diff options
Diffstat (limited to 'src/Simplex_tree/include/gudhi/Simplex_tree.h')
| -rw-r--r-- | src/Simplex_tree/include/gudhi/Simplex_tree.h | 354 |
1 files changed, 246 insertions, 108 deletions
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index 279327f7..6a47083c 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -28,6 +28,9 @@ #include <gudhi/Simplex_tree/Simplex_tree_iterators.h> #include <gudhi/Simplex_tree/indexing_tag.h> +#include <gudhi/reader_utils.h> +#include <gudhi/graph_simplicial_complex.h> + #include <boost/container/flat_map.hpp> #include <boost/iterator/transform_iterator.hpp> #include <boost/graph/adjacency_list.hpp> @@ -72,6 +75,17 @@ namespace Gudhi { * \copyright GNU General Public License v3. * @{ */ + +/// Model of SimplexTreeOptions. +struct Simplex_tree_options_full_featured { + typedef linear_indexing_tag Indexing_tag; + typedef int Vertex_handle; + typedef double Filtration_value; + typedef int Simplex_key; + static const bool store_key = true; + static const bool store_filtration = true; +}; + /** * \brief Simplex Tree data structure for representing simplicial complexes. * @@ -83,35 +97,63 @@ namespace Gudhi { * \implements FilteredComplex * */ -template<typename IndexingTag = linear_indexing_tag, -typename FiltrationValue = double, typename SimplexKey = int // must be a signed integer type -, typename VertexHandle = int // must be a signed integer type, int convertible to it -> + +template<typename SimplexTreeOptions = Simplex_tree_options_full_featured> class Simplex_tree { public: - typedef IndexingTag Indexing_tag; + typedef SimplexTreeOptions Options; + typedef typename Options::Indexing_tag Indexing_tag; /** \brief Type for the value of the filtration function. * * Must be comparable with <. */ - typedef FiltrationValue Filtration_value; + typedef typename Options::Filtration_value Filtration_value; /** \brief Key associated to each simplex. * * Must be a signed integer type. */ - typedef SimplexKey Simplex_key; + typedef typename Options::Simplex_key Simplex_key; /** \brief Type for the vertex handle. * * Must be a signed integer type. It admits a total order <. */ - typedef VertexHandle Vertex_handle; + typedef typename Options::Vertex_handle Vertex_handle; /* Type of node in the simplex tree. */ typedef Simplex_tree_node_explicit_storage<Simplex_tree> Node; /* Type of dictionary Vertex_handle -> Node for traversing the simplex tree. */ + // Note: this wastes space when Vertex_handle is 32 bits and Node is aligned on 64 bits. It would be better to use a flat_set (with our own comparator) where we can control the layout of the struct (put Vertex_handle and 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. */ typedef Simplex_tree_siblings<Simplex_tree, Dictionary> Siblings; + struct Key_simplex_base_real { + Key_simplex_base_real() : key_(-1) {} + void assign_key(Simplex_key k) { key_ = k; } + Simplex_key key() const { return key_; } + private: + Simplex_key key_; + }; + struct Key_simplex_base_dummy { + Key_simplex_base_dummy() {} + void assign_key(Simplex_key) { } + Simplex_key key() const { assert(false); return -1; } + }; + typedef typename std::conditional<Options::store_key, Key_simplex_base_real, Key_simplex_base_dummy>::type Key_simplex_base; + + struct Filtration_simplex_base_real { + Filtration_simplex_base_real() : filt_(0) {} + void assign_filtration(Filtration_value f) { filt_ = f; } + Filtration_value filtration() const { return filt_; } + private: + Filtration_value filt_; + }; + struct Filtration_simplex_base_dummy { + Filtration_simplex_base_dummy() {} + void assign_filtration(Filtration_value f) { assert(f == 0); } + Filtration_value filtration() const { return 0; } + }; + typedef typename std::conditional<Options::store_filtration, Filtration_simplex_base_real, Filtration_simplex_base_dummy>::type Filtration_simplex_base; + public: /** \brief Handle type to a simplex contained in the simplicial complex represented * by the simplex tree. */ @@ -170,12 +212,12 @@ class Simplex_tree { /** \brief Range over the simplices of the skeleton of the simplicial complex, for a given * dimension. */ typedef boost::iterator_range<Skeleton_simplex_iterator> Skeleton_simplex_range; + /** \brief Range over the simplices of the simplicial complex, ordered by the filtration. */ + typedef std::vector<Simplex_handle> Filtration_simplex_range; /** \brief Iterator over the simplices of the simplicial complex, ordered by the filtration. * * 'value_type' is Simplex_handle. */ - typedef typename std::vector<Simplex_handle>::iterator Filtration_simplex_iterator; - /** \brief Range over the simplices of the simplicial complex, ordered by the filtration. */ - typedef boost::iterator_range<Filtration_simplex_iterator> Filtration_simplex_range; + typedef typename Filtration_simplex_range::const_iterator Filtration_simplex_iterator; /* @} */ // end name range and iterator types /** \name Range and iterator methods @@ -226,17 +268,13 @@ class Simplex_tree { * order is used. * * The filtration must be valid. If the filtration has not been initialized yet, the - * method initializes it (i.e. order the simplices). */ - Filtration_simplex_range filtration_simplex_range(Indexing_tag) { + * method initializes it (i.e. order the simplices). If the complex has changed since the last time the filtration + * was initialized, please call `initialize_filtration()` to recompute it. */ + Filtration_simplex_range const& filtration_simplex_range(Indexing_tag=Indexing_tag()) { if (filtration_vect_.empty()) { initialize_filtration(); } - return Filtration_simplex_range(filtration_vect_.begin(), - filtration_vect_.end()); - } - - Filtration_simplex_range filtration_simplex_range() { - return filtration_simplex_range(Indexing_tag()); + return filtration_vect_; } /** \brief Returns a range over the vertices of a simplex. @@ -278,9 +316,47 @@ class Simplex_tree { Simplex_tree() : null_vertex_(-1), threshold_(0), - root_(NULL, null_vertex_), + root_(nullptr, null_vertex_), + filtration_vect_(), + dimension_(-1) { } + + /** \brief User-defined copy constructor reproduces the whole tree structure. */ + Simplex_tree(const Simplex_tree& simplex_source) + : null_vertex_(simplex_source.null_vertex_), + threshold_(simplex_source.threshold_), filtration_vect_(), - dimension_(-1) { + dimension_(simplex_source.dimension_) { + auto root_source = simplex_source.root_; + auto memb_source = root_source.members(); + root_ = Siblings(nullptr, null_vertex_, memb_source); + rec_copy(&root_, &root_source); + } + + /** \brief depth first search, inserts simplices when reaching a leaf. */ + void rec_copy(Siblings *sib, Siblings *sib_source) { + for (auto sh = sib->members().begin(), sh_source = sib_source->members().begin(); + sh != sib->members().end(); ++sh, ++sh_source) { + if (has_children(sh_source)) { + Siblings * newsib = new Siblings(sib, sh_source->first); + newsib->members_.reserve(sh_source->second.children()->members().size()); + for (auto & child : sh_source->second.children()->members()) + newsib->members_.emplace_hint(newsib->members_.end(), child.first, Node(sib, child.second.filtration())); + rec_copy(newsib, sh_source->second.children()); + sh->second.assign_children(newsib); + } + } + } + + /** \brief User-defined move constructor moves the whole tree structure. */ + Simplex_tree(Simplex_tree && old) + : null_vertex_(std::move(old.null_vertex_)), + threshold_(std::move(old.threshold_)), + root_(std::move(old.root_)), + filtration_vect_(std::move(old.filtration_vect_)), + dimension_(std::move(old.dimension_)) { + old.dimension_ = -1; + old.threshold_ = 0; + old.root_ = Siblings(nullptr, null_vertex_); } /** \brief Destructor; deallocates the whole tree structure. */ @@ -304,23 +380,63 @@ class Simplex_tree { } public: + /** \brief Checks if two simplex trees are equal. */ + bool operator==(Simplex_tree& st2) { + if ((null_vertex_ != st2.null_vertex_) || + (threshold_ != st2.threshold_) || + (dimension_ != st2.dimension_)) + return false; + return rec_equal(&root_, &st2.root_); + } + + /** \brief Checks if two simplex trees are different. */ + bool operator!=(Simplex_tree& st2) { + return (!(*this == st2)); + } + + private: + /** rec_equal: Checks recursively whether or not two simplex trees are equal, using depth first search. */ + bool rec_equal(Siblings* s1, Siblings* s2) { + if (s1->members().size() != s2->members().size()) + return false; + for (auto sh1 = s1->members().begin(), sh2 = s2->members().begin(); + (sh1 != s1->members().end() && sh2 != s2->members().end()); ++sh1, ++sh2) { + if (sh1->first != sh2->first || sh1->second.filtration() != sh2->second.filtration()) + return false; + if (has_children(sh1) != has_children(sh2)) + return false; + // Recursivity on children only if both have children + else if (has_children(sh1)) + if (!rec_equal(sh1->second.children(), sh2->second.children())) + return false; + } + return true; + } + + public: /** \brief Returns the key associated to a simplex. * - * The filtration must be initialized. */ + * The filtration must be initialized. + * \pre SimplexTreeOptions::store_key + */ static Simplex_key key(Simplex_handle sh) { return sh->second.key(); } /** \brief Returns the simplex associated to a key. * - * The filtration must be initialized. */ + * The filtration must be initialized. + * \pre SimplexTreeOptions::store_key + */ Simplex_handle simplex(Simplex_key key) const { return filtration_vect_[key]; } /** \brief Returns the filtration value of a simplex. * - * Called on the null_simplex, returns INFINITY. */ + * Called on the null_simplex, returns INFINITY. + * If SimplexTreeOptions::store_filtration is false, returns 0. + */ static Filtration_value filtration(Simplex_handle sh) { if (sh != null_simplex()) { return sh->second.filtration(); @@ -348,7 +464,7 @@ class Simplex_tree { * * One can call filtration(null_simplex()). */ static Simplex_handle null_simplex() { - return Dictionary_it(NULL); + return Dictionary_it(nullptr); } /** \brief Returns a key different for all keys associated to the @@ -395,7 +511,7 @@ class Simplex_tree { int dimension(Simplex_handle sh) { Siblings * curr_sib = self_siblings(sh); int dim = 0; - while (curr_sib != NULL) { + while (curr_sib != nullptr) { ++dim; curr_sib = curr_sib->oncles(); } @@ -413,26 +529,34 @@ class Simplex_tree { return (sh->second.children()->parent() == sh->first); } - public: - /** \brief Given a range of Vertex_handles, returns the Simplex_handle + /** \brief Given a range of Vertex_handles, returns the Simplex_handle * of the simplex in the simplicial complex containing the corresponding * vertices. Return null_simplex() if the simplex is not in the complex. * - * The type RandomAccessVertexRange must be a range for which .begin() and - * .end() return random access iterators, with <CODE>value_type</CODE> - * <CODE>Vertex_handle</CODE>. + * The type InputVertexRange must be a range of <CODE>Vertex_handle</CODE> + * on which we can call std::begin() function */ - template<class RandomAccessVertexRange> - Simplex_handle find(RandomAccessVertexRange & s) { - if (s.begin() == s.end()) // Empty simplex - return null_simplex(); - - sort(s.begin(), s.end()); + template<class InputVertexRange> + Simplex_handle find(const InputVertexRange & s) { + auto first = std::begin(s); + auto last = std::end(s); + + if (first == last) + return null_simplex(); // ----->> + + // Copy before sorting + std::vector<Vertex_handle> copy(first, last); + std::sort(std::begin(copy), std::end(copy)); + return find_simplex(copy); + } + private: + /** Find function, with a sorted range of vertices. */ + Simplex_handle find_simplex(const std::vector<Vertex_handle> & simplex) { Siblings * tmp_sib = &root_; Dictionary_it tmp_dit; - Vertex_handle last = s[s.size() - 1]; - for (auto v : s) { + Vertex_handle last = simplex.back(); + for (auto v : simplex) { tmp_dit = tmp_sib->members_.find(v); if (tmp_dit == tmp_sib->members_.end()) { return null_simplex(); @@ -450,43 +574,17 @@ class Simplex_tree { Simplex_handle find_vertex(Vertex_handle v) { return root_.members_.begin() + v; } - - /** \brief Insert a simplex, represented by a range of Vertex_handles, in the simplicial complex. - * - * @param[in] simplex range of Vertex_handles, representing the vertices of the new simplex - * @param[in] filtration the filtration value assigned to the new simplex. - * The return type is a pair. 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 - * to the new simplex. - * If the insertion fails (the simplex is already there), the bool is set to false. If the insertion - * fails and the simplex already in the complex has a filtration value strictly bigger than 'filtration', - * we assign this simplex with the new value 'filtration', and set the Simplex_handle filed of the - * output pair to the Simplex_handle of the simplex. Otherwise, we set the Simplex_handle part to - * null_simplex. - * - * All subsimplices do not necessary need to be already in the simplex tree to proceed to an - * insertion. However, the property of being a simplicial complex will be violated. This allows - * us to insert a stream of simplices contained in a simplicial complex without considering any - * order on them. - * - * The filtration value - * assigned to the new simplex must preserve the monotonicity of the filtration. - * - * The type RandomAccessVertexRange must be a range for which .begin() and - * .end() return random access iterators, with 'value_type' Vertex_handle. */ - template<class RandomAccessVertexRange> - std::pair<Simplex_handle, bool> insert_simplex(RandomAccessVertexRange & simplex, - Filtration_value filtration) { - if (simplex.empty()) { - return std::pair<Simplex_handle, bool>(null_simplex(), true); - } - // must be sorted in increasing order - sort(simplex.begin(), simplex.end()); + //{ return root_.members_.find(v); } + private: + /** \brief Inserts a simplex represented by a vector of vertex. + \warning the vector must be sorted by increasing vertex handle order */ + std::pair<Simplex_handle, bool> insert_vertex_vector(const std::vector<Vertex_handle>& simplex, + Filtration_value filtration) { Siblings * curr_sib = &root_; std::pair<Simplex_handle, bool> res_insert; - typename RandomAccessVertexRange::iterator vi; - for (vi = simplex.begin(); vi != simplex.end() - 1; ++vi) { + auto vi = simplex.begin(); + for (; vi != simplex.end() - 1; ++vi) { res_insert = curr_sib->members_.emplace(*vi, Node(curr_sib, filtration)); if (!(has_children(res_insert.first))) { res_insert.first->second.assign_children(new Siblings(curr_sib, *vi)); @@ -508,24 +606,77 @@ class Simplex_tree { return res_insert; } - /** \brief Insert a N-simplex and all his subfaces, from a N-simplex represented by a range of + public: + /** \brief Insert a simplex, represented by a range of Vertex_handles, in the simplicial complex. + * + * @param[in] simplex range of Vertex_handles, representing the vertices of the new simplex + * @param[in] filtration the filtration value assigned to the new simplex. + * The return type is a pair. 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 + * to the new simplex. + * If the insertion fails (the simplex is already there), the bool is set to false. If the insertion + * fails and the simplex already in the complex has a filtration value strictly bigger than 'filtration', + * we assign this simplex with the new value 'filtration', and set the Simplex_handle field of the + * output pair to the Simplex_handle of the simplex. Otherwise, we set the Simplex_handle part to + * null_simplex. + * + * All subsimplices do not necessary need to be already in the simplex tree to proceed to an + * insertion. However, the property of being a simplicial complex will be violated. This allows + * us to insert a stream of simplices contained in a simplicial complex without considering any + * order on them. + * + * The filtration value + * assigned to the new simplex must preserve the monotonicity of the filtration. + * + * The type InputVertexRange must be a range for which .begin() and + * .end() return input iterators, with 'value_type' Vertex_handle. */ + template<class InputVertexRange> + std::pair<Simplex_handle, bool> insert_simplex(const InputVertexRange & simplex, + Filtration_value filtration = 0) { + auto first = std::begin(simplex); + auto last = std::end(simplex); + + if (first == last) + return std::pair<Simplex_handle, bool>(null_simplex(), true); // ----->> + + // Copy before sorting + std::vector<Vertex_handle> copy(first, last); + std::sort(std::begin(copy), std::end(copy)); + return insert_vertex_vector(copy, filtration); + } + + /** \brief Insert a N-simplex and all his subfaces, from a N-simplex represented by a range of * Vertex_handles, in the simplicial complex. * * @param[in] Nsimplex range of Vertex_handles, representing the vertices of the new N-simplex * @param[in] filtration the filtration value assigned to the new N-simplex. + * The return type is a pair. 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 + * to the new simplex. + * If the insertion fails (the simplex is already there), the bool is set to false. If the insertion + * fails and the simplex already in the complex has a filtration value strictly bigger than 'filtration', + * we assign this simplex with the new value 'filtration', and set the Simplex_handle field of the + * output pair to the Simplex_handle of the simplex. Otherwise, we set the Simplex_handle part to + * null_simplex. */ - template<class RandomAccessVertexRange> - std::pair<Simplex_handle, bool> insert_simplex_and_subfaces(const RandomAccessVertexRange& Nsimplex, - Filtration_value filtration = 0.0) { - // Simplex copy - std::vector<Vertex_handle> the_simplex(Nsimplex.begin(), Nsimplex.end()); - // must be sorted in increasing order - std::sort(the_simplex.begin(), the_simplex.end()); + template<class InputVertexRange> + std::pair<Simplex_handle, bool> insert_simplex_and_subfaces(const InputVertexRange& Nsimplex, + Filtration_value filtration = 0) { + auto first = std::begin(Nsimplex); + auto last = std::end(Nsimplex); + + if (first == last) + return std::pair<Simplex_handle, bool>(null_simplex(), true); // ----->> + + // Copy before sorting + std::vector<Vertex_handle> copy(first, last); + std::sort(std::begin(copy), std::end(copy)); + std::vector<std::vector<Vertex_handle>> to_be_inserted; std::vector<std::vector<Vertex_handle>> to_be_propagated; - return rec_insert_simplex_and_subfaces(the_simplex, to_be_inserted, to_be_propagated, filtration); + return rec_insert_simplex_and_subfaces(copy, to_be_inserted, to_be_propagated, filtration); } - + private: std::pair<Simplex_handle, bool> rec_insert_simplex_and_subfaces(std::vector<Vertex_handle>& the_simplex, std::vector<std::vector<Vertex_handle>>& to_be_inserted, @@ -534,15 +685,15 @@ class Simplex_tree { std::pair<Simplex_handle, bool> insert_result; if (the_simplex.size() > 1) { // Get and remove last vertex - Vertex_handle last_vertex= the_simplex.back(); + Vertex_handle last_vertex = the_simplex.back(); the_simplex.pop_back(); // Recursive call after last vertex removal insert_result = rec_insert_simplex_and_subfaces(the_simplex, to_be_inserted, to_be_propagated, filtration); - + // Concatenation of to_be_inserted and to_be_propagated to_be_inserted.insert(to_be_inserted.begin(), to_be_propagated.begin(), to_be_propagated.end()); to_be_propagated = to_be_inserted; - + // to_be_inserted treatment for (auto& simplex_tbi : to_be_inserted) { simplex_tbi.push_back(last_vertex); @@ -557,26 +708,23 @@ class Simplex_tree { // insert all to_be_inserted for (auto& simplex_tbi : to_be_inserted) { - insert_result = insert_simplex(simplex_tbi, filtration); + insert_result = insert_vertex_vector(simplex_tbi, filtration); } - - } else if (the_simplex.size() == 1) { // When reaching the end of recursivity, vector of simplices shall be empty and filled on back recursive - if ((to_be_inserted.size() != 0) || (to_be_propagated.size() != 0)){ + if ((to_be_inserted.size() != 0) || (to_be_propagated.size() != 0)) { std::cerr << "Simplex_tree::rec_insert_simplex_and_subfaces - Error vector not empty" << std::endl; exit(-1); } std::vector<Vertex_handle> first_simplex(1, the_simplex.back()); // i.e. (0,1,2) => [to_be_inserted | to_be_propagated] = [(0) | ] to_be_inserted.push_back(first_simplex); - - insert_result = insert_simplex(first_simplex, filtration); + + insert_result = insert_vertex_vector(first_simplex, filtration); } else { std::cerr << "Simplex_tree::rec_insert_simplex_and_subfaces - Recursivity error" << std::endl; exit(-1); } - return insert_result; } @@ -603,17 +751,6 @@ class Simplex_tree { return sh->second.children(); } - // void display_simplex(Simplex_handle sh) - // { - // std::cout << " " << "[" << filtration(sh) << "] "; - // for( auto vertex : simplex_vertex_range(sh) ) - // { std::cout << vertex << " "; } - // } - - // void print(Simplex_handle sh, std::ostream& os = std::cout) - // { for(auto v : simplex_vertex_range(sh)) {os << v << " ";} - // os << std::endl; } - public: /** Returns a pointer to the root nodes of the simplex tree. */ Siblings * root() { @@ -778,8 +915,9 @@ class Simplex_tree { : st_(st) { } bool operator()(const Simplex_handle sh1, const Simplex_handle sh2) const { - if (st_->filtration(sh1) != st_->filtration(sh2)) { - return st_->filtration(sh1) < st_->filtration(sh2); + // Not using st_->filtration(sh1) because it uselessly tests for null_simplex. + if (sh1->second.filtration() != sh2->second.filtration()) { + return sh1->second.filtration() < sh2->second.filtration(); } // is sh1 a proper subface of sh2 return st_->reverse_lexicographic_order(sh1, sh2); @@ -925,7 +1063,7 @@ class Simplex_tree { while (true) { if (begin1->first == begin2->first) { Filtration_value filt = (std::max)({begin1->second.filtration(), begin2->second.filtration(), filtration_}); - intersection.emplace_back(begin1->first, Node(NULL, filt)); + intersection.emplace_back(begin1->first, Node(nullptr, filt)); if (++begin1 == end1 || ++begin2 == end2) return; // ----->> } else if (begin1->first < begin2->first) { @@ -947,7 +1085,7 @@ class Simplex_tree { * of the simplex, and fil is its filtration value. */ void print_hasse(std::ostream& os) { os << num_simplices() << " " << std::endl; - for (auto sh : filtration_simplex_range(Indexing_tag())) { + for (auto sh : filtration_simplex_range()) { os << dimension(sh) << " "; for (auto b_sh : boundary_simplex_range(sh)) { os << key(b_sh) << " "; |