multipers 2.2.3__cp312-cp312-win_amd64.whl → 2.3.0__cp312-cp312-win_amd64.whl

multipers/gudhi/mma_interface_matrix.h

@@ -1,282 +1,284 @@
-/*    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): Hannah
- * Schreiber
- *
- *    Copyright (C) 2022 Inria
- *
- *    Modification(s):
- *      - YYYY/MM Author: Description of the modification
- */
-/**
- * @file options.h
- * @author Hannah Schreiber
- * @brief Interface of the matrix for MMA
- */
-
-#ifndef MMA_INTERFACE_MATRIX_H
-#define MMA_INTERFACE_MATRIX_H
-
-#include <cstddef>
-#include <cstdint>
-#include <limits>
-#include <ostream>
-#include <utility>
-#include <vector>
-
-#include <gudhi/Matrix.h>
-#include <gudhi/persistence_matrix_options.h>
-
-namespace Gudhi {
-namespace multiparameter {
-namespace truc_interface {
-
-template <Gudhi::persistence_matrix::Column_types column_type = Gudhi::persistence_matrix::Column_types::INTRUSIVE_SET>
-struct Multi_persistence_options : Gudhi::persistence_matrix::Default_options<column_type, true> {
-  using Index = std::uint32_t;
-  static const bool has_matrix_maximal_dimension_access = false;
-  static const bool has_column_pairings = true;
-  static const bool has_vine_update = true;
-  static const bool can_retrieve_representative_cycles = true;
-};
-
-template <Gudhi::persistence_matrix::Column_types column_type = Gudhi::persistence_matrix::Column_types::INTRUSIVE_SET>
-struct Multi_persistence_Clement_options : Gudhi::persistence_matrix::Default_options<column_type, true> {
-  using Index = std::uint32_t;
-  static const bool has_matrix_maximal_dimension_access = false;
-  static const bool has_column_pairings = true;
-  static const bool has_vine_update = true;
-  static const bool is_of_boundary_type = false;
-  static const Gudhi::persistence_matrix::Column_indexation_types column_indexation_type =
-      Gudhi::persistence_matrix::Column_indexation_types::POSITION;
-  static const bool can_retrieve_representative_cycles = true;
-};
-
-template <Gudhi::persistence_matrix::Column_types column_type = Gudhi::persistence_matrix::Column_types::INTRUSIVE_SET>
-struct No_vine_multi_persistence_options : Gudhi::persistence_matrix::Default_options<column_type, true> {
-  using Index = std::uint32_t;
-  static const bool has_matrix_maximal_dimension_access = false;
-  static const bool has_column_pairings = true;
-  static const bool has_vine_update = false;
-};
-
-template <class Matrix_options, class Boundary_matrix_type>
-class Persistence_backend_matrix {
- public:
-  using matrix_type = Gudhi::persistence_matrix::Matrix<Matrix_options>;
-  using cycle_type = typename matrix_type::Cycle;
-  static const bool is_vine = Matrix_options::has_vine_update;
-
-  using bar = typename matrix_type::Bar;
-  //   using index = typename matrix_type::index;
-  //   using id_index = typename matrix_type::id_index;
-  using pos_index = typename matrix_type::Pos_index;
-  using Index = typename matrix_type::Index;
-  using dimension_type = typename matrix_type::Dimension;
-
-  class Barcode_iterator : public boost::iterator_facade<Barcode_iterator, const bar &, boost::forward_traversal_tag> {
-   public:
-    Barcode_iterator(const typename matrix_type::Barcode *barcode, const std::vector<Index> *inv)
-        : barcode_(barcode->size() == 0 ? nullptr : barcode), perm_(barcode->size() == 0 ? nullptr : inv), currPos_(0) {
-      if (barcode_ != nullptr && perm_ != nullptr) {
-        auto &b = barcode_->operator[](currPos_);
-        currBar_.dim = b.dim;
-        currBar_.birth = perm_->operator[](b.birth);
-        currBar_.death = b.death == static_cast<pos_index>(-1) ? -1 : perm_->operator[](b.death);
-      }
-    }
-
-    Barcode_iterator() : barcode_(nullptr), perm_(nullptr), currPos_(0) {}
-
-   private:
-    // mandatory for the boost::iterator_facade inheritance.
-    friend class boost::iterator_core_access;
-
-    const typename matrix_type::Barcode *barcode_;
-    const std::vector<Index> *perm_;
-    std::size_t currPos_;
-    bar currBar_;
-
-    bool equal(Barcode_iterator const &other) const {
-      return barcode_ == other.barcode_ && perm_ == other.perm_ && currPos_ == other.currPos_;
-    }
-
-    const bar &dereference() const { return currBar_; }
-
-    void increment() {
-      constexpr const bool debug = false;
-      ++currPos_;
-      if (currPos_ == barcode_->size()) {
-        barcode_ = nullptr;
-        perm_ = nullptr;
-        currPos_ = 0;
-      } else {
-        auto &b = barcode_->operator[](currPos_);
-        currBar_.dim = b.dim;
-        currBar_.birth = perm_->operator[](b.birth);
-        if (debug && currBar_.birth > std::numeric_limits<decltype(currBar_.birth)>::max() / 2) {
-          std::cout << currBar_ << std::endl;
-          std::cout << "while " << b.birth;
-          std::cout << "  " << perm_->size();
-        }
-        currBar_.death = b.death == static_cast<pos_index>(-1) ? -1 : perm_->operator[](b.death);
-      }
-    }
-  };
-
-  class Barcode {
-   public:
-    using iterator = Barcode_iterator;
-
-    Barcode(matrix_type &matrix, const std::vector<Index> *perm) : barcode_(&matrix.get_current_barcode()) {
-      const bool debug = false;
-      if constexpr (Matrix_options::has_vine_update) {
-        perm_ = perm;
-      } else {
-        perm_.reserve(perm->size());
-        for (const auto &stuff : *perm)
-          if (stuff < perm->size())  // number of generators
-            perm_.push_back(stuff);
-      }
-      if constexpr (debug) {
-        std::cout << "Built matrix of size " << matrix.get_number_of_columns() << " / " << perm->size() << std::endl;
-      }
-    }
-
-    iterator begin() const {
-      if constexpr (Matrix_options::has_vine_update) {
-        return Barcode_iterator(barcode_, perm_);
-      } else {
-        return Barcode_iterator(barcode_, &this->perm_);
-      }
-    }
-
-    iterator end() const { return Barcode_iterator(); }
-
-    /* using bar = typename matrix_type::Bar; */
-    /* const bar& operator[](std::size_t i){ */
-    /*   return barcode_->at(); */
-    /* } */
-    std::size_t size() const { return barcode_->size(); }
-
-    inline friend std::ostream &operator<<(std::ostream &stream, Barcode &structure) {
-      stream << "Barcode: " << structure.size() << "\n";
-      for (const auto bar : structure) {
-        stream << "[" << bar.dim << "] ";
-        stream << bar.birth << ", " << bar.death;
-        stream << "\n";
-      }
-      stream << "\n";
-      return stream;
-    }
-
-   private:
-    const typename matrix_type::Barcode *barcode_;
-    typename std::conditional<Matrix_options::has_vine_update, const std::vector<Index> *, std::vector<Index>>::type
-        perm_;
-  };
-
-  Persistence_backend_matrix() : permutation_(nullptr) {};
-
-  Persistence_backend_matrix(const Boundary_matrix_type &boundaries, std::vector<Index> &permutation)
-      : matrix_(boundaries.size()), permutation_(&permutation) {
-    static_assert(Matrix_options::is_of_boundary_type || Matrix_options::has_vine_update, "Clement implies vine.");
-    constexpr const bool verbose = false;
-    if constexpr (verbose) std::cout << "Constructing matrix..." << std::endl;
-    std::vector<Index> permutationInv(permutation_->size());
-    std::vector<Index> boundary_container;
-    std::size_t c = 0;
-    for (auto i : *permutation_) {
-      if (i >= boundaries.size()) {
-        c++;
-        continue;
-      }
-      permutationInv[i] = c++;
-      boundary_container.resize(boundaries[i].size());
-      if constexpr (verbose)
-        std::cout << i << "/" << permutation_->size() << " c= " << c << " dimension " << boundaries.dimension(i)
-                  << "..." << std::endl
-                  << std::flush;
-      for (std::size_t j = 0; j < boundaries[i].size(); ++j) {
-        boundary_container[j] = permutationInv[boundaries[i][j]];
-      }
-      std::sort(boundary_container.begin(), boundary_container.end());
-      matrix_.insert_boundary(c - 1, boundary_container, boundaries.dimension(i));
-    }
-  }
-
-  Persistence_backend_matrix(const Persistence_backend_matrix &toCopy)
-      : matrix_(toCopy.matrix_), permutation_(toCopy.permutation_) {}
-
-  Persistence_backend_matrix(Persistence_backend_matrix &&other) noexcept
-      : matrix_(std::move(other.matrix_)), permutation_(std::exchange(other.permutation_, nullptr)) {}
-
-  Persistence_backend_matrix &operator=(Persistence_backend_matrix other) {
-    swap(matrix_, other.matrix_);
-    std::swap(permutation_, other.permutation_);
-    return *this;
-  }
-
-  friend void swap(Persistence_backend_matrix &be1, Persistence_backend_matrix &be2) {
-    swap(be1.matrix_, be2.matrix_);
-    std::swap(be1.permutation_, be2.permutation_);
-  }
-
-  inline dimension_type get_dimension(pos_index i) { return matrix_.get_column_dimension(i); }
-
-  inline void vine_swap(pos_index i) { matrix_.vine_swap(i); }
-
-  inline Barcode get_barcode() { return Barcode(matrix_, permutation_); }
-
-  inline std::size_t size() { return this->matrix_.get_number_of_columns(); }
-
-  inline friend std::ostream &operator<<(std::ostream &stream, Persistence_backend_matrix &structure) {
-    stream << "[\n";
-    for (auto i = 0u; i < structure.matrix_.get_number_of_columns(); i++) {
-      stream << "[";
-      for (const auto &stuff : structure.matrix_.get_column(i)) stream << stuff << ", ";
-      stream << "]\n";
-    }
-
-    stream << "]\n";
-    return stream;
-  }
-
-  inline std::vector<std::vector<std::vector<unsigned int>>> get_representative_cycles(bool update,
-                                                                                       bool detailed = false) {
-    // Only used when vineyard, so shrunk permutation i.e.
-    // without the -1, is permutation as we keep inf values (they can become
-    // finite) cf barcode perm which is copied to remove the -1
-    std::vector<unsigned int> permutation2;
-    permutation2.reserve(permutation_->size());
-    for (auto i : *permutation_) {
-      if (i >= matrix_.get_number_of_columns()) {
-        continue;
-      }
-      permutation2.push_back(i);
-    }
-    constexpr const bool verbose = false;
-    if (update) [[likely]]
-      matrix_.update_representative_cycles();
-    std::vector<std::vector<std::vector<unsigned int>>> current_cycles =
-        matrix_.get_representative_cycles_as_borders(detailed);
-    for (auto &cycle : current_cycles) {
-      if constexpr (verbose) std::cout << "Cycle (matrix_ order): ";
-      for (auto &border : cycle) {
-        for (auto &b : border) {
-          b = permutation2[b];
-        }
-      }
-    }
-    return current_cycles;
-  }
-
-  inline void _update_permutation_ptr(std::vector<Index> &perm) { permutation_ = &perm; }
-
- private:
-  matrix_type matrix_;
-  std::vector<Index> *permutation_;
-};
-
-}}}  // namespace Gudhi::multiparameter::interface
-#endif  // MMA_INTERFACE_MATRIX_H
+/*    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): Hannah
+ * Schreiber
+ *
+ *    Copyright (C) 2022 Inria
+ *
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
+ */
+/**
+ * @file options.h
+ * @author Hannah Schreiber
+ * @brief Interface of the matrix for MMA
+ */
+
+#ifndef MMA_INTERFACE_MATRIX_H
+#define MMA_INTERFACE_MATRIX_H
+
+#include <cstddef>
+#include <cstdint>
+#include <limits>
+#include <ostream>
+#include <utility>
+#include <vector>
+
+#include <gudhi/Matrix.h>
+#include <gudhi/persistence_matrix_options.h>
+
+namespace Gudhi {
+namespace multiparameter {
+namespace truc_interface {
+
+template <Gudhi::persistence_matrix::Column_types column_type = Gudhi::persistence_matrix::Column_types::INTRUSIVE_SET>
+struct Multi_persistence_options : Gudhi::persistence_matrix::Default_options<column_type, true> {
+  using Index = std::uint32_t;
+  static const bool has_matrix_maximal_dimension_access = false;
+  static const bool has_column_pairings = true;
+  static const bool has_vine_update = true;
+  static const bool can_retrieve_representative_cycles = true;
+};
+
+template <Gudhi::persistence_matrix::Column_types column_type = Gudhi::persistence_matrix::Column_types::INTRUSIVE_SET>
+struct Multi_persistence_Clement_options : Gudhi::persistence_matrix::Default_options<column_type, true> {
+  using Index = std::uint32_t;
+  static const bool has_matrix_maximal_dimension_access = false;
+  static const bool has_column_pairings = true;
+  static const bool has_vine_update = true;
+  static const bool is_of_boundary_type = false;
+  static const Gudhi::persistence_matrix::Column_indexation_types column_indexation_type =
+      Gudhi::persistence_matrix::Column_indexation_types::POSITION;
+  static const bool can_retrieve_representative_cycles = true;
+};
+
+template <Gudhi::persistence_matrix::Column_types column_type = Gudhi::persistence_matrix::Column_types::INTRUSIVE_SET>
+struct No_vine_multi_persistence_options : Gudhi::persistence_matrix::Default_options<column_type, true> {
+  using Index = std::uint32_t;
+  static const bool has_matrix_maximal_dimension_access = false;
+  static const bool has_column_pairings = true;
+  static const bool has_vine_update = false;
+};
+
+template <class Matrix_options, class Boundary_matrix_type>
+class Persistence_backend_matrix {
+ public:
+  using matrix_type = Gudhi::persistence_matrix::Matrix<Matrix_options>;
+  using cycle_type = typename matrix_type::Cycle;
+  static const bool is_vine = Matrix_options::has_vine_update;
+
+  using bar = typename matrix_type::Bar;
+  //   using index = typename matrix_type::index;
+  //   using id_index = typename matrix_type::id_index;
+  using pos_index = typename matrix_type::Pos_index;
+  using Index = typename matrix_type::Index;
+  using dimension_type = typename matrix_type::Dimension;
+
+  class Barcode_iterator : public boost::iterator_facade<Barcode_iterator, const bar &, boost::forward_traversal_tag> {
+   public:
+    Barcode_iterator(const typename matrix_type::Barcode *barcode, const std::vector<Index> *inv)
+        : barcode_(barcode->size() == 0 ? nullptr : barcode), perm_(barcode->size() == 0 ? nullptr : inv), currPos_(0) {
+      if (barcode_ != nullptr && perm_ != nullptr) {
+        auto &b = barcode_->operator[](currPos_);
+        currBar_.dim = b.dim;
+        currBar_.birth = perm_->operator[](b.birth);
+        currBar_.death = b.death == static_cast<pos_index>(-1) ? -1 : perm_->operator[](b.death);
+      }
+    }
+
+    Barcode_iterator() : barcode_(nullptr), perm_(nullptr), currPos_(0) {}
+
+   private:
+    // mandatory for the boost::iterator_facade inheritance.
+    friend class boost::iterator_core_access;
+
+    const typename matrix_type::Barcode *barcode_;
+    const std::vector<Index> *perm_;
+    std::size_t currPos_;
+    bar currBar_;
+
+    bool equal(Barcode_iterator const &other) const {
+      return barcode_ == other.barcode_ && perm_ == other.perm_ && currPos_ == other.currPos_;
+    }
+
+    const bar &dereference() const { return currBar_; }
+
+    void increment() {
+      constexpr const bool debug = false;
+      ++currPos_;
+      if (currPos_ == barcode_->size()) {
+        barcode_ = nullptr;
+        perm_ = nullptr;
+        currPos_ = 0;
+      } else {
+        auto &b = barcode_->operator[](currPos_);
+        currBar_.dim = b.dim;
+        currBar_.birth = perm_->operator[](b.birth);
+        if (debug && currBar_.birth > std::numeric_limits<decltype(currBar_.birth)>::max() / 2) {
+          std::cout << currBar_ << std::endl;
+          std::cout << "while " << b.birth;
+          std::cout << "  " << perm_->size();
+        }
+        currBar_.death = b.death == static_cast<pos_index>(-1) ? -1 : perm_->operator[](b.death);
+      }
+    }
+  };
+
+  class Barcode {
+   public:
+    using iterator = Barcode_iterator;
+
+    Barcode(matrix_type &matrix, const std::vector<Index> *perm) : barcode_(&matrix.get_current_barcode()) {
+      const bool debug = false;
+      if constexpr (Matrix_options::has_vine_update) {
+        perm_ = perm;
+      } else {
+        perm_.reserve(perm->size());
+        for (const auto &stuff : *perm)
+          if (stuff < perm->size())  // number of generators
+            perm_.push_back(stuff);
+      }
+      if constexpr (debug) {
+        std::cout << "Built matrix of size " << matrix.get_number_of_columns() << " / " << perm->size() << std::endl;
+      }
+    }
+
+    iterator begin() const {
+      if constexpr (Matrix_options::has_vine_update) {
+        return Barcode_iterator(barcode_, perm_);
+      } else {
+        return Barcode_iterator(barcode_, &this->perm_);
+      }
+    }
+
+    iterator end() const { return Barcode_iterator(); }
+
+    /* using bar = typename matrix_type::Bar; */
+    /* const bar& operator[](std::size_t i){ */
+    /*   return barcode_->at(); */
+    /* } */
+    std::size_t size() const { return barcode_->size(); }
+
+    inline friend std::ostream &operator<<(std::ostream &stream, Barcode &structure) {
+      stream << "Barcode: " << structure.size() << "\n";
+      for (const auto bar : structure) {
+        stream << "[" << bar.dim << "] ";
+        stream << bar.birth << ", " << bar.death;
+        stream << "\n";
+      }
+      stream << "\n";
+      return stream;
+    }
+
+   private:
+    const typename matrix_type::Barcode *barcode_;
+    typename std::conditional<Matrix_options::has_vine_update, const std::vector<Index> *, std::vector<Index>>::type
+        perm_;
+  };
+
+  Persistence_backend_matrix() : permutation_(nullptr) {};
+
+  Persistence_backend_matrix(const Boundary_matrix_type &boundaries, std::vector<Index> &permutation)
+      : matrix_(boundaries.size()), permutation_(&permutation) {
+    static_assert(Matrix_options::is_of_boundary_type || Matrix_options::has_vine_update, "Clement implies vine.");
+    constexpr const bool verbose = false;
+    if constexpr (verbose) std::cout << "Constructing matrix..." << std::endl;
+    std::vector<Index> permutationInv(permutation_->size());
+    std::vector<Index> boundary_container;
+    std::size_t c = 0;
+    for (auto i : *permutation_) {
+      if (i >= boundaries.size()) {
+        c++;
+        continue;
+      }
+      permutationInv[i] = c++;
+      boundary_container.resize(boundaries[i].size());
+      if constexpr (verbose)
+        std::cout << i << "/" << permutation_->size() << " c= " << c << " dimension " << boundaries.dimension(i)
+                  << "..." << std::endl
+                  << std::flush;
+      for (std::size_t j = 0; j < boundaries[i].size(); ++j) {
+        boundary_container[j] = permutationInv[boundaries[i][j]];
+      }
+      std::sort(boundary_container.begin(), boundary_container.end());
+      matrix_.insert_boundary(c - 1, boundary_container, boundaries.dimension(i));
+    }
+  }
+
+  Persistence_backend_matrix(const Persistence_backend_matrix &toCopy)
+      : matrix_(toCopy.matrix_), permutation_(toCopy.permutation_) {}
+
+  Persistence_backend_matrix(Persistence_backend_matrix &&other) noexcept
+      : matrix_(std::move(other.matrix_)), permutation_(std::exchange(other.permutation_, nullptr)) {}
+
+  Persistence_backend_matrix &operator=(Persistence_backend_matrix other) {
+    swap(matrix_, other.matrix_);
+    std::swap(permutation_, other.permutation_);
+    return *this;
+  }
+
+  friend void swap(Persistence_backend_matrix &be1, Persistence_backend_matrix &be2) {
+    swap(be1.matrix_, be2.matrix_);
+    std::swap(be1.permutation_, be2.permutation_);
+  }
+
+  inline dimension_type get_dimension(pos_index i) { return matrix_.get_column_dimension(i); }
+
+  inline void vine_swap(pos_index i) { matrix_.vine_swap(i); }
+
+  inline Barcode get_barcode() { return Barcode(matrix_, permutation_); }
+
+  inline std::size_t size() { return this->matrix_.get_number_of_columns(); }
+
+  inline friend std::ostream &operator<<(std::ostream &stream, Persistence_backend_matrix &structure) {
+    stream << "[\n";
+    for (auto i = 0u; i < structure.matrix_.get_number_of_columns(); i++) {
+      stream << "[";
+      for (const auto &stuff : structure.matrix_.get_column(i)) stream << stuff << ", ";
+      stream << "]\n";
+    }
+
+    stream << "]\n";
+    return stream;
+  }
+
+  inline std::vector<std::vector<std::vector<unsigned int>>> get_representative_cycles(bool update,
+                                                                                       bool detailed = false) {
+    // Only used when vineyard, so shrunk permutation i.e.
+    // without the -1, is permutation as we keep inf values (they can become
+    // finite) cf barcode perm which is copied to remove the -1
+    std::vector<unsigned int> permutation2;
+    permutation2.reserve(permutation_->size());
+    for (auto i : *permutation_) {
+      if (i >= matrix_.get_number_of_columns()) {
+        continue;
+      }
+      permutation2.push_back(i);
+    }
+    constexpr const bool verbose = false;
+    if (update) [[likely]]
+      matrix_.update_representative_cycles();
+    std::vector<std::vector<std::vector<unsigned int>>> current_cycles =
+        matrix_.get_representative_cycles_as_borders(detailed);
+    for (auto &cycle : current_cycles) {
+      if constexpr (verbose) std::cout << "Cycle (matrix_ order): ";
+      for (auto &border : cycle) {
+        for (auto &b : border) {
+          b = permutation2[b];
+        }
+      }
+    }
+    return current_cycles;
+  }
+
+  inline void _update_permutation_ptr(std::vector<Index> &perm) { permutation_ = &perm; }
+
+ private:
+  matrix_type matrix_;
+  std::vector<Index> *permutation_;
+};
+
+}  // namespace truc_interface
+}  // namespace multiparameter
+}  // namespace Gudhi
+#endif  // MMA_INTERFACE_MATRIX_H