex_[idx]) Hasse_simp(cpx, cpx.simplex(idx));}); + for (int idx=0; idx < size; ++idx) + if (complex_[idx].boundary_.empty()) + vertices_.push_back(idx); +#else + for (int idx=0; idx < size; ++idx) { + new (&complex_[idx]) Hasse_simp(cpx, cpx.simplex(idx)); + if (complex_[idx].boundary_.empty()) + vertices_.push_back(idx); + } +#endif + } + + Hasse_complex() + : complex_() + , vertices_() + , num_vertices_(0) + , dim_max_(-1) { } + + size_t num_simplices() { + return complex_.size(); + } + + Filtration_simplex_range filtration_simplex_range() { + return Filtration_simplex_range(Filtration_simplex_iterator(0) + , Filtration_simplex_iterator(complex_.size())); + } + + Simplex_key key(Simplex_handle sh) { + return complex_[sh].key_; + } + + Simplex_key null_key() { + return -1; + } + + Simplex_handle simplex(Simplex_key key) { + if (key == null_key()) return null_simplex(); + return key; + } + + Simplex_handle null_simplex() { + return -1; + } + + Filtration_value filtration(Simplex_handle sh) { + if (sh == null_simplex()) { + return std::numeric_limits<Filtration_value>::infinity(); + } + return complex_[sh].filtration_; + } + + int dimension(Simplex_handle sh) { + if (complex_[sh].boundary_.empty()) return 0; + return complex_[sh].boundary_.size() - 1; + } + + int dimension() { + return dim_max_; + } + + std::pair<Simplex_handle, Simplex_handle> endpoints(Simplex_handle sh) { + return std::pair<Simplex_handle, Simplex_handle>(complex_[sh].boundary_[0] + , complex_[sh].boundary_[1]); + } + + void assign_key(Simplex_handle sh, Simplex_key key) { + complex_[sh].key_ = key; + } + + Boundary_simplex_range boundary_simplex_range(Simplex_handle sh) { + return Boundary_simplex_range(complex_[sh].boundary_.begin() + , complex_[sh].boundary_.end()); + } + + void display_simplex(Simplex_handle sh) { + std::cout << dimension(sh) << " "; + for (auto sh_b : boundary_simplex_range(sh)) std::cout << sh_b << " "; + std::cout << " " << filtration(sh) << " key=" << key(sh); + } + + void initialize_filtration() { + // Setting the keys is done by pcoh, Simplex_tree doesn't do it either. +#if 0 + Simplex_key key = 0; + for (auto & h_simp : complex_) + h_simp.key_ = key++; +#endif + } + + std::vector< Hasse_simp, Gudhi::no_init_allocator<Hasse_simp> > complex_; + std::vector<Simplex_handle> vertices_; + size_t num_vertices_; + int dim_max_; +}; + +template< typename T1, typename T2, typename T3 > +std::istream& operator>>(std::istream & is + , Hasse_complex< T1, T2, T3 > & hcpx) { + assert(hcpx.num_simplices() == 0); + + size_t num_simp; + is >> num_simp; + hcpx.complex_.reserve(num_simp); + + std::vector< typename Hasse_complex<T1, T2, T3>::Simplex_key > boundary; + typename Hasse_complex<T1, T2, T3>::Filtration_value fil; + typename Hasse_complex<T1, T2, T3>::Filtration_value max_fil = 0; + int max_dim = -1; + int key = 0; + // read all simplices in the file as a list of vertices + while (read_hasse_simplex(is, boundary, fil)) { + // insert every simplex in the simplex tree + hcpx.complex_.emplace_back(key, fil, boundary); + + if (max_dim < hcpx.dimension(key)) { + max_dim = hcpx.dimension(key); + } + if (hcpx.dimension(key) == 0) { + hcpx.vertices_.push_back(key); + } + if (max_fil < fil) { + max_fil = fil; + } + + ++key; + boundary.clear(); + } + + hcpx.dim_max_ = max_dim; + + return is; +} + +} // namespace Gudhi + +#endif // HASSE_COMPLEX_H_ |