multipers 2.3.3b6__cp313-cp313-macosx_10_13_x86_64.whl

multipers/gudhi/gudhi/Bitmap_cubical_complex.h

@@ -0,0 +1,450 @@
+/*    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):       Pawel Dlotko
+ *
+ *    Copyright (C) 2015 Inria
+ *
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
+ */
+
+#ifndef BITMAP_CUBICAL_COMPLEX_H_
+#define BITMAP_CUBICAL_COMPLEX_H_
+
+#include <gudhi/Debug_utils.h>
+#include <gudhi/Bitmap_cubical_complex_base.h>
+#include <gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h>
+
+#ifdef GUDHI_USE_TBB
+#include <tbb/parallel_sort.h>
+#endif
+
+#include <limits>
+#include <utility>    // for pair<>
+#include <algorithm>  // for sort
+#include <vector>
+#include <numeric>  // for iota
+#include <cstddef>
+#include <stdexcept>
+
+namespace Gudhi {
+
+namespace cubical_complex {
+
+template <typename T>
+class is_before_in_filtration;
+
+/**
+ * @brief Cubical complex represented as a bitmap.
+ * @ingroup cubical_complex
+ * @details This is a Bitmap_cubical_complex class. It joints a functionalities of Bitmap_cubical_complex_base and
+ * Bitmap_cubical_complex_periodic_boundary_conditions_base classes into
+ * Gudhi persistent homology engine. It is a template class that inherit from its template parameter. The template
+ * parameter is supposed to be either Bitmap_cubical_complex_base or
+ * Bitmap_cubical_complex_periodic_boundary_conditions_base class.
+ *
+ * This class implements the concept `FilteredComplex`.
+ **/
+template <typename T>
+class Bitmap_cubical_complex : public T {
+ public:
+  //*********************************************//
+  // Typedefs and typenames
+  //*********************************************//
+  typedef std::size_t Simplex_key;
+  typedef typename T::filtration_type Filtration_value;
+  typedef Simplex_key Simplex_handle;
+
+  //*********************************************//
+  // Constructors
+  //*********************************************//
+  // Over here we need to define various input types. I am proposing the following ones:
+  // Perseus style
+  // TODO(PD) H5 files?
+  // TODO(PD) binary files with little endians / big endians ?
+  // TODO(PD) constructor from a vector of elements of a type T. ?
+
+  /**
+   * @param[in] perseus_style_file The name of a \ref FileFormatsPerseus "Perseus-style file".
+   **/
+  explicit Bitmap_cubical_complex(const char* perseus_style_file)
+      : T(perseus_style_file), key_associated_to_simplex(num_simplices()) {
+#ifdef DEBUG_TRACES
+    std::clog << "Bitmap_cubical_complex( const char* perseus_style_file )\n";
+#endif
+  }
+
+  /**
+   * @param[in] dimensions The shape that should be used to interpret `cells` (in Fortran order).
+   * @param[in] cells The filtration values of the top-dimensional cells if `input_top_cells` is `true`,
+   * and of the vertices otherwise.
+   * @param[in] input_top_cells If `true`, `cells` represents top-dimensional cells. If `false`, it represents vertices.
+   **/
+  Bitmap_cubical_complex(const std::vector<unsigned>& dimensions,
+                         const std::vector<Filtration_value>& cells,
+                         bool input_top_cells = true)
+      : T(dimensions, cells, input_top_cells), key_associated_to_simplex(num_simplices()) {
+  }
+
+  /**
+   * @param[in] dimensions The shape that should be used to interpret `cells` (in Fortran order).
+   * @param[in] cells The filtration values of the top-dimensional cells if `input_top_cells` is `true`,
+   * and of the vertices otherwise.
+   * @param[in] directions_in_which_periodic_b_cond_are_to_be_imposed Specifies for each dimension (as per `dimensions`) if the space is periodic (`true`) or not (`false`), or in other words if the boundaries should be identified.
+   * @param[in] input_top_cells If `true`, `cells` represents top-dimensional cells. If `false`, it represents vertices.
+   **/
+  Bitmap_cubical_complex(const std::vector<unsigned>& dimensions,
+                         const std::vector<Filtration_value>& cells,
+                         const std::vector<bool>& directions_in_which_periodic_b_cond_are_to_be_imposed,
+                         bool input_top_cells = true)
+      : T(dimensions, cells, directions_in_which_periodic_b_cond_are_to_be_imposed, input_top_cells),
+        key_associated_to_simplex(num_simplices()) {
+  }
+
+  /**
+   * Destructor.
+   **/
+  virtual ~Bitmap_cubical_complex() {}
+
+  //*********************************************//
+  // Other 'easy' functions
+  //*********************************************//
+
+  /**
+   * Returns number of all cubes in the complex.
+   **/
+  std::size_t num_simplices() const { return this->data.size(); }
+
+  /**
+   * Returns a Simplex_handle to a cube that do not exist in this complex.
+   **/
+  static Simplex_handle null_simplex() {
+#ifdef DEBUG_TRACES
+    std::clog << "Simplex_handle null_simplex()\n";
+#endif
+    return std::numeric_limits<Simplex_handle>::max();
+  }
+
+  /**
+   * Returns dimension of the complex.
+   **/
+  inline std::size_t dimension() const { return this->sizes.size(); }
+
+  /**
+   * Return dimension of a cell pointed by the Simplex_handle.
+   **/
+  inline unsigned dimension(Simplex_handle sh) const {
+#ifdef DEBUG_TRACES
+    std::clog << "unsigned dimension(const Simplex_handle& sh)\n";
+#endif
+    GUDHI_CHECK(sh != null_simplex(), std::logic_error("Only real cells have a dimension"));
+    return this->get_dimension_of_a_cell(sh);
+  }
+
+  /**
+   * Return the filtration of a cell pointed by the Simplex_handle, or +inf for `null_simplex()`.
+   **/
+  Filtration_value filtration(Simplex_handle sh) {
+#ifdef DEBUG_TRACES
+    std::clog << "Filtration_value filtration(const Simplex_handle& sh)\n";
+#endif
+    // Returns the filtration value of a simplex.
+    if (sh != null_simplex()) return this->data[sh];
+    return std::numeric_limits<Filtration_value>::infinity();
+  }
+
+  /**
+   * Return a key which is not a key of any cube in the considered data structure.
+   **/
+  static Simplex_key null_key() {
+#ifdef DEBUG_TRACES
+    std::clog << "Simplex_key null_key()\n";
+#endif
+    return std::numeric_limits<Simplex_handle>::max();
+  }
+
+  /**
+   * Return the key of a cube pointed by the Simplex_handle.
+   **/
+  Simplex_key key(Simplex_handle sh) const {
+#ifdef DEBUG_TRACES
+    std::clog << "Simplex_key key(const Simplex_handle& sh)\n";
+#endif
+    GUDHI_CHECK(sh != null_simplex(), std::invalid_argument("key(null_simplex()) is not supported"));
+    return this->key_associated_to_simplex[sh];
+  }
+
+  /**
+   * Return the k-th Simplex_handle in filtration order.
+   *
+   * Only available after initialize_filtration() or filtration_simplex_range() has been called.
+   **/
+  Simplex_handle simplex(Simplex_key k) {
+#ifdef DEBUG_TRACES
+    std::clog << "Simplex_handle simplex(Simplex_key key)\n";
+#endif
+    GUDHI_CHECK (k != null_key(), std::invalid_argument("simplex(null_key()) is not supported"));
+    GUDHI_CHECK (!sorted_cells.empty(), std::logic_error("initialize_filtration() or filtration_simplex_range() must be called before simplex()"));
+    return this->sorted_cells[k];
+  }
+
+  /**
+   * Assign key to a cube pointed by the Simplex_handle
+   **/
+  void assign_key(Simplex_handle sh, Simplex_key key) {
+#ifdef DEBUG_TRACES
+    std::clog << "void assign_key(Simplex_handle& sh, Simplex_key key)\n";
+#endif
+    GUDHI_CHECK(sh != null_simplex(), std::invalid_argument("assign_key(null_simplex()) is not supported"));
+    this->key_associated_to_simplex[sh] = key;
+  }
+
+  /**
+   * Precompute a sorted list of the cells for filtration_simplex_range() and simplex().
+   * It is automatically called by filtration_simplex_range() if needed, but NOT by simplex().
+   **/
+  void initialize_filtration();
+
+  //*********************************************//
+  // Iterators
+  //*********************************************//
+
+  /**
+   * Boundary_simplex_range class provides ranges for boundary iterators.
+   **/
+  typedef typename std::vector<Simplex_handle>::iterator Boundary_simplex_iterator;
+  typedef typename std::vector<Simplex_handle> Boundary_simplex_range;
+
+  /**
+   * Range of all the cells in filtration order.
+   * Secondary criteria for filtration are:
+   * (1) Dimension of a cube (lower dimensional comes first).
+   * (2) Position in the data structure (the ones that are earliest in the data structure come first).
+   **/
+  typedef std::vector<Simplex_handle> Filtration_simplex_range;
+
+  //*********************************************//
+  // Methods to access iterators from the container:
+
+  /**
+   * boundary_simplex_range creates an object of a Boundary_simplex_range class
+   * that provides ranges for the Boundary_simplex_iterator.
+   **/
+  Boundary_simplex_range boundary_simplex_range(Simplex_handle sh) { return this->get_boundary_of_a_cell(sh); }
+
+  /**
+   * Range of all the cells in filtration order.
+   * Secondary criteria for filtration are:
+   * (1) Dimension of a cube (lower dimensional comes first).
+   * (2) Position in the data structure (the ones that are earliest in the data structure come first).
+   *
+   * This implicitly calls initialize_filtration() if it has never been called.
+   **/
+  Filtration_simplex_range const& filtration_simplex_range() {
+#ifdef DEBUG_TRACES
+    std::clog << "Filtration_simplex_range filtration_simplex_range()\n";
+#endif
+    if (sorted_cells.empty()) initialize_filtration();
+    return sorted_cells;
+  }
+  //*********************************************//
+
+  //*********************************************//
+  // Elements which are in Gudhi now, but I (and in all the cases I asked also Marc) do not understand why they are
+  // there.
+  // TODO(PD) the file IndexingTag.h in the Gudhi library contains an empty structure, so
+  // I understand that this is something that was planned (for simplicial maps?)
+  // but was never finished. The only idea I have here is to use the same empty structure from
+  // IndexingTag.h file, but only if the compiler needs it. If the compiler
+  // do not need it, then I would rather not add here elements which I do not understand.
+  // typedef Indexing_tag
+
+  /**
+   * Returns the extremities of edge `e`
+   **/
+  std::pair<Simplex_handle, Simplex_handle> endpoints(Simplex_handle e) {
+    std::vector<std::size_t> bdry = this->get_boundary_of_a_cell(e);
+#ifdef DEBUG_TRACES
+    std::clog << "std::pair<Simplex_handle, Simplex_handle> endpoints( Simplex_handle e )\n";
+    std::clog << "bdry.size() : " << bdry.size() << "\n";
+#endif
+    if (bdry.size() != 2)
+      throw(
+          "Error in endpoints in Bitmap_cubical_complex class. The cell is not an edge.");
+    return std::make_pair(bdry[0], bdry[1]);
+  }
+
+  class Skeleton_simplex_range;
+
+  class Skeleton_simplex_iterator {
+    // Iterator over all simplices of the complex in the order of the indexing scheme.
+   public:
+    typedef std::input_iterator_tag iterator_category;
+    typedef Simplex_handle value_type;
+    typedef std::ptrdiff_t difference_type;
+    typedef value_type* pointer;
+    typedef value_type reference;
+
+    Skeleton_simplex_iterator(Bitmap_cubical_complex* b, std::size_t d) : b(b), dimension(d) {
+#ifdef DEBUG_TRACES
+      std::clog << "Skeleton_simplex_iterator ( Bitmap_cubical_complex* b , std::size_t d )\n";
+#endif
+      // find the position of the first simplex of a dimension d
+      this->position = 0;
+      while ((this->position != b->data.size()) &&
+             (this->b->get_dimension_of_a_cell(this->position) != this->dimension)) {
+        ++this->position;
+      }
+    }
+
+    Skeleton_simplex_iterator() : b(NULL), position(0), dimension(0) {}
+
+    Skeleton_simplex_iterator operator++() {
+#ifdef DEBUG_TRACES
+      std::clog << "Skeleton_simplex_iterator operator++()\n";
+#endif
+      // increment the position as long as you did not get to the next element of the dimension dimension.
+      ++this->position;
+      while ((this->position != this->b->data.size()) &&
+             (this->b->get_dimension_of_a_cell(this->position) != this->dimension)) {
+        ++this->position;
+      }
+      return (*this);
+    }
+
+    Skeleton_simplex_iterator operator++(int) {
+      Skeleton_simplex_iterator result = *this;
+      ++(*this);
+      return result;
+    }
+
+    bool operator==(const Skeleton_simplex_iterator& rhs) const {
+#ifdef DEBUG_TRACES
+      std::clog << "bool operator ==\n";
+#endif
+      return (this->position == rhs.position);
+    }
+
+    bool operator!=(const Skeleton_simplex_iterator& rhs) const {
+#ifdef DEBUG_TRACES
+      std::clog << "bool operator != ( const Skeleton_simplex_iterator& rhs )\n";
+#endif
+      return !(*this == rhs);
+    }
+
+    Simplex_handle operator*() {
+#ifdef DEBUG_TRACES
+      std::clog << "Simplex_handle operator*() \n";
+#endif
+      return this->position;
+    }
+
+    friend class Skeleton_simplex_range;
+
+   private:
+    Bitmap_cubical_complex<T>* b;
+    std::size_t position;
+    unsigned dimension;
+  };
+
+  /**
+   * @brief A range containing all the cells of dimension at most k.
+   **/
+  class Skeleton_simplex_range {
+    // Range over the simplices of the complex in the order of the filtration.
+    // .begin() and .end() return type Skeleton_simplex_iterator.
+   public:
+    typedef Skeleton_simplex_iterator const_iterator;
+    typedef Skeleton_simplex_iterator iterator;
+
+    Skeleton_simplex_range(Bitmap_cubical_complex<T>* b, unsigned dimension) : b(b), dimension(dimension) {}
+
+    Skeleton_simplex_iterator begin() {
+#ifdef DEBUG_TRACES
+      std::clog << "Skeleton_simplex_iterator begin()\n";
+#endif
+      return Skeleton_simplex_iterator(this->b, this->dimension);
+    }
+
+    Skeleton_simplex_iterator end() {
+#ifdef DEBUG_TRACES
+      std::clog << "Skeleton_simplex_iterator end()\n";
+#endif
+      Skeleton_simplex_iterator it(this->b, this->dimension);
+      it.position = this->b->data.size();
+      return it;
+    }
+
+   private:
+    Bitmap_cubical_complex<T>* b;
+    unsigned dimension;
+  };
+
+  /**
+   * Returns a range containing all the cells of dimension at most `dimension`.
+   **/
+  Skeleton_simplex_range skeleton_simplex_range(unsigned dimension) {
+#ifdef DEBUG_TRACES
+    std::clog << "Skeleton_simplex_range skeleton_simplex_range( unsigned dimension )\n";
+#endif
+    return Skeleton_simplex_range(this, dimension);
+  }
+
+  friend class is_before_in_filtration<T>;
+
+ protected:
+  std::vector<std::size_t> key_associated_to_simplex;
+  std::vector<std::size_t> sorted_cells;
+};  // Bitmap_cubical_complex
+
+template <typename T>
+void Bitmap_cubical_complex<T>::initialize_filtration() {
+#ifdef DEBUG_TRACES
+  std::clog << "void Bitmap_cubical_complex<T>::initialize_elements_ordered_according_to_filtration() \n";
+#endif
+  this->sorted_cells.resize(this->data.size());
+  std::iota(std::begin(sorted_cells), std::end(sorted_cells), 0);
+#ifdef GUDHI_USE_TBB
+  tbb::parallel_sort(sorted_cells.begin(), sorted_cells.end(),
+                     is_before_in_filtration<T>(this));
+#else
+  std::sort(sorted_cells.begin(), sorted_cells.end(), is_before_in_filtration<T>(this));
+#endif
+}
+
+template <typename T>
+class is_before_in_filtration {
+ public:
+  explicit is_before_in_filtration(Bitmap_cubical_complex<T>* CC) : CC_(CC) {}
+
+  bool operator()(const typename Bitmap_cubical_complex<T>::Simplex_handle& sh1,
+                  const typename Bitmap_cubical_complex<T>::Simplex_handle& sh2) const {
+    // Not using st_->filtration(sh1) because it uselessly tests for null_simplex.
+    typedef typename T::filtration_type Filtration_value;
+    Filtration_value fil1 = CC_->data[sh1];
+    Filtration_value fil2 = CC_->data[sh2];
+    if (fil1 != fil2) {
+      return fil1 < fil2;
+    }
+    // in this case they are on the same filtration level, so the dimension decide.
+    std::size_t dim1 = CC_->get_dimension_of_a_cell(sh1);
+    std::size_t dim2 = CC_->get_dimension_of_a_cell(sh2);
+    if (dim1 != dim2) {
+      return dim1 < dim2;
+    }
+    // in this case both filtration and dimensions of the considered cubes are the same. To have stable sort, we simply
+    // compare their positions in the bitmap:
+    return sh1 < sh2;
+  }
+
+ protected:
+  Bitmap_cubical_complex<T>* CC_;
+};
+
+}  // namespace cubical_complex
+
+namespace Cubical_complex = cubical_complex;
+
+}  // namespace Gudhi
+
+#endif  // BITMAP_CUBICAL_COMPLEX_H_