Merge pull request #26 from hschreiber/ru_vine_opt

borders of representative cycles

multipers/gudhi/gudhi/Matrix.h

@@ -1220,7 +1220,7 @@ class Matrix {
     std::swap(matrix1.colSettings_, matrix2.colSettings_);
   }
 
-  void print();  // for debug
+  void print(Index startCol = 0, Index endCol = -1, Index startRow = 0, Index endRow = -1);  // for debug
 
   //TODO: change the behaviour for boundary matrices.
   /**
@@ -1344,21 +1344,23 @@ class Matrix {
    * returned.
    */
   void update_representative_cycles();
-  /**
-   * @brief Only available if @ref PersistenceMatrixOptions::can_retrieve_representative_cycles is true.
-   * Returns all representative cycles of the current filtration.
-   * 
-   * @return A const reference to the vector of representative cycles.
-   */
-  const std::vector<Cycle>& get_representative_cycles();
-  /**
-   * @brief Only available if @ref PersistenceMatrixOptions::can_retrieve_representative_cycles is true.
-   * Returns the cycle representing the given bar.
-   * 
-   * @param bar A bar from the current barcode.
-   * @return A const reference to the cycle representing @p bar.
-   */
-  const Cycle& get_representative_cycle(const Bar& bar);
+  // /**
+  //  * @brief Only available if @ref PersistenceMatrixOptions::can_retrieve_representative_cycles is true.
+  //  * Returns all representative cycles of the current filtration.
+  //  * 
+  //  * @return A const reference to the vector of representative cycles.
+  //  */
+  // const std::vector<Cycle>& get_representative_cycles();
+  // /**
+  //  * @brief Only available if @ref PersistenceMatrixOptions::can_retrieve_representative_cycles is true.
+  //  * Returns the cycle representing the given bar.
+  //  * 
+  //  * @param bar A bar from the current barcode.
+  //  * @return A const reference to the cycle representing @p bar.
+  //  */
+  // const Cycle& get_representative_cycle(const Bar& bar);
+  std::vector<std::vector<std::vector<typename Matrix<PersistenceMatrixOptions>::ID_index> > >
+  get_representative_cycles_as_borders(bool detailed = false);
 
  private:
   using Underlying_matrix = 
@@ -1931,9 +1933,9 @@ inline Matrix<PersistenceMatrixOptions>& Matrix<PersistenceMatrixOptions>::opera
 }
 
 template <class PersistenceMatrixOptions>
-inline void Matrix<PersistenceMatrixOptions>::print() 
+inline void Matrix<PersistenceMatrixOptions>::print(Index startCol, Index endCol, Index startRow, Index endRow) 
 {
-  return matrix_.print();
+  return matrix_.print(startCol, endCol, startRow, endRow);
 }
 
 template <class PersistenceMatrixOptions>
@@ -2035,20 +2037,28 @@ inline void Matrix<PersistenceMatrixOptions>::update_representative_cycles()
   matrix_.update_representative_cycles();
 }
 
-template <class PersistenceMatrixOptions>
-inline const std::vector<typename Matrix<PersistenceMatrixOptions>::Cycle>&
-Matrix<PersistenceMatrixOptions>::get_representative_cycles()
-{
-  static_assert(PersistenceMatrixOptions::can_retrieve_representative_cycles, "This method was not enabled.");
-  return matrix_.get_representative_cycles();
-}
+// template <class PersistenceMatrixOptions>
+// inline const std::vector<typename Matrix<PersistenceMatrixOptions>::Cycle>&
+// Matrix<PersistenceMatrixOptions>::get_representative_cycles()
+// {
+//   static_assert(PersistenceMatrixOptions::can_retrieve_representative_cycles, "This method was not enabled.");
+//   return matrix_.get_representative_cycles();
+// }
+
+// template <class PersistenceMatrixOptions>
+// inline const typename Matrix<PersistenceMatrixOptions>::Cycle&
+// Matrix<PersistenceMatrixOptions>::get_representative_cycle(const Bar& bar)
+// {
+//   static_assert(PersistenceMatrixOptions::can_retrieve_representative_cycles, "This method was not enabled.");
+//   return matrix_.get_representative_cycle(bar);
+// }
 
 template <class PersistenceMatrixOptions>
-inline const typename Matrix<PersistenceMatrixOptions>::Cycle&
-Matrix<PersistenceMatrixOptions>::get_representative_cycle(const Bar& bar)
-{
-  static_assert(PersistenceMatrixOptions::can_retrieve_representative_cycles, "This method was not enabled.");
-  return matrix_.get_representative_cycle(bar);
+inline std::vector<std::vector<std::vector<typename Matrix<PersistenceMatrixOptions>::ID_index> > >
+Matrix<PersistenceMatrixOptions>::get_representative_cycles_as_borders(bool detailed) {
+  static_assert(PersistenceMatrixOptions::can_retrieve_representative_cycles && PersistenceMatrixOptions::is_z2,
+                "This method was not enabled.");
+  return matrix_.get_representative_cycles_as_borders(detailed);
 }
 
 template <class PersistenceMatrixOptions>

multipers/gudhi/gudhi/Persistence_matrix/Base_matrix.h

@@ -316,7 +316,7 @@ class Base_matrix : public Master_matrix::template Base_swap_option<Base_matrix<
     }
   }
 
-  void print();  // for debug
+  void print(Index startCol = 0, Index endCol = -1, Index startRow = 0, Index endRow = -1);  // for debug
 
  private:
   using Swap_opt = typename Master_matrix::template Base_swap_option<Base_matrix<Master_matrix> >;
@@ -597,27 +597,32 @@ inline Base_matrix<Master_matrix>& Base_matrix<Master_matrix>::operator=(const B
 }
 
 template <class Master_matrix>
-inline void Base_matrix<Master_matrix>::print() 
+inline void Base_matrix<Master_matrix>::print(Index startCol, Index endCol, Index startRow, Index endRow) 
 {
   _orderRowsIfNecessary();
+  if (endCol == static_cast<Index>(-1)) endCol = nextInsertIndex_;
+  if (endRow == static_cast<Index>(-1)) endRow = nextInsertIndex_;
   std::cout << "Base_matrix:\n";
-  for (Index i = 0; i < nextInsertIndex_; ++i) {
+  for (Index i = startCol; i < endCol && i < nextInsertIndex_; ++i) {
     const Column& col = matrix_[i];
-    for (const auto& e : col.get_content(nextInsertIndex_)) {
-      if (e == 0u)
+    auto cont = col.get_content(endRow);
+    for (Index j = startRow; j < endRow; ++j) {
+      if (cont[j] == 0u)
         std::cout << "- ";
       else
-        std::cout << e << " ";
+        std::cout << cont[j] << " ";
     }
     std::cout << "\n";
   }
   std::cout << "\n";
   if constexpr (Master_matrix::Option_list::has_row_access) {
     std::cout << "Row Matrix:\n";
-    for (Index i = 0; i < nextInsertIndex_; ++i) {
+    for (Index i = startRow; i < endRow && i < nextInsertIndex_; ++i) {
       const auto& row = (*RA_opt::rows_)[i];
-      for (const auto& entry : row) {
-        std::cout << entry.get_column_index() << " ";
+      auto it = row.begin();
+      std::advance(it, startCol);
+      for (; it != row.end() && startCol < endCol; ++it, ++startCol) {
+        std::cout << it->get_column_index() << " ";
       }
       std::cout << "(" << i << ")\n";
     }

multipers/gudhi/gudhi/Persistence_matrix/Boundary_matrix.h

@@ -19,6 +19,7 @@
 
 #include <cassert>
 #include <iostream> //print() only
+#include <iterator>
 #include <vector>
 #include <utility>  //std::swap, std::move & std::exchange
 
@@ -349,7 +350,7 @@ class Boundary_matrix : public Master_matrix::Matrix_dimension_option,
     }
   }
 
-  void print();  // for debug
+  void print(Index startCol = 0, Index endCol = -1, Index startRow = 0, Index endRow = -1);  // for debug
 
  private:
   using Dim_opt = typename Master_matrix::Matrix_dimension_option;
@@ -709,29 +710,34 @@ inline Boundary_matrix<Master_matrix>& Boundary_matrix<Master_matrix>::operator=
 }
 
 template <class Master_matrix>
-inline void Boundary_matrix<Master_matrix>::print() 
+inline void Boundary_matrix<Master_matrix>::print(Index startCol, Index endCol, Index startRow, Index endRow) 
 {
+  if (endCol == static_cast<Index>(-1)) endCol = nextInsertIndex_;
+  if (endRow == static_cast<Index>(-1)) endRow = nextInsertIndex_;
   if constexpr (activeSwapOption) {
     if (Swap_opt::rowSwapped_) Swap_opt::_orderRows();
   }
   std::cout << "Boundary_matrix:\n";
-  for (Index i = 0; i < nextInsertIndex_; ++i) {
+  for (Index i = startCol; i < endCol && i < nextInsertIndex_; ++i) {
     Column& col = matrix_[i];
-    for (auto e : col.get_content(nextInsertIndex_)) {
-      if (e == 0u)
+    auto cont = col.get_content(endRow);
+    for (Index j = startRow; j < endRow; ++j) {
+      if (cont[j] == 0u)
         std::cout << "- ";
       else
-        std::cout << e << " ";
+        std::cout << cont[j] << " ";
     }
     std::cout << "\n";
   }
   std::cout << "\n";
   if constexpr (Master_matrix::Option_list::has_row_access) {
     std::cout << "Row Matrix:\n";
-    for (ID_index i = 0; i < nextInsertIndex_; ++i) {
+    for (ID_index i = startRow; i < endRow && i < nextInsertIndex_; ++i) {
       const auto& row = (*RA_opt::rows_)[i];
-      for (const typename Column::Entry& entry : row) {
-        std::cout << entry.get_column_index() << " ";
+      auto it = row.begin();
+      std::advance(it, startCol);
+      for (; it != row.end() && startCol < endCol; ++it, ++startCol) {
+        std::cout << it->get_column_index() << " ";
       }
       std::cout << "(" << i << ")\n";
     }

multipers/gudhi/gudhi/Persistence_matrix/RU_matrix.h

@@ -380,7 +380,7 @@ class RU_matrix : public Master_matrix::RU_pairing_option,
     std::swap(matrix1.operators_, matrix2.operators_);
   }
 
-  void print();  // for debug
+  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;
@@ -538,7 +538,7 @@ inline void RU_matrix<Master_matrix>::insert_boundary(ID_index cellIndex,
   if constexpr (Master_matrix::Option_list::has_vine_update) {
     if (cellIndex != nextEventIndex_) {
       Swap_opt::_positionToRowIdx().emplace(nextEventIndex_, cellIndex);
-      if (Master_matrix::Option_list::has_column_pairings) {
+      if constexpr (Master_matrix::Option_list::has_column_pairings) {
         Swap_opt::template RU_pairing<Master_matrix>::idToPosition_.emplace(cellIndex, nextEventIndex_);
       }
     }
@@ -733,12 +733,12 @@ inline RU_matrix<Master_matrix>& RU_matrix<Master_matrix>::operator=(const RU_ma
 }
 
 template <class Master_matrix>
-inline void RU_matrix<Master_matrix>::print()
+inline void RU_matrix<Master_matrix>::print(Index startCol, Index endCol, Index startRow, Index endRow)
 {
   std::cout << "R_matrix:\n";
-  reducedMatrixR_.print();
+  reducedMatrixR_.print(startCol, endCol, startRow, endRow);
   std::cout << "U_matrix:\n";
-  mirrorMatrixU_.print();
+  mirrorMatrixU_.print(startCol, endCol, startCol, endCol);
 }
 
 template <class Master_matrix>