diff options
Diffstat (limited to 'src/Simplex_tree/include')
4 files changed, 142 insertions, 6 deletions
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index d48f6616..4d94c037 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -187,6 +187,12 @@ class Simplex_tree { typedef Simplex_tree_boundary_simplex_iterator<Simplex_tree> Boundary_simplex_iterator; /** \brief Range over the simplices of the boundary of a simplex. */ typedef boost::iterator_range<Boundary_simplex_iterator> Boundary_simplex_range; + /** \brief Iterator over the simplices of the boundary of a simplex and their opposite vertices. + * + * 'value_type' is std::pair<Simplex_handle, Vertex_handle>. */ + typedef Simplex_tree_boundary_opposite_vertex_simplex_iterator<Simplex_tree> Boundary_opposite_vertex_simplex_iterator; + /** \brief Range over the simplices of the boundary of a simplex and their opposite vertices. */ + typedef boost::iterator_range<Boundary_opposite_vertex_simplex_iterator> Boundary_opposite_vertex_simplex_range; /** \brief Iterator over the simplices of the simplicial complex. * * 'value_type' is Simplex_handle. */ @@ -296,6 +302,23 @@ class Simplex_tree { Boundary_simplex_iterator(this)); } + /** \brief Given a simplex, returns a range over the simplices of its boundary and their opposite vertices. + * + * The boundary of a simplex is the set of codimension \f$1\f$ subsimplices of the simplex. + * If the simplex is \f$[v_0, \cdots ,v_d]\f$, with canonical orientation induced by \f$ v_0 < \cdots < v_d \f$, the + * iterator enumerates the simplices of the boundary in the order: + * \f$[v_0,\cdots,\widehat{v_i},\cdots,v_d]\f$ for \f$i\f$ from \f$d\f$ to \f$0\f$, where \f$\widehat{v_i}\f$ means + * that the vertex \f$v_i\f$, known as the opposite vertex, is omitted from boundary, but returned as the second + * element of a pair. + * + * @param[in] sh Simplex for which the boundary is computed. + */ + template<class SimplexHandle> + Boundary_opposite_vertex_simplex_range boundary_opposite_vertex_simplex_range(SimplexHandle sh) { + return Boundary_opposite_vertex_simplex_range(Boundary_opposite_vertex_simplex_iterator(this, sh), + Boundary_opposite_vertex_simplex_iterator(this)); + } + /** @} */ // end range and iterator methods /** \name Constructor/Destructor * @{ */ @@ -942,7 +965,7 @@ class Simplex_tree { // If we reached the end of the vertices, and the simplex has more vertices than the given simplex // => we found a coface - // Add a coface if we wan't the star or if the number of vertices of the current simplex matches with nbVertices + // Add a coface if we want the star or if the number of vertices of the current simplex matches with nbVertices bool addCoface = (star || curr_nbVertices == nbVertices); if (addCoface) cofaces.push_back(simplex); @@ -1060,8 +1083,8 @@ class Simplex_tree { * * Inserts all vertices and edges given by a OneSkeletonGraph. * OneSkeletonGraph must be a model of - * <a href="http://www.boost.org/doc/libs/1_76_0/libs/graph/doc/VertexAndEdgeListGraph.html">boost::VertexAndEdgeListGraph</a> - * and <a href="http://www.boost.org/doc/libs/1_76_0/libs/graph/doc/PropertyGraph.html">boost::PropertyGraph</a>. + * <a href="https://www.boost.org/doc/libs/release/libs/graph/doc/VertexAndEdgeListGraph.html">boost::VertexAndEdgeListGraph</a> + * and <a href="https://www.boost.org/doc/libs/release/libs/graph/doc/PropertyGraph.html">boost::PropertyGraph</a>. * * The vertex filtration value is accessible through the property tag * vertex_filtration_t. @@ -1468,7 +1491,7 @@ class Simplex_tree { int sh_dimension = dimension(sh); if (sh_dimension >= dimension_) - // Stop browsing as soon as the dimension is reached, no need to go furter + // Stop browsing as soon as the dimension is reached, no need to go further return false; new_dimension = (std::max)(new_dimension, sh_dimension); } diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h index e5522cc7..394c6ee1 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h @@ -5,6 +5,7 @@ * Copyright (C) 2014 Inria * * Modification(s): + * - 2022/04 Vincent Rouvreau: Add Simplex_tree_boundary_opposite_vertex_simplex_iterator for alpha and cech purpose * - YYYY/MM Author: Description of the modification */ @@ -17,6 +18,7 @@ #include <boost/container/static_vector.hpp> #include <vector> +#include <utility> // for std::pair namespace Gudhi { @@ -123,7 +125,7 @@ class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade< private: friend class boost::iterator_core_access; -// valid when iterating along the SAME boundary. + // valid when iterating along the SAME boundary. bool equal(Simplex_tree_boundary_simplex_iterator const& other) const { return sh_ == other.sh_; } @@ -178,6 +180,116 @@ class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade< Simplex_handle sh_; // current Simplex_handle in the boundary SimplexTree * st_; // simplex containing the simplicial complex }; + +/* \brief Iterator over the simplices of the boundary of a simplex and their opposite vertices. + * + * Forward iterator, value_type is std::pair<SimplexTree::Simplex_handle, SimplexTree::Vertex_handle>.*/ +template<class SimplexTree> +class Simplex_tree_boundary_opposite_vertex_simplex_iterator : public boost::iterator_facade< + Simplex_tree_boundary_opposite_vertex_simplex_iterator<SimplexTree>, + std::pair<typename SimplexTree::Simplex_handle, typename SimplexTree::Vertex_handle> const, boost::forward_traversal_tag> { + public: + using Simplex_handle = typename SimplexTree::Simplex_handle; + using Vertex_handle = typename SimplexTree::Vertex_handle; + using Siblings = typename SimplexTree::Siblings; + + // For cython purpose only. The object it initializes should be overwritten ASAP and never used before it is + // overwritten. + Simplex_tree_boundary_opposite_vertex_simplex_iterator() + : sib_(nullptr), + st_(nullptr) { + } + + // any end() iterator + explicit Simplex_tree_boundary_opposite_vertex_simplex_iterator(SimplexTree * st) + : last_(st->null_vertex()), + next_(st->null_vertex()), + sib_(nullptr), + baov_(st->null_simplex(), st->null_vertex()), + st_(st) { + } + + template<class SimplexHandle> + Simplex_tree_boundary_opposite_vertex_simplex_iterator(SimplexTree * st, SimplexHandle sh) + : last_(sh->first), + next_(st->null_vertex()), + sib_(nullptr), + baov_(st->null_simplex(), sh->first), + st_(st) { + // Only check once at the beginning instead of for every increment, as this is expensive. + if (SimplexTree::Options::contiguous_vertices) + GUDHI_CHECK(st_->contiguous_vertices(), "The set of vertices is not { 0, ..., n } without holes"); + Siblings * sib = st->self_siblings(sh); + next_ = sib->parent(); + sib_ = sib->oncles(); + if (sib_ != nullptr) { + if (SimplexTree::Options::contiguous_vertices && sib_->oncles() == nullptr) + // Only relevant for edges + baov_.first = sib_->members_.begin()+next_; + else + baov_.first = sib_->find(next_); + } + } + + private: + friend class boost::iterator_core_access; + + // valid when iterating along the SAME boundary. + bool equal(Simplex_tree_boundary_opposite_vertex_simplex_iterator const& other) const { + return (baov_.first == other.baov_.first); + } + + std::pair<Simplex_handle, Vertex_handle> const& dereference() const { + return baov_; + } + + void increment() { + if (sib_ == nullptr) { + baov_.first = st_->null_simplex(); + return; // ------>> + } + Siblings * for_sib = sib_; + Siblings * new_sib = sib_->oncles(); + auto rit = suffix_.rbegin(); + if (SimplexTree::Options::contiguous_vertices && new_sib == nullptr) { + // We reached the root, use a short-cut to find a vertex. + if (rit == suffix_.rend()) { + baov_.second = baov_.first->first; + // Segment, this vertex is the last boundary simplex + baov_.first = for_sib->members_.begin()+last_; + sib_ = nullptr; + return; + } else { + // Dim >= 2, initial step of the descent + baov_.first = for_sib->members_.begin()+*rit; + for_sib = baov_.first->second.children(); + ++rit; + } + } + for (; rit != suffix_.rend(); ++rit) { + baov_.first = for_sib->find(*rit); + for_sib = baov_.first->second.children(); + } + baov_.first = for_sib->find(last_); // baov_.first points to the right simplex now + suffix_.push_back(next_); + next_ = sib_->parent(); + sib_ = new_sib; + baov_.second = suffix_.back(); + } + + // Most of the storage should be moved to the range, iterators should be light. + Vertex_handle last_; // last vertex of the simplex + Vertex_handle next_; // next vertex to push in suffix_ + // 40 seems a conservative bound on the dimension of a Simplex_tree for now, + // as it would not fit on the biggest hard-drive. + boost::container::static_vector<Vertex_handle, 40> suffix_; + // static_vector still has some overhead compared to a trivial hand-made + // version using std::aligned_storage, or compared to making suffix_ static. + Siblings * sib_; // where the next search will start from + std::pair<Simplex_handle, Vertex_handle> baov_; // a pair containing the current Simplex_handle in the boundary and its opposite vertex + SimplexTree * st_; // simplex containing the simplicial complex +}; + /*---------------------------------------------------------------------------*/ /* \brief Iterator over the simplices of a simplicial complex. * diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h index ae140859..ad53710c 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h @@ -24,7 +24,7 @@ namespace Gudhi { * \brief Node of a simplex tree with filtration value * and simplex key. * - * It stores explicitely its own filtration value and its own Simplex_key. + * It stores explicitly its own filtration value and its own Simplex_key. */ template<class SimplexTree> struct Simplex_tree_node_explicit_storage : SimplexTree::Filtration_simplex_base, SimplexTree::Key_simplex_base { diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h index b53bad29..ae25d290 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h @@ -36,6 +36,7 @@ class Simplex_tree_siblings { template<class T> friend class Simplex_tree_boundary_simplex_iterator; template<class T> friend class Simplex_tree_complex_simplex_iterator; template<class T> friend class Simplex_tree_skeleton_simplex_iterator; + template<class T> friend class Simplex_tree_boundary_opposite_vertex_simplex_iterator; typedef typename SimplexTree::Vertex_handle Vertex_handle; typedef typename SimplexTree::Filtration_value Filtration_value; |