multipers 2.3.3b6__cp313-cp313-macosx_11_0_arm64.whl

multipers/gudhi/gudhi/Persistence_matrix/RU_matrix.h

@@ -0,0 +1,910 @@
+/*    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_matrix.h
+ * @author Hannah Schreiber
+ * @brief Contains the @ref Gudhi::persistence_matrix::RU_matrix class.
+ */
+
+#ifndef PM_RU_MATRIX_H
+#define PM_RU_MATRIX_H
+
+#include <vector>
+#include <utility>   //std::swap, std::move & std::exchange
+#include <iostream>  //print() only
+
+namespace Gudhi {
+namespace persistence_matrix {
+
+/**
+ * @class RU_matrix RU_matrix.h gudhi/Persistence_matrix/RU_matrix.h
+ * @ingroup persistence_matrix
+ *
+ * @brief %Matrix structure to store the ordered @ref boundarymatrix "boundary matrix" \f$ R \cdot U \f$ of a filtered
+ * complex in order to compute its persistent homology, as well as representative cycles.
+ * Supports vineyards (see @cite vineyards) and the removal of maximal cells while maintaining
+ * a valid barcode. Provides an access to its columns and rows.
+ *
+ * @tparam Master_matrix An instantiation of @ref Matrix from which all types and options are deduced.
+ */
+template <class Master_matrix>
+class RU_matrix : public Master_matrix::RU_pairing_option,
+                  public Master_matrix::RU_vine_swap_option,
+                  public Master_matrix::RU_representative_cycles_option
+{
+ public:
+  /**
+   * @brief Field operators class. Necessary only if @ref PersistenceMatrixOptions::is_z2 is false.
+   */
+  using Field_operators = typename Master_matrix::Field_operators;
+  using Field_element = typename Master_matrix::Element;                /**< Type of an field element. */
+  using Column = typename Master_matrix::Column;                        /**< Column type. */
+  using Row = typename Master_matrix::Row;                              /**< Row type,
+                                                                             only necessary with row access option. */
+  using Entry_constructor = typename Master_matrix::Entry_constructor;  /**< Factory of @ref Entry classes. */
+  using Column_settings = typename Master_matrix::Column_settings;      /**< Structure giving access to the columns to
+                                                                             necessary external classes. */
+  using Boundary = typename Master_matrix::Boundary;                    /**< Type of an input column. */
+  using Index = typename Master_matrix::Index;                          /**< @ref MatIdx index type. */
+  using ID_index = typename Master_matrix::ID_index;                    /**< @ref IDIdx index type. */
+  using Pos_index = typename Master_matrix::Pos_index;                  /**< @ref PosIdx index type. */
+  using Dimension = typename Master_matrix::Dimension;                  /**< Dimension value type. */
+
+  /**
+   * @brief Constructs an empty matrix.
+   *
+   * @param colSettings Pointer to an existing setting structure for the columns. The structure should contain all
+   * the necessary external classes specifically necessary for the choosen column type, such as custom allocators.
+   */
+  RU_matrix(Column_settings* colSettings);
+  /**
+   * @brief Constructs a new matrix from the given ranges of @ref Matrix::Entry_representative. Each range corresponds
+   * to a column (the order of the ranges are preserved). The content of the ranges is assumed to be sorted by
+   * increasing IDs. The IDs of the simplices are also assumed to be consecutive, ordered by filtration value, starting
+   * with 0.
+   *
+   * @tparam Boundary_range Range type for @ref Matrix::Entry_representative ranges.
+   * Assumed to have a begin(), end() and size() method.
+   * @param orderedBoundaries Range of boundaries: @p orderedBoundaries is interpreted as a boundary matrix of a
+   * filtered **simplicial** complex, whose boundaries are ordered by filtration order.
+   * Therefore, `orderedBoundaries[i]` should store the boundary of the \f$ i^{th} \f$ simplex in the filtration,
+   * as an ordered list of indices of its facets (again those indices correspond to their respective position
+   * in the matrix). That is why the indices of the simplices are assumed to be consecutive and starting with 0
+   * (an empty boundary is interpreted as a vertex boundary and not as a non existing simplex).
+   * All dimensions up to the maximal dimension of interest have to be present. If only a higher dimension is of
+   * interest and not everything should be stored, then use the @ref insert_boundary method instead (after creating the
+   * matrix with the @ref RU_matrix(unsigned int, Column_settings*) constructor preferably).
+   * @param colSettings Pointer to an existing setting structure for the columns. The structure should contain all
+   * the necessary external classes specifically necessary for the choosen column type, such as custom allocators.
+   */
+  template <class Boundary_range = Boundary>
+  RU_matrix(const std::vector<Boundary_range>& orderedBoundaries, Column_settings* colSettings);
+  /**
+   * @brief Constructs a new empty matrix and reserves space for the given number of columns.
+   *
+   * @param numberOfColumns Number of columns to reserve space for.
+   * @param colSettings Pointer to an existing setting structure for the columns. The structure should contain all
+   * the necessary external classes specifically necessary for the choosen column type, such as custom allocators.
+   */
+  RU_matrix(unsigned int numberOfColumns, Column_settings* colSettings);
+  /**
+   * @brief Copy constructor. If @p colSettings is not a null pointer, its value is kept
+   * instead of the one in the copied matrix.
+   *
+   * @param matrixToCopy Matrix to copy.
+   * @param colSettings Either a pointer to an existing setting structure for the columns or a null pointer.
+   * The structure should contain all the necessary external classes specifically necessary for the choosen column type,
+   * such as custom allocators. If null pointer, the pointer stored in @p matrixToCopy is used instead.
+   */
+  RU_matrix(const RU_matrix& matrixToCopy, Column_settings* colSettings = nullptr);
+  /**
+   * @brief Move constructor.
+   *
+   * @param other Matrix to move.
+   */
+  RU_matrix(RU_matrix&& other) noexcept;
+
+  /**
+   * @brief Inserts at the end of the matrix a new ordered column corresponding to the given boundary.
+   * This means that it is assumed that this method is called on boundaries in the order of the filtration.
+   * It also assumes that the cells in the given boundary are identified by their relative position in the filtration,
+   * starting at 0. If it is not the case, use the other
+   * @ref insert_boundary(ID_index, const Boundary_range&, Dimension) "insert_boundary" instead by indicating the
+   * cell ID used in the boundaries when the cell is inserted.
+   *
+   * Different to the constructor, the boundaries do not have to come from a simplicial complex, but also from
+   * a more general entry complex. This includes cubical complexes or Morse complexes for example.
+   *
+   * At the insertion, the boundary is stored in its reduced form and the barcode, if enabled, is updated.
+   *
+   * @tparam Boundary_range Range of @ref Matrix::Entry_representative. Assumed to have a begin(), end() and size()
+   * method.
+   * @param boundary Boundary generating the new column. The content should be ordered by ID.
+   * @param dim Dimension of the cell whose boundary is given. If the complex is simplicial,
+   * this parameter can be omitted as it can be deduced from the size of the boundary.
+   */
+  template <class Boundary_range = Boundary>
+  void insert_boundary(const Boundary_range& boundary, Dimension dim = -1);
+  /**
+   * @brief It does the same as the other version, but allows the boundary cells to be identified without restrictions
+   * except that all IDs have to be strictly increasing in the order of filtration. Note that you should avoid then
+   * to use the other insertion method to avoid overwriting IDs.
+   *
+   * As a cell has to be inserted before one of its cofaces in a valid filtration (recall that it is assumed that
+   * the cells are inserted by order of filtration), it is sufficient to indicate the ID of the cell being inserted.
+   *
+   * @tparam Boundary_range Range of @ref Matrix::Entry_representative. Assumed to have a begin(), end() and size()
+   * method.
+   * @param cellIndex @ref IDIdx index to use to identify the new cell.
+   * @param boundary Boundary generating the new column. The indices of the boundary have to correspond to the
+   * @p cellIndex values of precedent calls of the method for the corresponding cells and should be ordered in
+   * increasing order.
+   * @param dim Dimension of the cell whose boundary is given. If the complex is simplicial,
+   * this parameter can be omitted as it can be deduced from the size of the boundary.
+   */
+  template <class Boundary_range = Boundary>
+  void insert_boundary(ID_index cellIndex, const Boundary_range& boundary, Dimension dim = -1);
+  /**
+   * @brief Returns the column at the given @ref MatIdx index in \f$ R \f$ if @p inR is true and
+   * in \f$ U \f$ if @p inR is false.
+   * The type of the column depends on the choosen options, see @ref PersistenceMatrixOptions::column_type.
+   *
+   * Note that before returning the column, all column entries can eventually be reordered, if lazy swaps occurred.
+   * It is therefore recommended to avoid calling @ref get_column between vine swaps, otherwise the benefits
+   * of the the laziness is lost.
+   *
+   * @param columnIndex @ref MatIdx index of the column to return.
+   * @param inR If true, returns the column in \f$ R \f$, if false, returns the column in \f$ U \f$.
+   * Default value: true.
+   * @return Reference to the column.
+   */
+  Column& get_column(Index columnIndex, bool inR = true);
+  /**
+   * @brief Returns the row at the given @ref rowindex "row index" in \f$ R \f$ if @p inR is true and
+   * in \f$ U \f$ if @p inR is false.
+   * The type of the row depends on the choosen options, see @ref PersistenceMatrixOptions::has_intrusive_rows.
+   *
+   * Note that before returning the row, all column entries can eventually be reordered, if lazy swaps occurred.
+   * It is therefore recommended to avoid calling @ref get_row between vine swaps, otherwise the benefits
+   * of the the laziness is lost.
+   *
+   * @param rowIndex @ref rowindex "Row index" of the row to return.
+   * @param inR If true, returns the row in \f$ R \f$, if false, returns the row in \f$ U \f$.
+   * Default value: true.
+   * @return Reference to the row.
+   */
+  Row& get_row(Index rowIndex, bool inR = true);
+  /**
+   * @brief If @ref PersistenceMatrixOptions::has_row_access and @ref PersistenceMatrixOptions::has_removable_rows
+   * are true: assumes that the row is empty in \f$ R \f$ and removes it from \f$ R \f$. If the matrix is valid,
+   * a row will never be empty in \f$ U \f$, so \f$ U \f$ won't be affected.
+   * If @ref PersistenceMatrixOptions::has_map_column_container
+   * and @ref PersistenceMatrixOptions::has_column_and_row_swaps are true: cleans up maps used for the lazy row swaps.
+   * Otherwise, does nothing.
+   *
+   * @warning The removed rows are always assumed to be empty in \f$ R \f$. If it is not the case, the deleted row
+   * entries are not removed from their columns. And in the case of intrusive rows, this will generate a segmentation
+   * fault when the column entries are destroyed later. The row access is just meant as a "read only" access to the
+   * rows and the @ref erase_empty_row method just as a way to specify that a row is empty and can therefore be removed
+   * from dictionaries. This allows to avoid testing the emptiness of a row at each column entry removal, what can
+   * be quite frequent.
+   *
+   * @param rowIndex @ref rowindex "Row index" of the empty row.
+   */
+  void erase_empty_row(Index rowIndex);
+  /**
+   * @brief Only available if @ref PersistenceMatrixOptions::has_removable_columns and
+   * @ref PersistenceMatrixOptions::has_vine_update are true.
+   * Assumes that the cell is maximal in the current complex and removes it such that the matrix remains consistent
+   * (i.e., RU is still an upper triangular decomposition of the @ref boundarymatrix "boundary matrix").
+   * The maximality of the cell is not verified.
+   * Also updates the barcode if it is stored.
+   *
+   * See also @ref remove_last.
+   *
+   * @param columnIndex @ref MatIdx index of the cell to remove.
+   */
+  void remove_maximal_cell(Index columnIndex);
+  /**
+   * @brief Only available if @ref PersistenceMatrixOptions::has_removable_columns is true.
+   * Removes the last cell in the filtration from the matrix and updates the barcode if it is stored.
+   *
+   * See also @ref remove_maximal_cell.
+   */
+  void remove_last();
+
+  /**
+   * @brief Returns the maximal dimension of a cell stored in the matrix.
+   * Only available if @ref PersistenceMatrixOptions::has_matrix_maximal_dimension_access is true.
+   *
+   * @return The maximal dimension.
+   */
+  Dimension get_max_dimension() const;
+  /**
+   * @brief Returns the current number of columns in the matrix.
+   *
+   * @return The number of columns.
+   */
+  Index get_number_of_columns() const;
+  /**
+   * @brief Returns the dimension of the given column.
+   *
+   * @param columnIndex @ref MatIdx index of the column representing the cell.
+   * @return Dimension of the cell.
+   */
+  Dimension get_column_dimension(Index columnIndex) const;
+
+  /**
+   * @brief Adds column at @p sourceColumnIndex onto the column at @p targetColumnIndex in the matrix.
+   *
+   * @warning They will be no verification to ensure that the addition makes sense for the validity of a
+   * boundary matrix of a filtered complex. For example, a right-to-left addition could corrupt the computation
+   * of the barcode if done blindly. So should be used with care.
+   *
+   * @param sourceColumnIndex @ref MatIdx index of the source column.
+   * @param targetColumnIndex @ref MatIdx index of the target column.
+   */
+  void add_to(Index sourceColumnIndex, Index targetColumnIndex);
+  /**
+   * @brief Multiplies the target column with the coefficient and then adds the source column to it.
+   * That is: `targetColumn = (targetColumn * coefficient) + sourceColumn`.
+   *
+   * @warning They will be no verification to ensure that the addition makes sense for the validity of a
+   * boundary matrix of a filtered complex. For example, a right-to-left addition could corrupt the computation
+   * of the barcode if done blindly. So should be used with care.
+   *
+   * @param sourceColumnIndex @ref MatIdx index of the source column.
+   * @param coefficient Value to multiply.
+   * @param targetColumnIndex @ref MatIdx index of the target column.
+   */
+  void multiply_target_and_add_to(Index sourceColumnIndex, const Field_element& coefficient, Index targetColumnIndex);
+  /**
+   * @brief Multiplies the source column with the coefficient before adding it to the target column.
+   * That is: `targetColumn += (coefficient * sourceColumn)`. The source column will **not** be modified.
+   *
+   * @warning They will be no verification to ensure that the addition makes sense for the validity of a
+   * boundary matrix of a filtered complex. For example, a right-to-left addition could corrupt the computation
+   * of the barcode if done blindly. So should be used with care.
+   *
+   * @param coefficient Value to multiply.
+   * @param sourceColumnIndex @ref MatIdx index of the source column.
+   * @param targetColumnIndex @ref MatIdx index of the target column.
+   */
+  void multiply_source_and_add_to(const Field_element& coefficient, Index sourceColumnIndex, Index targetColumnIndex);
+
+  /**
+   * @brief Zeroes the entry at the given coordinates in \f$ R \f$ if @p inR is true or in
+   * \f$ U \f$ if @p inR is false. Should be used with care to not destroy the validity of the persistence
+   * related properties of the matrix.
+   *
+   * @param columnIndex @ref MatIdx index of the column of the entry.
+   * @param rowIndex @ref rowindex "Row index" of the row of the entry.
+   * @param inR Boolean indicating in which matrix to zero: if true in \f$ R \f$ and if false in \f$ U \f$.
+   * Default value: true.
+   */
+  void zero_entry(Index columnIndex, Index rowIndex, bool inR = true);
+  /**
+   * @brief Zeroes the column at the given index in \f$ R \f$ if @p inR is true or in
+   * \f$ U \f$ if @p inR is false. Should be used with care to not destroy the validity of the persistence
+   * related properties of the matrix.
+   *
+   * @param columnIndex @ref MatIdx index of the column to zero.
+   * @param inR Boolean indicating in which matrix to zero: if true in \f$ R \f$ and if false in \f$ U \f$.
+   * Default value: true.
+   */
+  void zero_column(Index columnIndex, bool inR = true);
+  /**
+   * @brief Indicates if the entry at given coordinates has value zero in \f$ R \f$
+   * if @p inR is true or in \f$ U \f$ if @p inR is false.
+   *
+   * @param columnIndex @ref MatIdx index of the column of the entry.
+   * @param rowIndex @ref rowindex "Row index" of the row of the entry.
+   * @param inR Boolean indicating in which matrix to look: if true in \f$ R \f$ and if false in \f$ U \f$.
+   * Default value: true.
+   * @return true If the entry has value zero.
+   * @return false Otherwise.
+   */
+  bool is_zero_entry(Index columnIndex, Index rowIndex, bool inR = true) const;
+  /**
+   * @brief Indicates if the column at given index has value zero in \f$ R \f$
+   * if @p inR is true or in \f$ U \f$ if @p inR is false.
+   *
+   * Note that if @p inR is false, this method should usually return false.
+   *
+   * @param columnIndex @ref MatIdx index of the column.
+   * @param inR Boolean indicating in which matrix to look: if true in \f$ R \f$ and if false in \f$ U \f$.
+   * Default value: true.
+   * @return true If the column has value zero.
+   * @return false Otherwise.
+   */
+  bool is_zero_column(Index columnIndex, bool inR = true);
+
+  /**
+   * @brief Returns the @ref MatIdx index of the column which has the given @ref rowindex "row index" as pivot in
+   * \f$ R \f$. Assumes that the pivot exists.
+   *
+   * @param cellIndex @ref rowindex "Row index" of the pivot.
+   * @return @ref MatIdx index of the column in \f$ R \f$ with the given pivot.
+   */
+  Index get_column_with_pivot(Index cellIndex) const;
+  /**
+   * @brief Returns the @ref rowindex "row index" of the pivot of the given column in \f$ R \f$.
+   *
+   * @param columnIndex @ref MatIdx index of the column in \f$ R \f$.
+   * @return The @ref rowindex "row index" of the pivot.
+   */
+  Index get_pivot(Index columnIndex);
+
+  /**
+   * @brief Resets the matrix to an empty matrix.
+   *
+   * @param colSettings Pointer to an existing setting structure for the columns. The structure should contain all
+   * the necessary external classes specifically necessary for the choosen column type, such as custom allocators.
+   */
+  void reset(Column_settings* colSettings) {
+    reducedMatrixR_.reset(colSettings);
+    mirrorMatrixU_.reset(colSettings);
+    pivotToColumnIndex_.clear();
+    nextEventIndex_ = 0;
+    if constexpr (!Master_matrix::Option_list::is_z2) {
+      operators_ = &(colSettings->operators);
+    }
+  }
+
+  /**
+   * @brief Assign operator.
+   */
+  RU_matrix& operator=(const RU_matrix& other);
+  /**
+   * @brief Swap operator.
+   */
+  friend void swap(RU_matrix& matrix1, RU_matrix& matrix2) {
+    swap(static_cast<typename Master_matrix::RU_pairing_option&>(matrix1),
+         static_cast<typename Master_matrix::RU_pairing_option&>(matrix2));
+    swap(static_cast<typename Master_matrix::RU_vine_swap_option&>(matrix1),
+         static_cast<typename Master_matrix::RU_vine_swap_option&>(matrix2));
+    swap(static_cast<typename Master_matrix::RU_representative_cycles_option&>(matrix1),
+         static_cast<typename Master_matrix::RU_representative_cycles_option&>(matrix2));
+    swap(matrix1.reducedMatrixR_, matrix2.reducedMatrixR_);
+    swap(matrix1.mirrorMatrixU_, matrix2.mirrorMatrixU_);
+    matrix1.pivotToColumnIndex_.swap(matrix2.pivotToColumnIndex_);
+    std::swap(matrix1.nextEventIndex_, matrix2.nextEventIndex_);
+    std::swap(matrix1.operators_, matrix2.operators_);
+  }
+
+  void print(Index startCol = 0, Index endCol = -1, Index startRow = 0, Index endRow = -1);  // for debug
+
+ private:
+  using Swap_opt = typename Master_matrix::RU_vine_swap_option;
+  using Pair_opt = typename Master_matrix::RU_pairing_option;
+  using Rep_opt = typename Master_matrix::RU_representative_cycles_option;
+  using Dictionary = typename Master_matrix::template Dictionary<Index>;
+  using Barcode = typename Master_matrix::Barcode;
+  using Bar_dictionary = typename Master_matrix::Bar_dictionary;
+  using R_matrix = typename Master_matrix::Master_boundary_matrix;
+  using U_matrix = typename Master_matrix::Master_base_matrix;
+
+  friend Rep_opt;   // direct access to the two matrices
+  friend Swap_opt;  // direct access to the two matrices
+
+  R_matrix reducedMatrixR_;       /**< R. */
+  // TODO: make U not accessible by default and add option to enable access? Inaccessible, it
+  // needs less options and we could avoid some ifs.
+  U_matrix mirrorMatrixU_;        /**< U. */
+  Dictionary pivotToColumnIndex_; /**< Map from pivot row index to column @ref MatIdx index. */
+  Pos_index nextEventIndex_;      /**< Next birth or death index. */
+  Field_operators* operators_;    /**< Field operators,
+                                       can be nullptr if @ref PersistenceMatrixOptions::is_z2 is true. */
+
+  void _insert_boundary(Index currentIndex);
+  void _initialize_U();
+  void _reduce();
+  void _reduce_last_column(Index lastIndex);
+  void _reduce_column(Index target, Index eventIndex);
+  void _reduce_column_by(Index target, Index source);
+  void _update_barcode(ID_index birthPivot, Pos_index death);
+  void _add_bar(Dimension dim, Pos_index birth);
+  void _remove_last_in_barcode(Pos_index eventIndex);
+
+  constexpr Bar_dictionary& _indexToBar();
+};
+
+template <class Master_matrix>
+inline RU_matrix<Master_matrix>::RU_matrix(Column_settings* colSettings)
+    : Pair_opt(),
+      Swap_opt(),
+      Rep_opt(),
+      reducedMatrixR_(colSettings),
+      mirrorMatrixU_(colSettings),
+      nextEventIndex_(0),
+      operators_(nullptr)
+{
+  if constexpr (!Master_matrix::Option_list::is_z2) {
+    operators_ = &(colSettings->operators);
+  }
+}
+
+template <class Master_matrix>
+template <class Boundary_range>
+inline RU_matrix<Master_matrix>::RU_matrix(const std::vector<Boundary_range>& orderedBoundaries,
+                                           Column_settings* colSettings)
+    : Pair_opt(),
+      Swap_opt(),
+      Rep_opt(),
+      reducedMatrixR_(orderedBoundaries, colSettings),
+      mirrorMatrixU_(orderedBoundaries.size(), colSettings),
+      nextEventIndex_(orderedBoundaries.size()),
+      operators_(nullptr)
+{
+  if constexpr (!Master_matrix::Option_list::is_z2) {
+    operators_ = &(colSettings->operators);
+  }
+
+  if constexpr (Master_matrix::Option_list::has_map_column_container) {
+    pivotToColumnIndex_.reserve(orderedBoundaries.size());
+  } else {
+    pivotToColumnIndex_.resize(orderedBoundaries.size(), -1);
+  }
+
+  _initialize_U();
+  _reduce();
+}
+
+template <class Master_matrix>
+inline RU_matrix<Master_matrix>::RU_matrix(unsigned int numberOfColumns, Column_settings* colSettings)
+    : Pair_opt(),
+      Swap_opt(),
+      Rep_opt(),
+      reducedMatrixR_(numberOfColumns, colSettings),
+      mirrorMatrixU_(numberOfColumns, colSettings),
+      nextEventIndex_(0),
+      operators_(nullptr)
+{
+  if constexpr (!Master_matrix::Option_list::is_z2) {
+    operators_ = &(colSettings->operators);
+  }
+
+  if constexpr (Master_matrix::Option_list::has_map_column_container) {
+    pivotToColumnIndex_.reserve(numberOfColumns);
+  } else {
+    pivotToColumnIndex_.resize(numberOfColumns, -1);
+  }
+  if constexpr (Master_matrix::Option_list::has_column_pairings) {
+    _indexToBar().reserve(numberOfColumns);
+  }
+  if constexpr (Master_matrix::Option_list::has_vine_update) {
+    Swap_opt::_positionToRowIdx().reserve(numberOfColumns);
+  }
+}
+
+template <class Master_matrix>
+inline RU_matrix<Master_matrix>::RU_matrix(const RU_matrix& matrixToCopy, Column_settings* colSettings)
+    : Pair_opt(static_cast<const Pair_opt&>(matrixToCopy)),
+      Swap_opt(static_cast<const Swap_opt&>(matrixToCopy)),
+      Rep_opt(static_cast<const Rep_opt&>(matrixToCopy)),
+      reducedMatrixR_(matrixToCopy.reducedMatrixR_, colSettings),
+      mirrorMatrixU_(matrixToCopy.mirrorMatrixU_, colSettings),
+      pivotToColumnIndex_(matrixToCopy.pivotToColumnIndex_),
+      nextEventIndex_(matrixToCopy.nextEventIndex_),
+      operators_(colSettings == nullptr ? matrixToCopy.operators_ : nullptr)
+{
+  if constexpr (!Master_matrix::Option_list::is_z2) {
+    if (colSettings != nullptr) operators_ = &(colSettings->operators);
+  }
+}
+
+template <class Master_matrix>
+inline RU_matrix<Master_matrix>::RU_matrix(RU_matrix&& other) noexcept
+    : Pair_opt(std::move(static_cast<Pair_opt&>(other))),
+      Swap_opt(std::move(static_cast<Swap_opt&>(other))),
+      Rep_opt(std::move(static_cast<Rep_opt&>(other))),
+      reducedMatrixR_(std::move(other.reducedMatrixR_)),
+      mirrorMatrixU_(std::move(other.mirrorMatrixU_)),
+      pivotToColumnIndex_(std::move(other.pivotToColumnIndex_)),
+      nextEventIndex_(std::exchange(other.nextEventIndex_, 0)),
+      operators_(std::exchange(other.operators_, nullptr))
+{}
+
+template <class Master_matrix>
+template <class Boundary_range>
+inline void RU_matrix<Master_matrix>::insert_boundary(const Boundary_range& boundary, Dimension dim)
+{
+  _insert_boundary(reducedMatrixR_.insert_boundary(boundary, dim));
+}
+
+template <class Master_matrix>
+template <class Boundary_range>
+inline void RU_matrix<Master_matrix>::insert_boundary(ID_index cellIndex,
+                                                      const Boundary_range& boundary,
+                                                      Dimension dim)
+{
+  // maps for possible shifting between column content and position indices used for birth events
+  if constexpr (Master_matrix::Option_list::has_column_pairings && !Master_matrix::Option_list::has_vine_update) {
+    if (cellIndex != nextEventIndex_) {
+      Pair_opt::idToPosition_.emplace(cellIndex, nextEventIndex_);
+      if constexpr (Master_matrix::Option_list::has_removable_columns) {
+        Pair_opt::PIDM::map_.emplace(nextEventIndex_, cellIndex);
+      }
+    }
+  }
+  if constexpr (Master_matrix::Option_list::has_vine_update) {
+    if (cellIndex != nextEventIndex_) {
+      Swap_opt::_positionToRowIdx().emplace(nextEventIndex_, cellIndex);
+      if constexpr (Master_matrix::Option_list::has_column_pairings) {
+        Swap_opt::template RU_pairing<Master_matrix>::idToPosition_.emplace(cellIndex, nextEventIndex_);
+      }
+    }
+  }
+  _insert_boundary(reducedMatrixR_.insert_boundary(cellIndex, boundary, dim));
+}
+
+template <class Master_matrix>
+inline typename RU_matrix<Master_matrix>::Column& RU_matrix<Master_matrix>::get_column(Index columnIndex, bool inR)
+{
+  if (inR) {
+    return reducedMatrixR_.get_column(columnIndex);
+  }
+  return mirrorMatrixU_.get_column(columnIndex);
+}
+
+template <class Master_matrix>
+inline typename RU_matrix<Master_matrix>::Row& RU_matrix<Master_matrix>::get_row(Index rowIndex, bool inR)
+{
+  static_assert(Master_matrix::Option_list::has_row_access, "'get_row' is not implemented for the chosen options.");
+
+  if (inR) {
+    return reducedMatrixR_.get_row(rowIndex);
+  }
+  return mirrorMatrixU_.get_row(rowIndex);
+}
+
+template <class Master_matrix>
+inline void RU_matrix<Master_matrix>::erase_empty_row(Index rowIndex)
+{
+  reducedMatrixR_.erase_empty_row(rowIndex);
+}
+
+template <class Master_matrix>
+inline void RU_matrix<Master_matrix>::remove_maximal_cell(Index columnIndex)
+{
+  static_assert(Master_matrix::Option_list::has_removable_columns && Master_matrix::Option_list::has_vine_update,
+                "'remove_maximal_cell' is not implemented for the chosen options.");
+
+  // TODO: is there an easy test to verify maximality even without row access?
+
+  for (Index curr = columnIndex; curr < nextEventIndex_ - 1; ++curr) {
+    Swap_opt::vine_swap(curr);
+  }
+
+  remove_last();
+}
+
+template <class Master_matrix>
+inline void RU_matrix<Master_matrix>::remove_last()
+{
+  static_assert(Master_matrix::Option_list::has_removable_columns,
+                "'remove_last' is not implemented for the chosen options.");
+
+  if (nextEventIndex_ == 0) return;  // empty matrix
+  --nextEventIndex_;
+
+  // assumes PosIdx == MatIdx for boundary matrices.
+  _remove_last_in_barcode(nextEventIndex_);
+
+  mirrorMatrixU_.remove_last();
+  if constexpr (Master_matrix::Option_list::has_map_column_container) {
+    pivotToColumnIndex_.erase(reducedMatrixR_.remove_last());
+  } else {
+    ID_index lastPivot = reducedMatrixR_.remove_last();
+    if (lastPivot != static_cast<ID_index>(-1)) pivotToColumnIndex_[lastPivot] = -1;
+  }
+
+  // if has_vine_update and has_column_pairings are both true,
+  // then the element is already removed in _remove_last_in_barcode
+  if constexpr (Master_matrix::Option_list::has_vine_update && !Master_matrix::Option_list::has_column_pairings) {
+    Swap_opt::_positionToRowIdx().erase(nextEventIndex_);
+  }
+}
+
+template <class Master_matrix>
+inline typename RU_matrix<Master_matrix>::Dimension RU_matrix<Master_matrix>::get_max_dimension() const
+{
+  return reducedMatrixR_.get_max_dimension();
+}
+
+template <class Master_matrix>
+inline typename RU_matrix<Master_matrix>::Index RU_matrix<Master_matrix>::get_number_of_columns() const
+{
+  return reducedMatrixR_.get_number_of_columns();
+}
+
+template <class Master_matrix>
+inline typename RU_matrix<Master_matrix>::Dimension RU_matrix<Master_matrix>::get_column_dimension(
+    Index columnIndex) const
+{
+  return reducedMatrixR_.get_column_dimension(columnIndex);
+}
+
+template <class Master_matrix>
+inline void RU_matrix<Master_matrix>::add_to(Index sourceColumnIndex, Index targetColumnIndex)
+{
+  reducedMatrixR_.add_to(sourceColumnIndex, targetColumnIndex);
+  // U transposed to avoid row operations
+  if constexpr (Master_matrix::Option_list::is_z2)
+    mirrorMatrixU_.add_to(targetColumnIndex, sourceColumnIndex);
+  else
+    mirrorMatrixU_.add_to(sourceColumnIndex, targetColumnIndex);
+}
+
+template <class Master_matrix>
+inline void RU_matrix<Master_matrix>::multiply_target_and_add_to(Index sourceColumnIndex,
+                                                                 const Field_element& coefficient,
+                                                                 Index targetColumnIndex)
+{
+  static_assert(!Master_matrix::Option_list::is_z2,
+                "Multiplication with something else than the identity is not allowed with Z2 coefficients.");
+  reducedMatrixR_.multiply_target_and_add_to(sourceColumnIndex, coefficient, targetColumnIndex);
+  mirrorMatrixU_.multiply_target_and_add_to(sourceColumnIndex, coefficient, targetColumnIndex);
+}
+
+template <class Master_matrix>
+inline void RU_matrix<Master_matrix>::multiply_source_and_add_to(const Field_element& coefficient,
+                                                                 Index sourceColumnIndex,
+                                                                 Index targetColumnIndex)
+{
+  static_assert(!Master_matrix::Option_list::is_z2,
+                "Multiplication with something else than the identity is not allowed with Z2 coefficients.");
+  reducedMatrixR_.multiply_source_and_add_to(coefficient, sourceColumnIndex, targetColumnIndex);
+  mirrorMatrixU_.multiply_source_and_add_to(coefficient, sourceColumnIndex, targetColumnIndex);
+}
+
+template <class Master_matrix>
+inline void RU_matrix<Master_matrix>::zero_entry(Index columnIndex, Index rowIndex, bool inR)
+{
+  if (inR) {
+    return reducedMatrixR_.zero_entry(columnIndex, rowIndex);
+  }
+  return mirrorMatrixU_.zero_entry(columnIndex, rowIndex);
+}
+
+template <class Master_matrix>
+inline void RU_matrix<Master_matrix>::zero_column(Index columnIndex, bool inR)
+{
+  if (inR) {
+    return reducedMatrixR_.zero_column(columnIndex);
+  }
+  return mirrorMatrixU_.zero_column(columnIndex);
+}
+
+template <class Master_matrix>
+inline bool RU_matrix<Master_matrix>::is_zero_entry(Index columnIndex, Index rowIndex, bool inR) const
+{
+  if (inR) {
+    return reducedMatrixR_.is_zero_entry(columnIndex, rowIndex);
+  }
+  return mirrorMatrixU_.is_zero_entry(columnIndex, rowIndex);
+}
+
+template <class Master_matrix>
+inline bool RU_matrix<Master_matrix>::is_zero_column(Index columnIndex, bool inR)
+{
+  if (inR) {
+    return reducedMatrixR_.is_zero_column(columnIndex);
+  }
+  return mirrorMatrixU_.is_zero_column(columnIndex);
+}
+
+template <class Master_matrix>
+inline typename RU_matrix<Master_matrix>::Index RU_matrix<Master_matrix>::get_column_with_pivot(Index cellIndex) const
+{
+  if constexpr (Master_matrix::Option_list::has_map_column_container) {
+    return pivotToColumnIndex_.at(cellIndex);
+  } else {
+    return pivotToColumnIndex_[cellIndex];
+  }
+}
+
+template <class Master_matrix>
+inline typename RU_matrix<Master_matrix>::Index RU_matrix<Master_matrix>::get_pivot(Index columnIndex)
+{
+  return reducedMatrixR_.get_column(columnIndex).get_pivot();
+}
+
+template <class Master_matrix>
+inline RU_matrix<Master_matrix>& RU_matrix<Master_matrix>::operator=(const RU_matrix& other)
+{
+  Swap_opt::operator=(other);
+  Pair_opt::operator=(other);
+  Rep_opt::operator=(other);
+  reducedMatrixR_ = other.reducedMatrixR_;
+  mirrorMatrixU_ = other.mirrorMatrixU_;
+  pivotToColumnIndex_ = other.pivotToColumnIndex_;
+  nextEventIndex_ = other.nextEventIndex_;
+  operators_ = other.operators_;
+  return *this;
+}
+
+template <class Master_matrix>
+inline void RU_matrix<Master_matrix>::print(Index startCol, Index endCol, Index startRow, Index endRow)
+{
+  std::cout << "R_matrix:\n";
+  reducedMatrixR_.print(startCol, endCol, startRow, endRow);
+  std::cout << "U_matrix:\n";
+  mirrorMatrixU_.print(startCol, endCol, startCol, endCol);
+}
+
+template <class Master_matrix>
+inline void RU_matrix<Master_matrix>::_insert_boundary(Index currentIndex)
+{
+  if constexpr (Master_matrix::Option_list::is_z2) {
+    mirrorMatrixU_.insert_column({currentIndex});
+  } else {
+    mirrorMatrixU_.insert_column({{currentIndex, 1}});
+  }
+
+  if constexpr (!Master_matrix::Option_list::has_map_column_container) {
+    ID_index pivot = reducedMatrixR_.get_column(currentIndex).get_pivot();
+    if (pivot != static_cast<ID_index>(-1) && pivotToColumnIndex_.size() <= pivot)
+      pivotToColumnIndex_.resize((pivot + 1) * 2, -1);
+  }
+
+  _reduce_last_column(currentIndex);
+  ++nextEventIndex_;
+}
+
+template <class Master_matrix>
+inline void RU_matrix<Master_matrix>::_initialize_U()
+{
+  typename std::conditional<Master_matrix::Option_list::is_z2, Index, std::pair<Index, Field_element> >::type id;
+  if constexpr (!Master_matrix::Option_list::is_z2) id.second = 1;
+
+  for (ID_index i = 0; i < reducedMatrixR_.get_number_of_columns(); i++) {
+    if constexpr (Master_matrix::Option_list::is_z2)
+      id = i;
+    else
+      id.first = i;
+    mirrorMatrixU_.insert_column({id});
+  }
+}
+
+template <class Master_matrix>
+inline void RU_matrix<Master_matrix>::_reduce()
+{
+  if constexpr (Master_matrix::Option_list::has_column_pairings) {
+    _indexToBar().reserve(reducedMatrixR_.get_number_of_columns());
+  }
+
+  for (Index i = 0; i < reducedMatrixR_.get_number_of_columns(); i++) {
+    if (!(reducedMatrixR_.is_zero_column(i))) {
+      _reduce_column(i, i);
+    } else {
+      _add_bar(get_column_dimension(i), i);
+    }
+  }
+}
+
+template <class Master_matrix>
+inline void RU_matrix<Master_matrix>::_reduce_last_column(Index lastIndex)
+{
+  if (reducedMatrixR_.get_column(lastIndex).is_empty()) {
+    _add_bar(get_column_dimension(lastIndex), nextEventIndex_);
+    return;
+  }
+
+  _reduce_column(lastIndex, nextEventIndex_);
+}
+
+template <class Master_matrix>
+inline void RU_matrix<Master_matrix>::_reduce_column(Index target, Index eventIndex)
+{
+  auto get_column_with_pivot_ = [&](ID_index pivot) -> Index {
+    if (pivot == static_cast<ID_index>(-1)) return -1;
+    if constexpr (Master_matrix::Option_list::has_map_column_container) {
+      auto it = pivotToColumnIndex_.find(pivot);
+      if (it == pivotToColumnIndex_.end())
+        return -1;
+      else
+        return it->second;
+    } else {
+      return pivotToColumnIndex_[pivot];
+    }
+  };
+
+  Column& curr = reducedMatrixR_.get_column(target);
+  ID_index pivot = curr.get_pivot();
+  Index currIndex = get_column_with_pivot_(pivot);
+
+  while (pivot != static_cast<ID_index>(-1) && currIndex != static_cast<Index>(-1)) {
+    _reduce_column_by(target, currIndex);
+    pivot = curr.get_pivot();
+    currIndex = get_column_with_pivot_(pivot);
+  }
+
+  if (pivot != static_cast<ID_index>(-1)) {
+    if constexpr (Master_matrix::Option_list::has_map_column_container) {
+      pivotToColumnIndex_.try_emplace(pivot, target);
+    } else {
+      pivotToColumnIndex_[pivot] = target;
+    }
+    _update_barcode(pivot, eventIndex);
+  } else {
+    _add_bar(get_column_dimension(target), eventIndex);
+  }
+}
+
+template <class Master_matrix>
+inline void RU_matrix<Master_matrix>::_reduce_column_by(Index target, Index source)
+{
+  Column& curr = reducedMatrixR_.get_column(target);
+  if constexpr (Master_matrix::Option_list::is_z2) {
+    curr += reducedMatrixR_.get_column(source);
+    // to avoid having to do line operations during vineyards, U is transposed
+    // TODO: explain this somewhere in the documentation...
+    mirrorMatrixU_.get_column(source).push_back(*mirrorMatrixU_.get_column(target).begin());
+  } else {
+    Column& toadd = reducedMatrixR_.get_column(source);
+    Field_element coef = toadd.get_pivot_value();
+    coef = operators_->get_inverse(coef);
+    operators_->multiply_inplace(coef, operators_->get_characteristic() - curr.get_pivot_value());
+
+    curr.multiply_source_and_add(toadd, coef);
+    // but no transposition for Zp, careful if there will be vineyard or rep cycles in Zp one day
+    // TODO: explain this somewhere in the documentation...
+    mirrorMatrixU_.multiply_source_and_add_to(coef, source, target);
+  }
+}
+
+template <class Master_matrix>
+inline void RU_matrix<Master_matrix>::_update_barcode(ID_index birthPivot, Pos_index death)
+{
+  if constexpr (Master_matrix::Option_list::has_column_pairings) {
+    if constexpr (Master_matrix::Option_list::has_vine_update)
+      Swap_opt::template RU_pairing<Master_matrix>::_update_barcode(birthPivot, death);
+    else
+      Pair_opt::_update_barcode(birthPivot, death);
+  }
+}
+
+template <class Master_matrix>
+inline void RU_matrix<Master_matrix>::_add_bar(Dimension dim, Pos_index birth)
+{
+  if constexpr (Master_matrix::Option_list::has_column_pairings) {
+    if constexpr (Master_matrix::Option_list::has_vine_update)
+      Swap_opt::template RU_pairing<Master_matrix>::_add_bar(dim, birth);
+    else
+      Pair_opt::_add_bar(dim, birth);
+  }
+}
+
+template <class Master_matrix>
+inline void RU_matrix<Master_matrix>::_remove_last_in_barcode(Pos_index eventIndex)
+{
+  if constexpr (Master_matrix::Option_list::has_column_pairings) {
+    if constexpr (Master_matrix::Option_list::has_vine_update)
+      Swap_opt::template RU_pairing<Master_matrix>::_remove_last(eventIndex);
+    else
+      Pair_opt::_remove_last(eventIndex);
+  }
+}
+
+template <class Master_matrix>
+inline constexpr typename RU_matrix<Master_matrix>::Bar_dictionary& RU_matrix<Master_matrix>::_indexToBar()
+{
+  if constexpr (Master_matrix::Option_list::has_vine_update)
+    return Swap_opt::template RU_pairing<Master_matrix>::indexToBar_;
+  else
+    return Pair_opt::indexToBar_;
+}
+
+}  // namespace persistence_matrix
+}  // namespace Gudhi
+
+#endif  // PM_RU_MATRIX_H