replacing remaining -1s in the matrix module

src/Persistence_matrix/concept/PersistenceMatrixColumn.h

@@ -242,18 +242,19 @@ class PersistenceMatrixColumn :
 
   /**
    * @brief Reorders the column with the given map of row indices. Also changes the column index stored in the
-   * entries if row access is enabled and @p columnIndex is not -1.
+   * entries if row access is enabled and @p columnIndex is not the @ref Matrix::get_null_value "null index".
    *
    * Only useful for @ref basematrix "base" and @ref boundarymatrix "boundary matrices" using lazy swaps.
    * 
    * @tparam Row_index_map Map with an %at() method.
    * @param valueMap Map such that `valueMap.at(i)` indicates the new row index of the entry
    * at current row index `i`.
-   * @param columnIndex New @ref MatIdx column index of the column. If -1, the index does not change. Ignored if
-   * the row access is not enabled. Default value: -1.
+   * @param columnIndex New @ref MatIdx column index of the column. If @ref Matrix::get_null_value "null index",
+   * the index does not change. Ignored if the row access is not enabled.
+   * Default value: @ref Matrix::get_null_value "null index".
    */
   template <class Row_index_map>
-  void reorder(const Row_index_map& valueMap, [[maybe_unused]] Index columnIndex = -1);
+  void reorder(const Row_index_map& valueMap, [[maybe_unused]] Index columnIndex = Matrix::get_null_value<Index>());
   /**
    * @brief Zeros/empties the column.
    * 
@@ -275,11 +276,12 @@ class PersistenceMatrixColumn :
   void clear(ID_index rowIndex);
 
   /**
-   * @brief Returns the row index of the pivot. If the column does not have a pivot, returns -1.
+   * @brief Returns the row index of the pivot. If the column does not have a pivot,
+   * returns @ref Matrix::get_null_value "null index".
    *
    * Only useful for @ref boundarymatrix "boundary" and @ref chainmatrix "chain matrices".
    * 
-   * @return Row index of the pivot or -1.
+   * @return Row index of the pivot or @ref Matrix::get_null_value "null index".
    */
   ID_index get_pivot();
   /**
@@ -429,7 +431,7 @@ class PersistenceMatrixColumn :
   /**
    * @brief Adds a copy of the given entry at the end of the column. It is therefore assumed that the row index
    * of the entry is higher than the current pivot of the column. Not available for @ref chainmatrix "chain matrices"
-   * and is only needed for @ref rumatrix "RU matrices".
+   * and is only needed for @ref boundarymatrix "RU matrices".
    * 
    * @param entry Entry to push back.
    */

src/Persistence_matrix/include/gudhi/Matrix.h

@@ -164,7 +164,6 @@ class Matrix {
   using Characteristic = typename Field_operators::Characteristic;
 
   /**
-   * @private
    * @brief Returns value from a type when not set.
    */
   template <typename T>
@@ -774,7 +773,7 @@ class Matrix {
    * chains used to reduce the boundary. Otherwise, nothing.
    */
   template <class Boundary_range = Boundary>
-  Insertion_return insert_boundary(const Boundary_range& boundary, Dimension dim = -1);
+  Insertion_return insert_boundary(const Boundary_range& boundary, Dimension dim = Matrix::get_null_value<Dimension>());
   /**
    * @brief Only available for @ref mp_matrices "non-basic matrices".
    * It does the same as the other version, but allows the boundary cells to be identified without restrictions
@@ -796,7 +795,8 @@ class Matrix {
    * chains used to reduce the boundary. Otherwise, nothing.
    */
   template <class Boundary_range = Boundary>
-  Insertion_return insert_boundary(ID_index cellIndex, const Boundary_range& boundary, Dimension dim = -1);
+  Insertion_return insert_boundary(ID_index cellIndex, const Boundary_range& boundary,
+                                   Dimension dim = Matrix::get_null_value<Dimension>());
 
   /**
    * @brief Returns the column at the given @ref MatIdx index.

src/Persistence_matrix/include/gudhi/Persistence_matrix/Base_matrix.h

@@ -133,7 +133,8 @@ class Base_matrix : public Master_matrix::template Base_swap_option<Base_matrix<
    * @param dim Ignored.
    */
   template <class Boundary_range>
-  void insert_boundary(const Boundary_range& boundary, Dimension dim = -1);
+  void insert_boundary(const Boundary_range& boundary,
+                       Dimension dim = Master_matrix::template get_null_value<Dimension>());
   /**
    * @brief Returns the column at the given @ref MatIdx index.
    * The type of the column depends on the choosen options, see @ref PersistenceMatrixOptions::column_type.
@@ -438,7 +439,7 @@ template <class Master_matrix>
 template <class Boundary_range>
 inline void Base_matrix<Master_matrix>::insert_boundary(const Boundary_range& boundary, Dimension dim) 
 {
-  if (dim == -1) dim = boundary.size() == 0 ? 0 : boundary.size() - 1;
+  if (dim == Master_matrix::template get_null_value<Dimension>()) dim = boundary.size() == 0 ? 0 : boundary.size() - 1;
   //TODO: dim not actually stored right now, so either get rid of it or store it again
   _insert(boundary, nextInsertIndex_++, dim);
 }

src/Persistence_matrix/include/gudhi/Persistence_matrix/Base_matrix_with_column_compression.h

@@ -180,7 +180,8 @@ class Base_matrix_with_column_compression : protected Master_matrix::Matrix_row_
    * @param dim Ignored.
    */
   template <class Boundary_range>
-  void insert_boundary(const Boundary_range& boundary, Dimension dim = -1);
+  void insert_boundary(const Boundary_range& boundary,
+                       Dimension dim = Master_matrix::template get_null_value<Dimension>());
   /**
    * @brief Returns the column at the given @ref MatIdx index.
    * The type of the column depends on the choosen options, see @ref PersistenceMatrixOptions::column_type.
@@ -450,7 +451,7 @@ inline void Base_matrix_with_column_compression<Master_matrix>::insert_boundary(
   // handles a dimension which is not actually stored.
   // TODO: verify if this is not a problem for the cohomology algorithm and if yes,
   // change how Column_dimension_option is choosen.
-  if (dim == -1) dim = boundary.size() == 0 ? 0 : boundary.size() - 1;
+  if (dim == Master_matrix::template get_null_value<Dimension>()) dim = boundary.size() == 0 ? 0 : boundary.size() - 1;
 
   if constexpr (Master_matrix::Option_list::has_row_access && !Master_matrix::Option_list::has_removable_rows) {
     if (boundary.begin() != boundary.end()) {

src/Persistence_matrix/include/gudhi/Persistence_matrix/Boundary_matrix.h

@@ -141,7 +141,8 @@ class Boundary_matrix : public Master_matrix::Matrix_dimension_option,
    * @return The @ref MatIdx index of the inserted boundary.
    */
   template <class Boundary_range = Boundary>
-  Index insert_boundary(const Boundary_range& boundary, Dimension dim = -1);
+  Index insert_boundary(const Boundary_range& boundary,
+                        Dimension dim = Master_matrix::template get_null_value<Dimension>());
   /**
    * @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
@@ -161,7 +162,8 @@ class Boundary_matrix : public Master_matrix::Matrix_dimension_option,
    * @return The @ref MatIdx index of the inserted boundary.
    */
   template <class Boundary_range = Boundary>
-  Index insert_boundary(ID_index cellIndex, const Boundary_range& boundary, Dimension dim = -1);
+  Index insert_boundary(ID_index cellIndex, const Boundary_range& boundary,
+                        Dimension dim = Master_matrix::template get_null_value<Dimension>());
   /**
    * @brief Returns the column at the given @ref MatIdx index.
    * The type of the column depends on the choosen options, see @ref PersistenceMatrixOptions::column_type.
@@ -384,7 +386,7 @@ class Boundary_matrix : public Master_matrix::Matrix_dimension_option,
 
 template <class Master_matrix>
 inline Boundary_matrix<Master_matrix>::Boundary_matrix(Column_settings* colSettings)
-    : Dim_opt(-1),
+    : Dim_opt(Master_matrix::template get_null_value<Dimension>()),
       Swap_opt(),
       Pair_opt(),
       RA_opt(),
@@ -396,7 +398,7 @@ template <class Master_matrix>
 template <class Boundary_range>
 inline Boundary_matrix<Master_matrix>::Boundary_matrix(const std::vector<Boundary_range>& orderedBoundaries,
                                                        Column_settings* colSettings)
-    : Dim_opt(-1),
+    : Dim_opt(Master_matrix::template get_null_value<Dimension>()),
       Swap_opt(orderedBoundaries.size()),
       Pair_opt(),
       RA_opt(orderedBoundaries.size()),
@@ -413,7 +415,7 @@ inline Boundary_matrix<Master_matrix>::Boundary_matrix(const std::vector<Boundar
 template <class Master_matrix>
 inline Boundary_matrix<Master_matrix>::Boundary_matrix(unsigned int numberOfColumns, 
                                                        Column_settings* colSettings)
-    : Dim_opt(-1),
+    : Dim_opt(Master_matrix::template get_null_value<Dimension>()),
       Swap_opt(numberOfColumns),
       Pair_opt(),
       RA_opt(numberOfColumns),
@@ -471,7 +473,7 @@ template <class Boundary_range>
 inline typename Boundary_matrix<Master_matrix>::Index Boundary_matrix<Master_matrix>::insert_boundary(
     ID_index cellIndex, const Boundary_range& boundary, Dimension dim) 
 {
-  if (dim == -1) dim = boundary.size() == 0 ? 0 : boundary.size() - 1;
+  if (dim == Master_matrix::template get_null_value<Dimension>()) dim = boundary.size() == 0 ? 0 : boundary.size() - 1;
 
   _orderRowsIfNecessary();
 
@@ -543,7 +545,7 @@ inline typename Boundary_matrix<Master_matrix>::Index Boundary_matrix<Master_mat
   static_assert(Master_matrix::Option_list::has_removable_columns,
                 "'remove_last' is not implemented for the chosen options.");
 
-  if (nextInsertIndex_ == 0) return -1;  // empty matrix
+  if (nextInsertIndex_ == 0) return Master_matrix::template get_null_value<Index>();  // empty matrix
   --nextInsertIndex_;
 
   //updates dimension max

src/Persistence_matrix/include/gudhi/Persistence_matrix/Chain_matrix.h

@@ -247,7 +247,8 @@ class Chain_matrix : public Master_matrix::Matrix_dimension_option,
    * @return The @ref MatIdx indices of the unpaired chains used to reduce the boundary.
    */
   template <class Boundary_range = Boundary>
-  std::vector<Entry_representative> insert_boundary(const Boundary_range& boundary, Dimension dim = -1);
+  std::vector<Entry_representative> insert_boundary(
+      const Boundary_range& boundary, Dimension dim = Master_matrix::template get_null_value<Dimension>());
   /**
    * @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
@@ -267,9 +268,10 @@ class Chain_matrix : public Master_matrix::Matrix_dimension_option,
    * @return The @ref MatIdx index of the inserted boundary.
    */
   template <class Boundary_range = Boundary>
-  std::vector<Entry_representative> insert_boundary(ID_index cellID,
-                                                    const Boundary_range& boundary,
-                                                    Dimension dim = -1);
+  std::vector<Entry_representative> insert_boundary(
+      ID_index cellID,
+      const Boundary_range& boundary,
+      Dimension dim = Master_matrix::template get_null_value<Dimension>());
   /**
    * @brief Returns the column at the given @ref MatIdx index.
    * The type of the column depends on the choosen options, see @ref PersistenceMatrixOptions::column_type.
@@ -523,7 +525,7 @@ class Chain_matrix : public Master_matrix::Matrix_dimension_option,
 
 template <class Master_matrix>
 inline Chain_matrix<Master_matrix>::Chain_matrix(Column_settings* colSettings)
-    : Dim_opt(-1),
+    : Dim_opt(Master_matrix::template get_null_value<Dimension>()),
       Pair_opt(),
       Swap_opt(),
       Rep_opt(),
@@ -536,7 +538,7 @@ template <class Master_matrix>
 template <class Boundary_range>
 inline Chain_matrix<Master_matrix>::Chain_matrix(const std::vector<Boundary_range>& orderedBoundaries,
                                                  Column_settings* colSettings)
-    : Dim_opt(-1),
+    : Dim_opt(Master_matrix::template get_null_value<Dimension>()),
       Pair_opt(),
       Swap_opt(),
       Rep_opt(),
@@ -548,7 +550,7 @@ inline Chain_matrix<Master_matrix>::Chain_matrix(const std::vector<Boundary_rang
   if constexpr (Master_matrix::Option_list::has_map_column_container) {
     pivotToColumnIndex_.reserve(orderedBoundaries.size());
   } else {
-    pivotToColumnIndex_.resize(orderedBoundaries.size(), -1);
+    pivotToColumnIndex_.resize(orderedBoundaries.size(), Master_matrix::template get_null_value<Index>());
   }
 
   for (const Boundary_range& b : orderedBoundaries) {
@@ -559,7 +561,7 @@ inline Chain_matrix<Master_matrix>::Chain_matrix(const std::vector<Boundary_rang
 template <class Master_matrix>
 inline Chain_matrix<Master_matrix>::Chain_matrix(unsigned int numberOfColumns, 
                                                  Column_settings* colSettings)
-    : Dim_opt(-1),
+    : Dim_opt(Master_matrix::template get_null_value<Dimension>()),
       Pair_opt(),
       Swap_opt(),
       Rep_opt(),
@@ -571,7 +573,7 @@ inline Chain_matrix<Master_matrix>::Chain_matrix(unsigned int numberOfColumns,
   if constexpr (Master_matrix::Option_list::has_map_column_container) {
     pivotToColumnIndex_.reserve(numberOfColumns);
   } else {
-    pivotToColumnIndex_.resize(numberOfColumns, -1);
+    pivotToColumnIndex_.resize(numberOfColumns, Master_matrix::template get_null_value<Index>());
   }
 }
 
@@ -580,7 +582,7 @@ template <typename BirthComparatorFunction, typename DeathComparatorFunction>
 inline Chain_matrix<Master_matrix>::Chain_matrix(Column_settings* colSettings,
                                                  const BirthComparatorFunction& birthComparator,
                                                  const DeathComparatorFunction& deathComparator)
-    : Dim_opt(-1),
+    : Dim_opt(Master_matrix::template get_null_value<Dimension>()),
       Pair_opt(),
       Swap_opt(birthComparator, deathComparator),
       Rep_opt(),
@@ -595,7 +597,7 @@ inline Chain_matrix<Master_matrix>::Chain_matrix(const std::vector<Boundary_rang
                                                  Column_settings* colSettings,
                                                  const BirthComparatorFunction& birthComparator,
                                                  const DeathComparatorFunction& deathComparator)
-    : Dim_opt(-1),
+    : Dim_opt(Master_matrix::template get_null_value<Dimension>()),
       Pair_opt(),
       Swap_opt(birthComparator, deathComparator),
       Rep_opt(),
@@ -607,7 +609,7 @@ inline Chain_matrix<Master_matrix>::Chain_matrix(const std::vector<Boundary_rang
   if constexpr (Master_matrix::Option_list::has_map_column_container) {
     pivotToColumnIndex_.reserve(orderedBoundaries.size());
   } else {
-    pivotToColumnIndex_.resize(orderedBoundaries.size(), -1);
+    pivotToColumnIndex_.resize(orderedBoundaries.size(), Master_matrix::template get_null_value<Index>());
   }
   for (const Boundary_range& b : orderedBoundaries) {
     insert_boundary(b);
@@ -620,7 +622,7 @@ inline Chain_matrix<Master_matrix>::Chain_matrix(unsigned int numberOfColumns,
                                                  Column_settings* colSettings,
                                                  const BirthComparatorFunction& birthComparator,
                                                  const DeathComparatorFunction& deathComparator)
-    : Dim_opt(-1),
+    : Dim_opt(Master_matrix::template get_null_value<Dimension>()),
       Pair_opt(),
       Swap_opt(birthComparator, deathComparator),
       Rep_opt(),
@@ -632,7 +634,7 @@ inline Chain_matrix<Master_matrix>::Chain_matrix(unsigned int numberOfColumns,
   if constexpr (Master_matrix::Option_list::has_map_column_container) {
     pivotToColumnIndex_.reserve(numberOfColumns);
   } else {
-    pivotToColumnIndex_.resize(numberOfColumns, -1);
+    pivotToColumnIndex_.resize(numberOfColumns, Master_matrix::template get_null_value<Index>());
   }
 }
 
@@ -685,7 +687,7 @@ inline std::vector<typename Master_matrix::Entry_representative> Chain_matrix<Ma
 {
   if constexpr (!Master_matrix::Option_list::has_map_column_container) {
     if (pivotToColumnIndex_.size() <= cellID) {
-      pivotToColumnIndex_.resize(cellID * 2 + 1, -1);
+      pivotToColumnIndex_.resize(cellID * 2 + 1, Master_matrix::template get_null_value<Index>());
     }
   }
 
@@ -694,7 +696,8 @@ inline std::vector<typename Master_matrix::Entry_representative> Chain_matrix<Ma
       Swap_opt::CP::pivotToPosition_.try_emplace(cellID, _nextPosition());
     } else {
       if (Swap_opt::CP::pivotToPosition_.size() <= cellID)
-        Swap_opt::CP::pivotToPosition_.resize(pivotToColumnIndex_.size(), -1);
+        Swap_opt::CP::pivotToPosition_.resize(pivotToColumnIndex_.size(),
+                                              Master_matrix::template get_null_value<Pos_index>());
       Swap_opt::CP::pivotToPosition_[cellID] = _nextPosition();
     }
   }
@@ -1215,7 +1218,7 @@ inline void Chain_matrix<Master_matrix>::_remove_last(Index lastIndex)
     }
 
     if (colToErase.is_paired()) matrix_.at(colToErase.get_paired_chain_index()).unassign_paired_chain();
-    pivotToColumnIndex_[pivot] = -1;
+    pivotToColumnIndex_[pivot] = Master_matrix::template get_null_value<Index>();
     matrix_.pop_back();
     // TODO: resize matrix_ when a lot is removed? Could be not the best strategy if user inserts a lot back afterwards.
   }
@@ -1231,7 +1234,7 @@ inline void Chain_matrix<Master_matrix>::_remove_last(Index lastIndex)
     if (bar->death == Master_matrix::template get_null_value<Pos_index>())
       _barcode().erase(bar);
     else
-      bar->death = -1;
+      bar->death = Master_matrix::template get_null_value<Pos_index>();
 
     _indexToBar().erase(it);
     if constexpr (Master_matrix::Option_list::has_vine_update) Swap_opt::CP::pivotToPosition_.erase(pivot);
@@ -1268,7 +1271,7 @@ template <class Master_matrix>
 inline void Chain_matrix<Master_matrix>::_add_bar(Dimension dim)
 {
   if constexpr (Master_matrix::Option_list::has_column_pairings) {
-    _barcode().emplace_back(_nextPosition(), -1, dim);
+    _barcode().emplace_back(_nextPosition(), Master_matrix::template get_null_value<Pos_index>(), dim);
     if constexpr (Master_matrix::Option_list::has_removable_columns) {
       _indexToBar().try_emplace(_nextPosition(), --_barcode().end());
     } else {