multipers 2.4.0b1__cp312-cp312-macosx_11_0_arm64.whl

multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_iterators.h

@@ -0,0 +1,559 @@
+/*    This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ *    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+ *    Author(s):       Clément Maria
+ *
+ *    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
+ */
+
+#ifndef SIMPLEX_TREE_SIMPLEX_TREE_ITERATORS_H_
+#define SIMPLEX_TREE_SIMPLEX_TREE_ITERATORS_H_
+
+#include <gudhi/Debug_utils.h>
+
+#include <boost/iterator/iterator_facade.hpp>
+
+#include <utility>  // for std::pair
+
+namespace Gudhi {
+
+/** \addtogroup simplex_tree
+ * Iterators and range types for the Simplex_tree.
+ *  @{
+ */
+
+/** \brief Iterator over the vertices of a simplex
+ * in a SimplexTree.
+ *
+ * Forward iterator, 'value_type' is SimplexTree::Vertex_handle.*/
+template<class SimplexTree>
+class Simplex_tree_simplex_vertex_iterator : public boost::iterator_facade<
+    Simplex_tree_simplex_vertex_iterator<SimplexTree>,
+    typename SimplexTree::Vertex_handle const, boost::forward_traversal_tag,
+    typename SimplexTree::Vertex_handle const> {
+ public:
+  typedef typename SimplexTree::Simplex_handle Simplex_handle;
+  typedef typename SimplexTree::Siblings Siblings;
+  typedef typename SimplexTree::Vertex_handle Vertex_handle;
+
+  explicit Simplex_tree_simplex_vertex_iterator(SimplexTree const* st)
+      :  // any end() iterator
+        sib_(nullptr),
+        v_(st->null_vertex()) {
+  }
+
+  Simplex_tree_simplex_vertex_iterator(SimplexTree const* st, Simplex_handle sh)
+      : sib_(st->self_siblings(sh)),
+        v_(sh->first) {
+  }
+
+ private:
+  friend class boost::iterator_core_access;
+
+  bool equal(Simplex_tree_simplex_vertex_iterator const &other) const {
+    return sib_ == other.sib_ && v_ == other.v_;
+  }
+
+  Vertex_handle const& dereference() const {
+    return v_;
+  }
+
+  void increment() {
+    v_ = sib_->parent();
+    sib_ = sib_->oncles();
+  }
+
+  Siblings const* sib_;
+  Vertex_handle v_;
+};
+
+/*---------------------------------------------------------------------------*/
+/** \brief Iterator over the simplices of the boundary of a
+ *  simplex.
+ *
+ * Forward iterator, value_type is SimplexTree::Simplex_handle.*/
+template<class SimplexTree>
+class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade<
+    Simplex_tree_boundary_simplex_iterator<SimplexTree>,
+    typename SimplexTree::Simplex_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;
+  using Static_vertex_vector = typename SimplexTree::Static_vertex_vector;
+
+  // For cython purpose only. The object it initializes should be overwritten ASAP and never used before it is overwritten.
+  Simplex_tree_boundary_simplex_iterator()
+      : sib_(nullptr),
+        st_(nullptr)  {
+  }
+
+// any end() iterator
+  explicit Simplex_tree_boundary_simplex_iterator(SimplexTree const* st)
+      : last_(st->null_vertex()),
+        next_(st->null_vertex()),
+        sib_(nullptr),
+        sh_(st->null_simplex()),
+        st_(st)  {
+  }
+
+  template<class SimplexHandle>
+  Simplex_tree_boundary_simplex_iterator(SimplexTree const* st, SimplexHandle sh)
+      : last_(sh->first),
+        next_(st->null_vertex()),
+        sib_(nullptr),
+        sh_(st->null_simplex()),
+        st_(st) {
+    // Only check once at the beginning instead of for every increment, as this is expensive.
+    if constexpr (SimplexTree::Options::contiguous_vertices)
+      GUDHI_CHECK(st_->contiguous_vertices(), "The set of vertices is not { 0, ..., n } without holes");
+    Siblings const* sib = st->self_siblings(sh);
+    next_ = sib->parent();
+    sib_ = sib->oncles();
+    if (sib_ != nullptr) {
+      if constexpr (SimplexTree::Options::contiguous_vertices &&
+                    !SimplexTree::Options::stable_simplex_handles)
+      {
+        if (sib_->oncles() == nullptr)  // Only relevant for edges
+          sh_ = sib_->members_.begin() + next_;
+        else
+          sh_ = sib_->find(next_);
+      } else {
+        sh_ = sib_->find(next_);
+      }
+    }
+  }
+
+ private:
+  friend class boost::iterator_core_access;
+  // valid when iterating along the SAME boundary.
+  bool equal(Simplex_tree_boundary_simplex_iterator const& other) const {
+    return sh_ == other.sh_;
+  }
+
+  Simplex_handle const& dereference() const {
+    assert(sh_ != st_->null_simplex());
+    return sh_;
+  }
+
+  void increment() {
+    if (sib_ == nullptr) {
+      sh_ = st_->null_simplex();
+      return;
+    }
+
+    Siblings const* for_sib = sib_;
+    Siblings const* new_sib = sib_->oncles();
+    auto rit = suffix_.rbegin();
+    if constexpr (SimplexTree::Options::contiguous_vertices && !SimplexTree::Options::stable_simplex_handles) {
+      if (new_sib == nullptr) {
+        // We reached the root, use a short-cut to find a vertex.
+        if (rit == suffix_.rend()) {
+          // Segment, this vertex is the last boundary simplex
+          sh_ = for_sib->members_.begin() + last_;
+          sib_ = nullptr;
+          return;
+        } else {
+          // Dim >= 2, initial step of the descent
+          sh_ = for_sib->members_.begin() + *rit;
+          for_sib = sh_->second.children();
+          ++rit;
+        }
+      }
+    }
+
+    for (; rit != suffix_.rend(); ++rit) {
+      sh_ = for_sib->find(*rit);
+      for_sib = sh_->second.children();
+    }
+    sh_ = for_sib->find(last_);  // sh_ points to the right simplex now
+    suffix_.push_back(next_);
+    next_ = sib_->parent();
+    sib_ = new_sib;
+  }
+
+  // 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_
+  Static_vertex_vector suffix_;
+  Siblings const* sib_;  // where the next search will start from
+  Simplex_handle sh_;  // current Simplex_handle in the boundary
+  SimplexTree const* 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;
+  using Static_vertex_vector = typename SimplexTree::Static_vertex_vector;
+
+  // 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 const* 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 const* 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 constexpr (SimplexTree::Options::contiguous_vertices)
+      GUDHI_CHECK(st_->contiguous_vertices(), "The set of vertices is not { 0, ..., n } without holes");
+    Siblings const* sib = st->self_siblings(sh);
+    next_ = sib->parent();
+    sib_ = sib->oncles();
+    if (sib_ != nullptr) {
+      if constexpr (SimplexTree::Options::contiguous_vertices &&
+                    !SimplexTree::Options::stable_simplex_handles) {
+        if (sib_->oncles() == nullptr)
+          // Only relevant for edges
+          baov_.first = sib_->members_.begin() + next_;
+        else
+          baov_.first = sib_->find(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 const* for_sib = sib_;
+    Siblings const* new_sib = sib_->oncles();
+    auto rit = suffix_.rbegin();
+    if constexpr (SimplexTree::Options::contiguous_vertices && !SimplexTree::Options::stable_simplex_handles) {
+      if (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_
+  Static_vertex_vector suffix_;
+  Siblings const* 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 const* st_;  // simplex containing the simplicial complex
+};
+
+/*---------------------------------------------------------------------------*/
+/** \brief Iterator over the simplices of a simplicial complex.
+ *
+ * Forward iterator, value_type is SimplexTree::Simplex_handle.*/
+template<class SimplexTree>
+class Simplex_tree_complex_simplex_iterator : public boost::iterator_facade<
+    Simplex_tree_complex_simplex_iterator<SimplexTree>,
+    typename SimplexTree::Simplex_handle const, boost::forward_traversal_tag> {
+ public:
+  typedef typename SimplexTree::Simplex_handle Simplex_handle;
+  typedef typename SimplexTree::Siblings Siblings;
+  typedef typename SimplexTree::Vertex_handle Vertex_handle;
+
+// any end() iterator
+  Simplex_tree_complex_simplex_iterator()
+      : sib_(nullptr),
+        st_(nullptr) {
+  }
+
+  explicit Simplex_tree_complex_simplex_iterator(SimplexTree const* st)
+      : sib_(nullptr),
+        st_(st) {
+    if (st == nullptr || st->root() == nullptr || st->root()->members().empty()) {
+      st_ = nullptr;
+    } else {
+      sh_ = st->root()->members().begin();
+      sib_ = st->root();
+      while (st->has_children(sh_)) {
+        sib_ = sh_->second.children();
+        sh_ = sib_->members().begin();
+      }
+    }
+  }
+ private:
+  friend class boost::iterator_core_access;
+
+// valid when iterating along the SAME boundary.
+  bool equal(Simplex_tree_complex_simplex_iterator const& other) const {
+    if (other.st_ == nullptr) {
+      return (st_ == nullptr);
+    }
+    if (st_ == nullptr) {
+      return false;
+    }
+    return (&(sh_->second) == &(other.sh_->second));
+  }
+
+  Simplex_handle const& dereference() const {
+    return sh_;
+  }
+
+// Depth first traversal.
+  void increment() {
+    ++sh_;
+    if (sh_ == sib_->members().end()) {
+      if (sib_->oncles() == nullptr) {
+        st_ = nullptr;
+        return;
+      }  // reach the end
+      sh_ = sib_->oncles()->members().find(sib_->parent());
+      sib_ = sib_->oncles();
+      return;
+    }
+    while (st_->has_children(sh_)) {
+      sib_ = sh_->second.children();
+      sh_ = sib_->members().begin();
+    }
+  }
+
+  Simplex_handle sh_;
+  Siblings const* sib_;
+  SimplexTree const* st_;
+};
+
+/** \brief Iterator over the simplices of the skeleton of a given
+ * dimension of the simplicial complex.
+ *
+ * Forward iterator, value_type is SimplexTree::Simplex_handle.*/
+template<class SimplexTree>
+class Simplex_tree_skeleton_simplex_iterator : public boost::iterator_facade<
+    Simplex_tree_skeleton_simplex_iterator<SimplexTree>,
+    typename SimplexTree::Simplex_handle const, boost::forward_traversal_tag> {
+ public:
+  typedef typename SimplexTree::Simplex_handle Simplex_handle;
+  typedef typename SimplexTree::Siblings Siblings;
+  typedef typename SimplexTree::Vertex_handle Vertex_handle;
+
+// any end() iterator
+  Simplex_tree_skeleton_simplex_iterator()
+      : sib_(nullptr),
+        st_(nullptr),
+        dim_skel_(0),
+        curr_dim_(0) {
+  }
+
+  Simplex_tree_skeleton_simplex_iterator(SimplexTree const* st, int dim_skel)
+      : sib_(nullptr),
+        st_(st),
+        dim_skel_(dim_skel),
+        curr_dim_(0) {
+    if (st == nullptr || st->root() == nullptr || st->root()->members().empty()) {
+      st_ = nullptr;
+    } else {
+      sh_ = st->root()->members().begin();
+      sib_ = st->root();
+      while (st->has_children(sh_) && curr_dim_ < dim_skel_) {
+        sib_ = sh_->second.children();
+        sh_ = sib_->members().begin();
+        ++curr_dim_;
+      }
+    }
+  }
+ private:
+  friend class boost::iterator_core_access;
+
+// valid when iterating along the SAME boundary.
+  bool equal(Simplex_tree_skeleton_simplex_iterator const& other) const {
+    if (other.st_ == nullptr) {
+      return (st_ == nullptr);
+    }
+    if (st_ == nullptr) {
+      return false;
+    }
+    return (&(sh_->second) == &(other.sh_->second));
+  }
+
+  Simplex_handle const& dereference() const {
+    return sh_;
+  }
+
+// Depth first traversal of the skeleton.
+  void increment() {
+    ++sh_;
+    if (sh_ == sib_->members().end()) {
+      if (sib_->oncles() == nullptr) {
+        st_ = nullptr;
+        return;
+      }  // reach the end
+      sh_ = sib_->oncles()->members().find(sib_->parent());
+      sib_ = sib_->oncles();
+      --curr_dim_;
+      return;
+    }
+    while (st_->has_children(sh_) && curr_dim_ < dim_skel_) {
+      sib_ = sh_->second.children();
+      sh_ = sib_->members().begin();
+      ++curr_dim_;
+    }
+  }
+
+  Simplex_handle sh_;
+  Siblings const* sib_;
+  SimplexTree const* st_;
+  int dim_skel_;
+  int curr_dim_;
+};
+
+/** \brief Iterator over the simplices of the simplicial complex that match the dimension specified by the parameter.
+ *
+ * Forward iterator, value_type is SimplexTree::Simplex_handle.*/
+template<class SimplexTree>
+class Simplex_tree_dimension_simplex_iterator : public boost::iterator_facade<
+    Simplex_tree_dimension_simplex_iterator<SimplexTree>,
+    typename SimplexTree::Simplex_handle const, boost::forward_traversal_tag> {
+ public:
+  typedef typename SimplexTree::Simplex_handle Simplex_handle;
+  typedef typename SimplexTree::Siblings Siblings;
+  typedef typename SimplexTree::Vertex_handle Vertex_handle;
+
+// any end() iterator
+  Simplex_tree_dimension_simplex_iterator()
+      : sib_(nullptr),
+        st_(nullptr),
+        dim_(0),
+        curr_dim_(0) {
+  }
+
+  Simplex_tree_dimension_simplex_iterator(SimplexTree const* st, int dim)
+      : sib_(nullptr),
+        st_(st),
+        dim_(dim),
+        curr_dim_(0) {
+    if (st == nullptr || st->root() == nullptr || st->root()->members().empty() ||
+        st->upper_bound_dimension() < dim || dim < 0) {
+      st_ = nullptr;
+    } else {
+      sh_ = st->root()->members().begin();
+      sib_ = st->root();
+      until_leaf_or_dim();
+      // if we reached a leaf that does not respect the required dimension - call increment
+      if (curr_dim_ != dim_)
+        increment();
+    }
+  }
+ private:
+  friend class boost::iterator_core_access;
+
+// valid when iterating along the SAME boundary.
+  bool equal(Simplex_tree_dimension_simplex_iterator const& other) const {
+    if (other.st_ == nullptr) {
+      return (st_ == nullptr);
+    }
+    if (st_ == nullptr) {
+      return false;
+    }
+    return (&(sh_->second) == &(other.sh_->second));
+  }
+
+  Simplex_handle const& dereference() const {
+    return sh_;
+  }
+
+  void until_leaf_or_dim() {
+    while (st_->has_children(sh_) && curr_dim_ != dim_) {
+      sib_ = sh_->second.children();
+      sh_ = sib_->members().begin();
+      ++curr_dim_;
+    }
+#ifdef DEBUG_TRACES
+    std::clog << "Simplex_tree::dimension_simplex_range until_leaf_or_dim reached (";
+    for (auto vertex : st_->simplex_vertex_range(sh_)) {
+      std::clog << vertex << ",";
+    }
+    std::clog << ")\n";
+#endif  // DEBUG_TRACES
+  }
+  // Depth first traversal of the tree structure. Returns when reaching a simplex with a given dimension
+  void increment() {
+    ++sh_;
+    while (sh_ == sib_->members().end()) {
+      if (sib_->oncles() == nullptr) {
+        st_ = nullptr;
+        return;
+      }  // reach the end
+      sh_ = sib_->oncles()->members().find(sib_->parent());
+      sib_ = sib_->oncles();
+      --curr_dim_;
+      ++sh_;
+      until_leaf_or_dim();
+    }
+    // It seems we do it twice here, but necessary when coming from the constructor
+    until_leaf_or_dim();
+    // if we reached a leaf that does not respect the dimension - recall increment
+    if (curr_dim_ != dim_)
+      increment();
+  }
+
+  Simplex_handle sh_;
+  Siblings const* sib_;
+  SimplexTree const* st_;
+  int dim_;
+  int curr_dim_;
+};
+
+/** @}*/  // end addtogroup simplex_tree
+
+}  // namespace Gudhi
+
+#endif  // SIMPLEX_TREE_SIMPLEX_TREE_ITERATORS_H_

multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h

@@ -0,0 +1,83 @@
+/*    This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ *    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+ *    Author(s):       Clément Maria
+ *
+ *    Copyright (C) 2014 Inria
+ *
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
+ */
+
+#ifndef SIMPLEX_TREE_SIMPLEX_TREE_NODE_EXPLICIT_STORAGE_H_
+#define SIMPLEX_TREE_SIMPLEX_TREE_NODE_EXPLICIT_STORAGE_H_
+
+// Empty base optimization for MSVC - https://learn.microsoft.com/en-us/cpp/cpp/empty-bases
+#if _MSC_VER
+ #define GUDHI_EMPTY_BASE_CLASS_OPTIMIZATION __declspec(empty_bases)
+#else
+ #define GUDHI_EMPTY_BASE_CLASS_OPTIMIZATION
+#endif
+
+#include <boost/core/empty_value.hpp>
+
+namespace Gudhi {
+
+/** \addtogroup simplex_tree
+ * Represents a node of a Simplex_tree.
+ * @{
+ */
+
+/** \brief Node of a simplex tree with filtration value
+ * and simplex key.
+ *
+ * It stores explicitly its own filtration value and its own Simplex_key.
+ */
+template <class SimplexTree>
+struct GUDHI_EMPTY_BASE_CLASS_OPTIMIZATION Simplex_tree_node_explicit_storage
+    : SimplexTree::Filtration_simplex_base,
+      SimplexTree::Key_simplex_base,
+      SimplexTree::Hooks_simplex_base,
+      boost::empty_value<typename SimplexTree::Simplex_data> {
+  typedef typename SimplexTree::Siblings Siblings;
+  typedef typename SimplexTree::Filtration_value Filtration_value;
+  typedef typename SimplexTree::Simplex_key Simplex_key;
+  typedef typename SimplexTree::Simplex_data Simplex_data;
+
+  Simplex_tree_node_explicit_storage() : children_(nullptr) {}
+
+  Simplex_tree_node_explicit_storage(Siblings* sib, const Filtration_value& filtration = Filtration_value())
+      : SimplexTree::Filtration_simplex_base(filtration), children_(sib)
+  {}
+
+  //will fail to compile when called with SimplexTree::Options::store_key is false.
+  Simplex_tree_node_explicit_storage(Siblings* sib, Filtration_value filtration, Simplex_key key)
+      : SimplexTree::Filtration_simplex_base(filtration), SimplexTree::Key_simplex_base(key), children_(sib)
+  {}
+
+  /*
+   * Assign children to the node
+   */
+  void assign_children(Siblings * children) {
+    children_ = children;
+  }
+
+  /* Careful -> children_ can be NULL*/
+  Siblings * children() {
+    return children_;
+  }
+  const Siblings * children() const {
+    return children_;
+  }
+
+  Simplex_data& data() { return boost::empty_value<Simplex_data>::get(); }
+  const Simplex_data& data() const { return boost::empty_value<Simplex_data>::get(); }
+
+ private:
+  Siblings * children_;
+};
+
+/** @}*/  // end addtogroup simplex_tree
+
+}  // namespace Gudhi
+
+#endif  // SIMPLEX_TREE_SIMPLEX_TREE_NODE_EXPLICIT_STORAGE_H_