diff options
Diffstat (limited to 'src/Simplex_tree/include/gudhi/Simplex_tree.h')
| -rw-r--r-- | src/Simplex_tree/include/gudhi/Simplex_tree.h | 139 |
1 files changed, 107 insertions, 32 deletions
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index 889dbd00..4177a0b8 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -24,6 +24,8 @@ #include <boost/iterator/transform_iterator.hpp> #include <boost/graph/adjacency_list.hpp> #include <boost/range/adaptor/reversed.hpp> +#include <boost/range/adaptor/transformed.hpp> +#include <boost/range/size.hpp> #include <boost/container/static_vector.hpp> #ifdef GUDHI_USE_TBB @@ -42,6 +44,10 @@ namespace Gudhi { +/** \addtogroup simplex_tree + * @{ + */ + /** * \class Extended_simplex_type Simplex_tree.h gudhi/Simplex_tree.h * \brief Extended simplex type data structure for representing the type of simplices in an extended filtration. @@ -97,8 +103,7 @@ class Simplex_tree { // Simplex_key next to each other). typedef typename boost::container::flat_map<Vertex_handle, Node> Dictionary; - /* \brief Set of nodes sharing a same parent in the simplex tree. */ - /* \brief Set of nodes sharing a same parent in the simplex tree. */ + /** \brief Set of nodes sharing a same parent in the simplex tree. */ typedef Simplex_tree_siblings<Simplex_tree, Dictionary> Siblings; @@ -187,6 +192,12 @@ 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 +307,23 @@ 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 * @{ */ @@ -676,10 +704,10 @@ class Simplex_tree { return true; } - private: - /** \brief Inserts a simplex represented by a vector of vertex. - * @param[in] simplex vector of Vertex_handles, representing the vertices of the new simplex. The vector must be - * sorted by increasing vertex handle order. + protected: + /** \brief Inserts a simplex represented by a range of vertex. + * @param[in] simplex range of Vertex_handles, representing the vertices of the new simplex. The range must be + * sorted by increasing vertex handle order, and not empty. * @param[in] filtration the filtration value assigned to the new simplex. * @return If the new simplex is inserted successfully (i.e. it was not in the * simplicial complex yet) the bool is set to true and the Simplex_handle is the handle assigned @@ -691,12 +719,13 @@ class Simplex_tree { * null_simplex. * */ - std::pair<Simplex_handle, bool> insert_vertex_vector(const std::vector<Vertex_handle>& simplex, + template <class RandomVertexHandleRange = std::initializer_list<Vertex_handle>> + std::pair<Simplex_handle, bool> insert_simplex_raw(const RandomVertexHandleRange& simplex, Filtration_value filtration) { Siblings * curr_sib = &root_; std::pair<Simplex_handle, bool> res_insert; auto vi = simplex.begin(); - for (; vi != simplex.end() - 1; ++vi) { + for (; vi != std::prev(simplex.end()); ++vi) { GUDHI_CHECK(*vi != null_vertex(), "cannot use the dummy null_vertex() as a real vertex"); res_insert = curr_sib->members_.emplace(*vi, Node(curr_sib, filtration)); if (!(has_children(res_insert.first))) { @@ -717,9 +746,10 @@ class Simplex_tree { return std::pair<Simplex_handle, bool>(null_simplex(), false); } // otherwise the insertion has succeeded - size is a size_type - if (static_cast<int>(simplex.size()) - 1 > dimension_) { + int dim = static_cast<int>(boost::size(simplex)) - 1; + if (dim > dimension_) { // Update dimension if needed - dimension_ = static_cast<int>(simplex.size()) - 1; + dimension_ = dim; } return res_insert; } @@ -760,7 +790,7 @@ class Simplex_tree { // Copy before sorting std::vector<Vertex_handle> copy(first, last); std::sort(std::begin(copy), std::end(copy)); - return insert_vertex_vector(copy, filtration); + return insert_simplex_raw(copy, filtration); } /** \brief Insert a N-simplex and all his subfaces, from a N-simplex represented by a range of @@ -942,7 +972,7 @@ 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 +1090,8 @@ 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_65_1/libs/graph/doc/EdgeListGraph.html">boost::EdgeListGraph</a> - * and <a href="http://www.boost.org/doc/libs/1_65_1/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. @@ -1081,7 +1111,10 @@ class Simplex_tree { // the simplex tree must be empty assert(num_simplices() == 0); - if (boost::num_vertices(skel_graph) == 0) { + // is there a better way to let the compiler know that we don't mean Simplex_tree::num_vertices? + using boost::num_vertices; + + if (num_vertices(skel_graph) == 0) { return; } if (num_edges(skel_graph) == 0) { @@ -1090,25 +1123,21 @@ class Simplex_tree { dimension_ = 1; } - root_.members_.reserve(boost::num_vertices(skel_graph)); + root_.members_.reserve(num_vertices(skel_graph)); // probably useless in most cases + auto verts = vertices(skel_graph) | boost::adaptors::transformed([&](auto v){ + return Dit_value_t(v, Node(&root_, get(vertex_filtration_t(), skel_graph, v))); }); + root_.members_.insert(boost::begin(verts), boost::end(verts)); + // This automatically sorts the vertices, the graph concept doesn't guarantee the order in which we iterate. - typename boost::graph_traits<OneSkeletonGraph>::vertex_iterator v_it, - v_it_end; - for (std::tie(v_it, v_it_end) = boost::vertices(skel_graph); v_it != v_it_end; - ++v_it) { - root_.members_.emplace_hint( - root_.members_.end(), *v_it, - Node(&root_, boost::get(vertex_filtration_t(), skel_graph, *v_it))); - } std::pair<typename boost::graph_traits<OneSkeletonGraph>::edge_iterator, - typename boost::graph_traits<OneSkeletonGraph>::edge_iterator> boost_edges = boost::edges(skel_graph); + typename boost::graph_traits<OneSkeletonGraph>::edge_iterator> boost_edges = edges(skel_graph); // boost_edges.first is the equivalent to boost_edges.begin() // boost_edges.second is the equivalent to boost_edges.end() for (; boost_edges.first != boost_edges.second; boost_edges.first++) { auto edge = *(boost_edges.first); auto u = source(edge, skel_graph); auto v = target(edge, skel_graph); - if (u == v) throw "Self-loops are not simplicial"; + if (u == v) throw std::invalid_argument("Self-loops are not simplicial"); // We cannot skip edges with the wrong orientation and expect them to // come a second time with the right orientation, that does not always // happen in practice. emplace() should be a NOP when an element with the @@ -1123,10 +1152,25 @@ class Simplex_tree { } sh->second.children()->members().emplace(v, - Node(sh->second.children(), boost::get(edge_filtration_t(), skel_graph, edge))); + Node(sh->second.children(), get(edge_filtration_t(), skel_graph, edge))); } } + /** \brief Inserts several vertices. + * @param[in] vertices A range of Vertex_handle + * @param[in] filt filtration value of the new vertices (the same for all) + * + * This may be faster than inserting the vertices one by one, especially in a random order. + * The complex does not need to be empty before calling this function. However, if a vertex is + * already present, its filtration value is not modified, unlike with other insertion functions. */ + template <class VertexRange> + void insert_batch_vertices(VertexRange const& vertices, Filtration_value filt = 0) { + auto verts = vertices | boost::adaptors::transformed([&](auto v){ + return Dit_value_t(v, Node(&root_, filt)); }); + root_.members_.insert(boost::begin(verts), boost::end(verts)); + if (dimension_ < 0 && !root_.members_.empty()) dimension_ = 0; + } + /** \brief Expands the Simplex_tree containing only its one skeleton * until dimension max_dim. * @@ -1280,6 +1324,7 @@ class Simplex_tree { Siblings * new_sib = new Siblings(siblings, // oncles simplex->first, // parent boost::adaptors::reverse(intersection)); // boost::container::ordered_unique_range_t + simplex->second.assign_children(new_sib); std::vector<Vertex_handle> blocked_new_sib_vertex_list; // As all intersections are inserted, we can call the blocker function on all new_sib members for (auto new_sib_member = new_sib->members().begin(); @@ -1302,7 +1347,6 @@ class Simplex_tree { new_sib->members().erase(blocked_new_sib_member); } // ensure recursive call - simplex->second.assign_children(new_sib); siblings_expansion_with_blockers(new_sib, max_dim, k - 1, block_simplex); } } else { @@ -1312,7 +1356,7 @@ class Simplex_tree { } } - /* \private Returns the Simplex_handle composed of the vertex list (from the Simplex_handle), plus the given + /** \private Returns the Simplex_handle composed of the vertex list (from the Simplex_handle), plus the given * Vertex_handle if the Vertex_handle is found in the Simplex_handle children list. * Returns null_simplex() if it does not exist */ @@ -1465,7 +1509,7 @@ 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); } @@ -1569,7 +1613,7 @@ class Simplex_tree { Simplex_tree st_copy = *this; // Add point for coning the simplicial complex - this->insert_simplex({maxvert}, -3); + this->insert_simplex_raw({maxvert}, -3); // For each simplex std::vector<Vertex_handle> vr; @@ -1667,6 +1711,37 @@ class Simplex_tree { return sh; // None of its faces has the same filtration. } + public: + /** \brief This function resets the filtration value of all the simplices of dimension at least min_dim. Resets all + * the Simplex_tree when `min_dim = 0`. + * `reset_filtration` may break the filtration property with `min_dim > 0`, and it is the user's responsibility to + * make it a valid filtration (using a large enough `filt_value`, or calling `make_filtration_non_decreasing` + * afterwards for instance). + * @param[in] filt_value The new filtration value. + * @param[in] min_dim The minimal dimension. Default value is 0. + */ + void reset_filtration(Filtration_value filt_value, int min_dim = 0) { + rec_reset_filtration(&root_, filt_value, min_dim); + clear_filtration(); // Drop the cache. + } + + private: + /** \brief Recursively resets filtration value when minimal depth <= 0. + * @param[in] sib Siblings to be parsed. + * @param[in] filt_value The new filtration value. + * @param[in] min_depth The minimal depth. + */ + void rec_reset_filtration(Siblings * sib, Filtration_value filt_value, int min_depth) { + for (auto sh = sib->members().begin(); sh != sib->members().end(); ++sh) { + if (min_depth <= 0) { + sh->second.assign_filtration(filt_value); + } + if (has_children(sh)) { + rec_reset_filtration(sh->second.children(), filt_value, min_depth - 1); + } + } + } + private: Vertex_handle null_vertex_; /** \brief Total number of simplices in the complex, without the empty simplex.*/ @@ -1744,7 +1819,7 @@ struct Simplex_tree_options_fast_persistence { static const bool contiguous_vertices = true; }; -/** @} */ // end defgroup simplex_tree +/** @}*/ // end addtogroup simplex_tree } // namespace Gudhi |