multipers 2.4.0b1__cp312-cp312-macosx_11_0_arm64.whl

multipers/gudhi/gudhi/Persistence_matrix/index_mapper.h

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+/*    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) 2022-24 Inria
+ *
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
+ */
+
+/**
+ * @file index_mapper.h
+ * @author Hannah Schreiber
+ * @brief Contains the Gudhi::persistence_matrix::Index_mapper class and
+ * Gudhi::persistence_matrix::Dummy_index_mapper structure.
+ */
+
+#ifndef PM_INDEX_MAPPER_H
+#define PM_INDEX_MAPPER_H
+
+namespace Gudhi {
+namespace persistence_matrix {
+
+// Note: this would be a good candidate for std::optional instead of a mixin as its only role for now
+// is to store a map. If this does not change later.
+
+/**
+ * @private
+ * @ingroup persistence_matrix
+ *
+ * @brief Empty structure.
+ * Inherited instead of @ref Index_mapper.
+ */
+struct Dummy_index_mapper {
+  friend void swap([[maybe_unused]] Dummy_index_mapper& d1, [[maybe_unused]] Dummy_index_mapper& d2) noexcept {}
+};
+
+/**
+ * @private
+ * @ingroup persistence_matrix
+ *
+ * @brief Map container. Though for translation between different index types.
+ *
+ * @tparam Map Map type
+ */
+template <class Map>
+struct Index_mapper {
+  using Index_map = Map;
+
+  Index_map map_;
+
+  friend void swap(Index_mapper& mapper1, Index_mapper& mapper2) noexcept { mapper1.map_.swap(mapper2.map_); }
+};
+
+}  // namespace persistence_matrix
+}  // namespace Gudhi
+
+#endif  // PM_INDEX_MAPPER_H

multipers/gudhi/gudhi/Persistence_matrix/matrix_dimension_holders.h

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+/*    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) 2022-24 Inria
+ *
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
+ */
+
+/**
+ * @file matrix_dimension_holders.h
+ * @author Hannah Schreiber
+ * @brief Contains the @ref Gudhi::persistence_matrix::Matrix_max_dimension_holder
+ * @ref Gudhi::persistence_matrix::Matrix_all_dimension_holder classes
+ * and the @ref Gudhi::persistence_matrix::Dummy_matrix_dimension_holder structure.
+ */
+
+#ifndef PM_MATRIX_DIM_HOLDER_H
+#define PM_MATRIX_DIM_HOLDER_H
+
+#include <utility>  //std::swap, std::move & std::exchange
+#include <vector>
+
+namespace Gudhi {
+namespace persistence_matrix {
+
+/**
+ * @ingroup persistence_matrix
+ *
+ * @brief Empty structure.
+ * Inherited instead of @ref Matrix_max_dimension_holder or @ref Matrix_all_dimension_holder, when the maximal
+ * dimension of a matrix is not stored.
+ */
+struct Dummy_matrix_dimension_holder {
+  template <typename Dimension>
+  Dummy_matrix_dimension_holder([[maybe_unused]] Dimension maximalDimension)
+  {}
+
+  friend void swap([[maybe_unused]] Dummy_matrix_dimension_holder& d1,
+                   [[maybe_unused]] Dummy_matrix_dimension_holder& d2) noexcept
+  {}
+};
+
+// TODO: find an easy way to give access to get_null_value<Dimension>() to replace the -1s
+
+/**
+ * @ingroup persistence_matrix
+ *
+ * @brief Class managing the maximal dimension of a cell represented in the inheriting matrix, when the option of
+ * cell removal is not enabled.
+ *
+ * @tparam Dimension Dimension value type. Has to be an integer type.
+ * If unsigned, the maximal value of the type should not be attained during a run.
+ */
+template <typename Dimension>
+class Matrix_max_dimension_holder
+{
+ public:
+  /**
+   * @brief Default constructor. If a dimension is specified, stores it as the maximal value.
+   *
+   * @param maximalDimension Value of the maximal dimension. Has to be either positive or -1. Default value: -1.
+   */
+  Matrix_max_dimension_holder(Dimension maximalDimension = -1) : maxDim_(maximalDimension) {};
+  /**
+   * @brief Copy constructor.
+   *
+   * @param toCopy Matrix to copy.
+   */
+  Matrix_max_dimension_holder(const Matrix_max_dimension_holder& toCopy) = default;
+  /**
+   * @brief Move constructor.
+   *
+   * @param other Matrix to move.
+   */
+  Matrix_max_dimension_holder(Matrix_max_dimension_holder&& other) noexcept
+      : maxDim_(std::exchange(other.maxDim_, -1)) {};
+
+  ~Matrix_max_dimension_holder() = default;
+
+  /**
+   * @brief Returns the maximal dimension of a cell represented in the matrix.
+   *
+   * @return The maximal dimension.
+   */
+  Dimension get_max_dimension() const { return maxDim_; };
+
+  /**
+   * @brief Assign operator.
+   */
+  Matrix_max_dimension_holder& operator=(const Matrix_max_dimension_holder& other) = default;
+
+  /**
+   * @brief Move assign operator.
+   */
+  Matrix_max_dimension_holder& operator=(Matrix_max_dimension_holder&& other) noexcept
+  {
+    if (this == &other) return *this;
+
+    maxDim_ = std::exchange(other.maxDim_, -1);
+    return *this;
+  };
+
+  /**
+   * @brief Swap operator.
+   */
+  friend void swap(Matrix_max_dimension_holder& matrix1, Matrix_max_dimension_holder& matrix2) noexcept
+  {
+    std::swap(matrix1.maxDim_, matrix2.maxDim_);
+  }
+
+ protected:
+  void _update_up(Dimension dimension)
+  {
+    if (maxDim_ == -1 || maxDim_ < dimension) maxDim_ = dimension;
+  };
+
+  void _reset() { maxDim_ = -1; }
+
+ private:
+  Dimension maxDim_; /**< Current maximal dimension. */
+};
+
+/**
+ * @ingroup persistence_matrix
+ *
+ * @brief Class managing the maximal dimension of a cell represented in the inheriting matrix, when the option of
+ * cell removal is enabled.
+ *
+ * @tparam Dimension Dimension value type. Has to be an integer type.
+ * If unsigned, the maximal value of the type should not be attained during a run.
+ */
+template <typename Dimension>
+class Matrix_all_dimension_holder
+{
+ public:
+  /**
+   * @brief Default constructor. If a dimension is specified, stores it as the maximal value.
+   *
+   * @param maximalDimension Value of the maximal dimension. Has to be either positive or -1. Default value: -1.
+   */
+  Matrix_all_dimension_holder(Dimension maximalDimension = -1)
+      : dimensions_(maximalDimension < 0 ? 0 : maximalDimension + 1, 0), maxDim_(maximalDimension)
+  {
+    if (maxDim_ != -1) dimensions_[maxDim_] = 1;
+  };
+
+  /**
+   * @brief Copy constructor.
+   *
+   * @param toCopy Matrix to copy.
+   */
+  Matrix_all_dimension_holder(const Matrix_all_dimension_holder& toCopy) = default;
+  /**
+   * @brief Move constructor.
+   *
+   * @param other Matrix to move.
+   */
+  Matrix_all_dimension_holder(Matrix_all_dimension_holder&& other) noexcept
+      : dimensions_(std::move(other.dimensions_)), maxDim_(std::exchange(other.maxDim_, -1)) {};
+
+  ~Matrix_all_dimension_holder() = default;
+
+  /**
+   * @brief Returns the maximal dimension of a cell represented in the matrix.
+   *
+   * @return The maximal dimension.
+   */
+  Dimension get_max_dimension() const { return maxDim_; };
+
+  /**
+   * @brief Assign operator.
+   */
+  Matrix_all_dimension_holder& operator=(const Matrix_all_dimension_holder& other) = default;
+
+  /**
+   * @brief Move assign operator.
+   */
+  Matrix_all_dimension_holder& operator=(Matrix_all_dimension_holder&& other) noexcept
+  {
+    if (this == &other) return *this;
+
+    dimensions_ = std::move(other.dimensions_);
+    maxDim_ = std::exchange(other.maxDim_, -1);
+    return *this;
+  };
+
+  /**
+   * @brief Swap operator.
+   */
+  friend void swap(Matrix_all_dimension_holder& matrix1, Matrix_all_dimension_holder& matrix2) noexcept
+  {
+    std::swap(matrix1.maxDim_, matrix2.maxDim_);
+    matrix1.dimensions_.swap(matrix2.dimensions_);
+  }
+
+ protected:
+  void _update_up(unsigned int dimension)
+  {
+    if (dimensions_.size() <= dimension) dimensions_.resize(dimension + 1, 0);
+    ++(dimensions_[dimension]);
+    maxDim_ = dimensions_.size() - 1;
+  };
+
+  void _update_down(unsigned int dimension)
+  {
+    --(dimensions_[dimension]);  // assumes dimension already exists and is not 0
+    while (!dimensions_.empty() && dimensions_.back() == 0) dimensions_.pop_back();
+    maxDim_ = dimensions_.size() - 1;
+  };
+
+  void _reset()
+  {
+    dimensions_.clear();
+    maxDim_ = -1;
+  }
+
+ private:
+  std::vector<unsigned int> dimensions_; /**< Number of cells by dimension. */
+  Dimension maxDim_;                     /**< Current maximal dimension. */
+};
+
+}  // namespace persistence_matrix
+}  // namespace Gudhi
+
+#endif  // PM_MATRIX_DIM_HOLDER_H

multipers/gudhi/gudhi/Persistence_matrix/matrix_row_access.h

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+/*    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) 2022-24 Inria
+ *
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
+ */
+
+/**
+ * @file matrix_row_access.h
+ * @author Hannah Schreiber
+ * @brief Contains the @ref Gudhi::persistence_matrix::Matrix_row_access class and
+ * @ref Gudhi::persistence_matrix::Dummy_matrix_row_access structure.
+ */
+
+#ifndef PM_BASE_MATRIX_RA_H
+#define PM_BASE_MATRIX_RA_H
+
+#include <utility>  //std::move
+
+namespace Gudhi {
+namespace persistence_matrix {
+
+/**
+ * @ingroup persistence_matrix
+ *
+ * @brief Empty structure.
+ * Inherited instead of @ref Matrix_row_access, when the the row access is not enabled.
+ */
+struct Dummy_matrix_row_access {
+  Dummy_matrix_row_access([[maybe_unused]] unsigned int numberOfRows = 0) {};
+
+  friend void swap([[maybe_unused]] Dummy_matrix_row_access& d1, [[maybe_unused]] Dummy_matrix_row_access& d2) noexcept
+  {}
+};
+
+/**
+ * @class Matrix_row_access matrix_row_access.h gudhi/Persistence_matrix/matrix_row_access.h
+ * @ingroup persistence_matrix
+ *
+ * @brief Class managing the row access for the inheriting matrix.
+ *
+ * @tparam Row Either boost::intrusive::list<Matrix_entry,...> if @ref PersistenceMatrixOptions::has_intrusive_rows
+ * is true, or std::set<Matrix_entry, RowEntryComp> otherwise.
+ * @tparam Row_container Either std::map<Index,Row> if @ref PersistenceMatrixOptions::has_removable_rows is
+ *  true, or std::vector<Row> otherwise.
+ * @tparam has_removable_rows Value of @ref PersistenceMatrixOptions::has_removable_rows.
+ * @tparam ID_index @ref IDIdx index type.
+ */
+template <typename Row, typename Row_container, bool has_removable_rows, typename ID_index>
+class Matrix_row_access
+{
+ public:
+  /**
+   * @brief Default constructor.
+   */
+  Matrix_row_access() : rows_(new Row_container()) {};
+
+  /**
+   * @brief Constructor reserving space for the given number of rows.
+   *
+   * Has only an effect if @ref PersistenceMatrixOptions::has_removable_rows is false.
+   *
+   * @param numberOfRows Number of rows to reserve space for.
+   */
+  Matrix_row_access(unsigned int numberOfRows) : rows_(new Row_container())
+  {
+    if constexpr (!has_removable_rows) {
+      rows_->resize(numberOfRows);
+    }
+  }
+
+  /**
+   * @brief Copy constructor.
+   *
+   * @param toCopy Matrix to copy.
+   */
+  Matrix_row_access(const Matrix_row_access& toCopy)
+      : rows_(new Row_container())  // as the matrix is rebuild, the rows should not be copied.
+  {
+    if constexpr (!has_removable_rows) {
+      rows_->resize(toCopy.rows_->size());
+    }
+  }
+
+  /**
+   * @brief Move constructor.
+   *
+   * @param other Matrix to move.
+   */
+  Matrix_row_access(Matrix_row_access&& other) noexcept : rows_(std::exchange(other.rows_, nullptr)) {}
+
+  /**
+   * @brief Destructor.
+   */
+  ~Matrix_row_access() { delete rows_; }
+
+  /**
+   * @brief Returns the row at the given @ref rowindex "row index".
+   * The type of the row depends on the chosen options, see @ref PersistenceMatrixOptions::has_intrusive_rows.
+   *
+   * @param rowIndex @ref rowindex "Row index" of the row to return: @ref IDIdx for @ref chainmatrix "chain matrices"
+   * or updated @ref IDIdx for @ref boundarymatrix "boundary matrices" if swaps occurred.
+   * @return Reference to the row.
+   */
+  Row& get_row(ID_index rowIndex)
+  {
+    if constexpr (has_removable_rows) {
+      return rows_->at(rowIndex);
+    } else {
+      return rows_->operator[](rowIndex);
+    }
+  }
+
+  /**
+   * @brief Returns the row at the given @ref rowindex "row index".
+   * The type of the row depends on the chosen options, see @ref PersistenceMatrixOptions::has_intrusive_rows.
+   *
+   * @param rowIndex @ref rowindex "Row index" of the row to return: @ref IDIdx for @ref chainmatrix "chain matrices"
+   * or updated @ref IDIdx for @ref boundarymatrix "boundary matrices" if swaps occurred.
+   * @return Const reference to the row.
+   */
+  const Row& get_row(ID_index rowIndex) const
+  {
+    if constexpr (has_removable_rows) {
+      return rows_->at(rowIndex);
+    } else {
+      return rows_->operator[](rowIndex);
+    }
+  }
+
+  /**
+   * @brief Only available if @ref PersistenceMatrixOptions::has_removable_rows is true. Removes the given row
+   * from the row container if the row exists and is empty.
+   *
+   * @param rowIndex @ref rowindex "Row index" of the row to remove.
+   */
+  void erase_empty_row(ID_index rowIndex)
+  {
+    static_assert(has_removable_rows, "'erase_empty_row' is not implemented for the chosen options.");
+
+    auto it = rows_->find(rowIndex);
+    if (it != rows_->end() && it->second.empty()) rows_->erase(it);
+  }
+
+  /**
+   * @brief Assign operator.
+   */
+  Matrix_row_access& operator=(const Matrix_row_access& other)
+  {
+    if constexpr (has_removable_rows)
+      rows_->reserve(other.rows_->size());
+    else
+      rows_->resize(other.rows_->size());
+    return *this;
+  }
+
+  /**
+   * @brief Move assign operator.
+   */
+  Matrix_row_access& operator=(Matrix_row_access&& other) noexcept
+  {
+    if (this == &other) return *this;
+
+    rows_ = std::exchange(other.rows_, nullptr);
+    return *this;
+  }
+
+  /**
+   * @brief Swap operator.
+   */
+  friend void swap(Matrix_row_access& matrix1, Matrix_row_access& matrix2) noexcept
+  {
+    std::swap(matrix1.rows_, matrix2.rows_);
+  }
+
+ protected:
+  Row_container* _get_rows_ptr() const { return rows_; }
+
+  void _resize(ID_index size)
+  {
+    static_assert(!has_removable_rows, "'_resize' is not implemented for the chosen options.");
+
+    if (rows_->size() <= size) rows_->resize(size + 1);
+  }
+
+ private:
+  /**
+   * @brief Row container. A pointer to facilitate column swaps when two matrices are swapped.
+   * Has to be destroyed after matrix_, therefore has to be inherited.
+   */
+  Row_container* rows_;
+};
+
+}  // namespace persistence_matrix
+}  // namespace Gudhi
+
+#endif  // PM_BASE_MATRIX_RA_H

multipers/gudhi/gudhi/Persistence_matrix/ru_pairing.h

@@ -0,0 +1,166 @@
+/*    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) 2022-24 Inria
+ *
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
+ */
+
+/**
+ * @file ru_pairing.h
+ * @author Hannah Schreiber
+ * @brief Contains the @ref Gudhi::persistence_matrix::RU_pairing class and
+ * @ref Gudhi::persistence_matrix::Dummy_ru_pairing structure.
+ */
+
+#ifndef PM_RU_PAIRING_H
+#define PM_RU_PAIRING_H
+
+#include <unordered_map>
+
+namespace Gudhi {
+namespace persistence_matrix {
+
+template <typename Master_matrix>
+class RU_barcode_swap;
+
+/**
+ * @ingroup persistence_matrix
+ *
+ * @brief Empty structure.
+ * Inherited instead of @ref RU_pairing, when the computation of the barcode was not enabled or if the pairing
+ * is already managed by the vine update classes.
+ */
+struct Dummy_ru_pairing {
+  friend void swap([[maybe_unused]] Dummy_ru_pairing& d1, [[maybe_unused]] Dummy_ru_pairing& d2) noexcept {}
+};
+
+/**
+ * @class RU_pairing ru_pairing.h gudhi/Persistence_matrix/ru_pairing.h
+ * @ingroup persistence_matrix
+ *
+ * @brief Class managing the barcode for @ref RU_matrix if the option was enabled.
+ *
+ * @tparam Master_matrix An instantiation of @ref Matrix from which all types and options are deduced.
+ */
+template <class Master_matrix>
+class RU_pairing
+{
+ public:
+  using Barcode = typename Master_matrix::Barcode; /**< Barcode type. */
+
+  /**
+   * @brief Default constructor.
+   */
+  RU_pairing() = default;
+
+  /**
+   * @brief Returns the current barcode which is maintained at any insertion, removal or vine swap.
+   *
+   * @return Const reference to the barcode.
+   */
+  const Barcode& get_current_barcode() const { return barcode_; }
+
+  /**
+   * @brief Swap operator.
+   */
+  friend void swap(RU_pairing& pairing1, RU_pairing& pairing2) noexcept
+  {
+    pairing1.barcode_.swap(pairing2.barcode_);
+    pairing1.indexToBar_.swap(pairing2.indexToBar_);
+    pairing1.idToPosition_.swap(pairing2.idToPosition_);
+  }
+
+ protected:
+  using Pos_index = typename Master_matrix::Pos_index;
+  using ID_index = typename Master_matrix::ID_index;
+  using Dimension = typename Master_matrix::Dimension;
+
+  void _reserve(unsigned int numberOfColumns) { indexToBar_.reserve(numberOfColumns); }
+
+  void _update_barcode(ID_index birthPivot, Pos_index death)
+  {
+    auto it = idToPosition_.find(birthPivot);
+    Pos_index pivotBirth = it == idToPosition_.end() ? birthPivot : it->second;
+    if constexpr (Master_matrix::hasFixedBarcode || !Master_matrix::Option_list::has_removable_columns) {
+      barcode_[indexToBar_[pivotBirth]].death = death;
+      indexToBar_.push_back(indexToBar_[pivotBirth]);
+    } else {
+      auto& barIt = indexToBar_.at(pivotBirth);
+      barIt->death = death;
+      indexToBar_.try_emplace(death, barIt);  // list so iterators are stable
+    }
+  }
+
+  void _add_bar(Dimension dim, Pos_index birth)
+  {
+    barcode_.emplace_back(birth, Master_matrix::template get_null_value<Pos_index>(), dim);
+    if constexpr (Master_matrix::hasFixedBarcode || !Master_matrix::Option_list::has_removable_columns) {
+      indexToBar_.push_back(barcode_.size() - 1);
+    } else {
+      indexToBar_.try_emplace(birth, --barcode_.end());
+    }
+  }
+
+  void _remove_last(Pos_index eventIndex)
+  {
+    static_assert(Master_matrix::Option_list::has_removable_columns, "_remove_last not available.");
+    constexpr const Pos_index nullDeath = Master_matrix::template get_null_value<Pos_index>();
+
+    if constexpr (Master_matrix::hasFixedBarcode) {
+      auto& bar = barcode_[indexToBar_[eventIndex]];
+      if (bar.death == nullDeath) {  // birth
+        barcode_.pop_back();         // sorted by birth and eventIndex has to be the highest one
+      } else {                       // death
+        bar.death = nullDeath;
+      };
+      indexToBar_.pop_back();
+    } else {  // birth order eventually shuffled by vine updates. No sort possible to keep the matchings.
+      auto it = indexToBar_.find(eventIndex);
+      typename Barcode::iterator bar = it->second;
+
+      if (bar->death == nullDeath)
+        barcode_.erase(bar);
+      else
+        bar->death = nullDeath;
+
+      indexToBar_.erase(it);
+    }
+
+    auto& map = static_cast<typename Master_matrix::Master_RU_matrix*>(this)->positionToID_;
+    auto it = map.find(eventIndex);
+    if (it != map.end()) {
+      idToPosition_.erase(it->second);
+      map.erase(it);
+    }
+  }
+
+  void _insert_id_position(ID_index id, Pos_index pos) { idToPosition_.emplace(id, pos); }
+
+  void _reset()
+  {
+    barcode_.clear();
+    indexToBar_.clear();
+  }
+
+ private:
+  using Dictionary = typename Master_matrix::Bar_dictionary;
+
+  // could also just mark everything as protected as RU_barcode_swap inherits from RU_pairing
+  // but this way, it marks a better difference between "class using this mixin" with "class extending this mixin"
+  friend RU_barcode_swap<Master_matrix>;
+
+  Barcode barcode_;       /**< Bar container. */
+  Dictionary indexToBar_; /**< Map from @ref MatIdx index to bar index. */
+  /**
+   * @brief Map from cell ID to cell position. Only stores a pair if ID != position.
+   */
+  std::unordered_map<ID_index, Pos_index> idToPosition_;  // TODO: test other map types
+};
+
+}  // namespace persistence_matrix
+}  // namespace Gudhi
+
+#endif  // PM_RU_PAIRING_H