diff options
Diffstat (limited to 'src/Simplex_tree/include/gudhi')
4 files changed, 48 insertions, 62 deletions
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index 6430c300..9b3de20a 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -20,20 +20,22 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#ifndef GUDHI_SIMPLEX_TREE_H -#define GUDHI_SIMPLEX_TREE_H +#ifndef SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_H_ +#define SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_H_ + +#include <gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h> +#include <gudhi/Simplex_tree/Simplex_tree_siblings.h> +#include <gudhi/Simplex_tree/Simplex_tree_iterators.h> +#include <gudhi/Simplex_tree/indexing_tag.h> -#include <algorithm> -#include <utility> -#include <vector> -#include "gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h" -#include "gudhi/Simplex_tree/Simplex_tree_siblings.h" -#include "gudhi/Simplex_tree/Simplex_tree_iterators.h" -#include "gudhi/Simplex_tree/indexing_tag.h" #include <boost/container/flat_map.hpp> #include <boost/iterator/transform_iterator.hpp> #include <boost/graph/adjacency_list.hpp> +#include <algorithm> +#include <utility> +#include <vector> + namespace Gudhi { /** \defgroup simplex_tree Filtered Complexes Package @@ -107,18 +109,12 @@ class Simplex_tree { /* Type of dictionary Vertex_handle -> Node for traversing the simplex tree. */ typedef typename boost::container::flat_map<Vertex_handle, Node> Dictionary; - friend class Simplex_tree_node_explicit_storage< - Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> > ; - friend class Simplex_tree_siblings< - Simplex_tree<FiltrationValue, SimplexKey, VertexHandle>, Dictionary> ; - friend class Simplex_tree_simplex_vertex_iterator< - Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> > ; - friend class Simplex_tree_boundary_simplex_iterator< - Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> > ; - friend class Simplex_tree_complex_simplex_iterator< - Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> > ; - friend class Simplex_tree_skeleton_simplex_iterator< - Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> > ; + friend class Simplex_tree_node_explicit_storage< Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> >; + friend class Simplex_tree_siblings< Simplex_tree<FiltrationValue, SimplexKey, VertexHandle>, Dictionary>; + friend class Simplex_tree_simplex_vertex_iterator< Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> >; + friend class Simplex_tree_boundary_simplex_iterator< Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> >; + friend class Simplex_tree_complex_simplex_iterator< Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> >; + friend class Simplex_tree_skeleton_simplex_iterator< Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> >; template<class T1, class T2> friend class Persistent_cohomology; /* \brief Set of nodes sharing a same parent in the simplex tree. */ @@ -400,7 +396,7 @@ class Simplex_tree { * <CODE>Vertex_handle</CODE>. */ template<class RandomAccessVertexRange> - Simplex_handle find(RandomAccessVertexRange & s) { + Simplex_handle find(const RandomAccessVertexRange & s) { if (s.begin() == s.end()) std::cerr << "Empty simplex \n"; @@ -597,7 +593,7 @@ class Simplex_tree { * Reverse lexicographic order has the property to always consider the subsimplex of a simplex * to be smaller. The filtration function must be monotonic. */ struct is_before_in_filtration { - is_before_in_filtration(Simplex_tree * st) + explicit is_before_in_filtration(Simplex_tree * st) : st_(st) { } @@ -632,7 +628,7 @@ class Simplex_tree { * boost::graph_traits<OneSkeletonGraph>::directed_category * must be undirected_tag. */ template<class OneSkeletonGraph> - void insert_graph(OneSkeletonGraph & skel_graph) { + void insert_graph(const OneSkeletonGraph& skel_graph) { assert(num_simplices() == 0); // the simplex tree must be empty if (boost::num_vertices(skel_graph) == 0) { @@ -738,25 +734,22 @@ class Simplex_tree { } /** \brief Intersects Dictionary 1 [begin1;end1) with Dictionary 2 [begin2,end2) * and assigns the maximal possible Filtration_value to the Nodes. */ - void intersection(std::vector<std::pair<Vertex_handle, Node> > & intersection, + void intersection(std::vector<std::pair<Vertex_handle, Node> >& intersection, Dictionary_it begin1, Dictionary_it end1, Dictionary_it begin2, Dictionary_it end2, Filtration_value filtration) { if (begin1 == end1 || begin2 == end2) - return; // 0; + return; // ----->> while (true) { if (begin1->first == begin2->first) { intersection.push_back( std::pair<Vertex_handle, Node>( begin1->first, - Node( - NULL, - maximum(begin1->second.filtration(), - begin2->second.filtration(), filtration)))); + Node(NULL, maximum(begin1->second.filtration(), begin2->second.filtration(), filtration)))); ++begin1; ++begin2; if (begin1 == end1 || begin2 == end2) - return; + return; // ----->> } else { if (begin1->first < begin2->first) { ++begin1; @@ -765,7 +758,7 @@ class Simplex_tree { } else { ++begin2; if (begin2 == end2) - return; + return; // ----->> } } } @@ -784,7 +777,7 @@ class Simplex_tree { * dim idx_1 ... idx_k fil where dim is the dimension of the simplex, * idx_1 ... idx_k are the row index (starting from 0) of the simplices of the boundary * of the simplex, and fil is its filtration value. */ - void print_hasse(std::ostream & os) { + void print_hasse(std::ostream& os) { os << num_simplices() << " " << std::endl; for (auto sh : filtration_simplex_range(Indexing_tag())) { os << dimension(sh) << " "; @@ -832,7 +825,7 @@ std::istream& operator>>(std::istream & is, Simplex_tree<T1, T2, T3> & st) { size_t num_simplices = 0; while (read_simplex(is, simplex, fil)) { // read all simplices in the file as a list of vertices ++num_simplices; - int dim = (int) simplex.size() - 1; // Warning : simplex_size needs to be casted in int - Can be 0 + int dim = static_cast<int>(simplex.size() - 1); // Warning : simplex_size needs to be casted in int - Can be 0 if (max_dim < dim) { max_dim = dim; } @@ -852,4 +845,4 @@ std::istream& operator>>(std::istream & is, Simplex_tree<T1, T2, T3> & st) { /** @} */ // end defgroup simplex_tree } // namespace Gudhi -#endif // GUDHI_SIMPLEX_TREE_H +#endif // SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_H_ 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 54d4d296..06462c88 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 @@ -20,12 +20,13 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#ifndef SIMPLEX_TREE_ITERATORS_H -#define SIMPLEX_TREE_ITERATORS_H +#ifndef SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_SIMPLEX_TREE_ITERATORS_H_ +#define SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_SIMPLEX_TREE_ITERATORS_H_ -#include <vector> #include <boost/iterator/iterator_facade.hpp> +#include <vector> + namespace Gudhi { /* \addtogroup simplex_tree @@ -47,7 +48,7 @@ class Simplex_tree_simplex_vertex_iterator : public boost::iterator_facade< typedef typename SimplexTree::Siblings Siblings; typedef typename SimplexTree::Vertex_handle Vertex_handle; - Simplex_tree_simplex_vertex_iterator(SimplexTree * st) + explicit Simplex_tree_simplex_vertex_iterator(SimplexTree * st) : // any end() iterator sib_(NULL), v_(st->null_vertex()) { @@ -93,7 +94,7 @@ class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade< typedef typename SimplexTree::Siblings Siblings; // any end() iterator - Simplex_tree_boundary_simplex_iterator(SimplexTree * st) + explicit Simplex_tree_boundary_simplex_iterator(SimplexTree * st) : last_(st->null_vertex()), sib_(NULL) { } @@ -166,7 +167,7 @@ class Simplex_tree_complex_simplex_iterator : public boost::iterator_facade< : st_(NULL) { } - Simplex_tree_complex_simplex_iterator(SimplexTree * st) + explicit Simplex_tree_complex_simplex_iterator(SimplexTree * st) : st_(st) { if (st == NULL || st->root() == NULL || st->root()->members().empty()) { st_ = NULL; @@ -302,4 +303,4 @@ class Simplex_tree_skeleton_simplex_iterator : public boost::iterator_facade< /* @} */ // end addtogroup simplex_tree } // namespace Gudhi -#endif // SIMPLEX_TREE_ITERATORS_H +#endif // SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_SIMPLEX_TREE_ITERATORS_H_ 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 27120f00..1f1a34cc 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 @@ -20,11 +20,10 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#ifndef GUDHI_SIMPLEX_TREE_NODE_EXPLICIT_STORAGE_H -#define GUDHI_SIMPLEX_TREE_NODE_EXPLICIT_STORAGE_H +#ifndef SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_SIMPLEX_TREE_NODE_EXPLICIT_STORAGE_H_ +#define SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_SIMPLEX_TREE_NODE_EXPLICIT_STORAGE_H_ #include <vector> -#include <iostream> namespace Gudhi { @@ -42,14 +41,10 @@ namespace Gudhi { template<class SimplexTree> class Simplex_tree_node_explicit_storage { public: -// friend SimplexTree; - typedef typename SimplexTree::Siblings Siblings; typedef typename SimplexTree::Filtration_value Filtration_value; typedef typename SimplexTree::Simplex_key Simplex_key; - //private: - //friend class Simplex_tree; // Default constructor. Simplex_tree_node_explicit_storage() : children_(NULL), @@ -69,13 +64,6 @@ class Simplex_tree_node_explicit_storage { } /* - * Return true if the node has children, - * false otherwise. - */ - //bool has_children(Vertex label) - //{ //if(children_ == NULL) return false; //for root simplices - // return (children_->parent() == label);} - /* * Assign a children to the node */ void assign_children(Siblings * children) { @@ -92,7 +80,7 @@ class Simplex_tree_node_explicit_storage { return filtration_; } - /* Careful -> has_children() must be true*/ + /* Careful -> children_ can be NULL*/ Siblings * children() { return children_; } @@ -106,11 +94,10 @@ class Simplex_tree_node_explicit_storage { // Data attached to simplex, explicit storage Simplex_key simplex_key_; - Filtration_value filtration_; //value in the filtration - + Filtration_value filtration_; // value in the filtration }; /* @} */ // end addtogroup simplex_tree -}// namespace Gudhi +} // namespace Gudhi -#endif // GUDHI_SIMPLEX_TREE_NODE_EXPLICIT_STORAGE_H +#endif // SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_SIMPLEX_TREE_NODE_EXPLICIT_STORAGE_H_ diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h b/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h index 680458a5..69ffa44b 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h @@ -20,6 +20,9 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ +#ifndef SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_INDEXING_TAG_H_ +#define SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_INDEXING_TAG_H_ + namespace Gudhi { /** \brief Tag for a linear ordering of simplices. @@ -31,4 +34,6 @@ struct linear_indexing_tag { /* \brief Tag for a zigzag ordering of simplices. */ // struct zigzag_indexing_tag {}; -}// namespace Gudhi +} // namespace Gudhi + +#endif // SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_INDEXING_TAG_H_ |