multipers 2.2.3__cp310-cp310-win_amd64.whl → 2.3.0__cp310-cp310-win_amd64.whl

multipers/gudhi/gudhi/Persistence_matrix/base_pairing.h

@@ -1,230 +1,230 @@
-/*    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 base_pairing.h
- * @author Hannah Schreiber
- * @brief Contains the @ref Gudhi::persistence_matrix::Base_pairing class and
- * @ref Gudhi::persistence_matrix::Dummy_base_pairing structure.
- */
-
-#ifndef PM_BASE_PAIRING_H
-#define PM_BASE_PAIRING_H
-
-#include <utility>  //std::swap & std::move
-#include <unordered_map>
-#include <algorithm>
-#include <vector>
-
-#include "boundary_cell_position_to_id_mapper.h"
-
-namespace Gudhi {
-namespace persistence_matrix {
-
-/**
- * @ingroup persistence_matrix
- *
- * @brief Empty structure.
- * Inherited instead of @ref Base_pairing, when the computation of the barcode was not enabled or if the pairing
- * is already managed by the vine update classes.
- */
-struct Dummy_base_pairing {
-  friend void swap([[maybe_unused]] Dummy_base_pairing& d1, [[maybe_unused]] Dummy_base_pairing& d2) {}
-};
-
-/**
- * @class Base_pairing base_pairing.h gudhi/Persistence_matrix/base_pairing.h
- * @ingroup persistence_matrix
- *
- * @brief Class managing the barcode for @ref Boundary_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 Base_pairing : public std::conditional<
-                       Master_matrix::Option_list::has_removable_columns,
-                       Cell_position_to_ID_mapper<typename Master_matrix::ID_index, typename Master_matrix::Pos_index>,
-                       Dummy_pos_mapper
-                    >::type
-{
- public:
-  using Bar = typename Master_matrix::Bar;                            /**< Bar type. */
-  using Barcode = typename Master_matrix::Barcode;                    /**< Barcode type. */
-  using Column_container = typename Master_matrix::Column_container;  /**< Column container type. */
-  using Index = typename Master_matrix::Index;                        /**< Container index type. */
-  using Dimension = typename Master_matrix::Dimension;                /**< Dimension value type. */
-
-  /**
-   * @brief Default constructor.
-   */
-  Base_pairing();
-
-  /**
-   * @brief Reduces the matrix stored in @ref Boundary_matrix and computes the corresponding barcode.
-   *
-   * @warning The barcode will not be recomputed if the matrix is modified later after calling this method
-   * for the first time. So call it only once the matrix is finalized. This behaviour could be changed in the future,
-   * if the need is mentioned.
-   * 
-   * @return Const reference to the barcode.
-   */
-  const Barcode& get_current_barcode();
-
-  /**
-   * @brief Swap operator.
-   */
-  friend void swap(Base_pairing& pairing1, Base_pairing& pairing2) {
-    if constexpr (Master_matrix::Option_list::has_removable_columns) {
-      swap(static_cast<Cell_position_to_ID_mapper<ID_index, Pos_index>&>(pairing1),
-           static_cast<Cell_position_to_ID_mapper<ID_index, Pos_index>&>(pairing2));
-    }
-    pairing1.barcode_.swap(pairing2.barcode_);
-    pairing1.deathToBar_.swap(pairing2.deathToBar_);
-    pairing1.idToPosition_.swap(pairing2.idToPosition_);
-    std::swap(pairing1.isReduced_, pairing2.isReduced_);
-  }
-
- protected:
-  using Pos_index = typename Master_matrix::Pos_index;
-  using ID_index = typename Master_matrix::ID_index;
-  using Dictionary = typename Master_matrix::Bar_dictionary;
-  using Base_matrix = typename Master_matrix::Master_boundary_matrix;
-  //PIDM = Position to ID Map
-  using PIDM = typename std::conditional<Master_matrix::Option_list::has_removable_columns,
-                                         Cell_position_to_ID_mapper<ID_index, Pos_index>,
-                                         Dummy_pos_mapper
-                                        >::type;
-
-  Barcode barcode_;       /**< Bar container. */
-  Dictionary deathToBar_; /**< Map from death 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
-  bool isReduced_;        /**< True if `_reduce()` was called. */
-
-  void _reduce();
-  void _remove_last(Pos_index columnIndex);
-
-  //access to inheriting Boundary_matrix class
-  constexpr Base_matrix* _matrix() { return static_cast<Base_matrix*>(this); }
-  constexpr const Base_matrix* _matrix() const { return static_cast<const Base_matrix*>(this); }
-};
-
-template <class Master_matrix>
-inline Base_pairing<Master_matrix>::Base_pairing() : PIDM(), isReduced_(false) 
-{}
-
-template <class Master_matrix>
-inline const typename Base_pairing<Master_matrix>::Barcode& Base_pairing<Master_matrix>::get_current_barcode() 
-{
-  if (!isReduced_) _reduce();
-  return barcode_;
-}
-
-template <class Master_matrix>
-inline void Base_pairing<Master_matrix>::_reduce() 
-{
-  std::unordered_map<Index, Index> negativeColumns(_matrix()->get_number_of_columns());
-
-  auto dim = _matrix()->get_max_dimension();
-  std::vector<std::vector<Index> > columnsByDim(dim + 1);
-  for (unsigned int i = 0; i < _matrix()->get_number_of_columns(); i++) {
-    columnsByDim[dim - _matrix()->get_column_dimension(i)].push_back(i);
-  }
-
-  for (const auto& cols : columnsByDim) {
-    for (Index i : cols) {
-      auto& curr = _matrix()->get_column(i);
-      if (curr.is_empty()) {
-        if (negativeColumns.find(i) == negativeColumns.end()) {
-          barcode_.emplace_back(i, -1, dim);
-        }
-      } else {
-        ID_index pivot = curr.get_pivot();
-        auto it = idToPosition_.find(pivot);
-        Index pivotColumnNumber = it == idToPosition_.end() ? pivot : it->second;
-        auto itNeg = negativeColumns.find(pivotColumnNumber);
-        Index pivotKiller = itNeg == negativeColumns.end() ? -1 : itNeg->second;
-
-        while (pivot != static_cast<ID_index>(-1) && pivotKiller != static_cast<Index>(-1)) {
-          if constexpr (Master_matrix::Option_list::is_z2) {
-            curr += _matrix()->get_column(pivotKiller);
-          } else {
-            auto& toadd = _matrix()->get_column(pivotKiller);
-            typename Master_matrix::Element coef = toadd.get_pivot_value();
-            auto& operators = _matrix()->colSettings_->operators;
-            coef = operators.get_inverse(coef);
-            operators.multiply_inplace(coef, operators.get_characteristic() - curr.get_pivot_value());
-            curr.multiply_source_and_add(toadd, coef);
-          }
-
-          pivot = curr.get_pivot();
-          it = idToPosition_.find(pivot);
-          pivotColumnNumber = it == idToPosition_.end() ? pivot : it->second;
-          itNeg = negativeColumns.find(pivotColumnNumber);
-          pivotKiller = itNeg == negativeColumns.end() ? -1 : itNeg->second;
-        }
-
-        if (pivot != static_cast<ID_index>(-1)) {
-          negativeColumns.emplace(pivotColumnNumber, i);
-          _matrix()->get_column(pivotColumnNumber).clear();
-          barcode_.emplace_back(pivotColumnNumber, i, dim - 1);
-        } else {
-          curr.clear();
-          barcode_.emplace_back(i, -1, dim);
-        }
-      }
-    }
-    --dim;
-  }
-
-  if constexpr (Master_matrix::Option_list::has_removable_columns) {
-    // sort barcode by birth such that a removal is trivial
-    std::sort(barcode_.begin(), barcode_.end(), [](const Bar& b1, const Bar& b2) { return b1.birth < b2.birth; });
-    // map can only be constructed once barcode is sorted
-    for (Index i = 0; i < barcode_.size(); ++i) {
-      auto d = barcode_[i].death;
-      if (d != static_cast<Pos_index>(-1)) {
-        deathToBar_.emplace(d, i);
-      }
-    }
-  }
-
-  isReduced_ = true;
-}
-
-template <class Master_matrix>
-inline void Base_pairing<Master_matrix>::_remove_last(Pos_index columnIndex) 
-{
-  static_assert(Master_matrix::Option_list::has_removable_columns, "remove_last not available.");
-
-  if (isReduced_) {
-    auto it = deathToBar_.find(columnIndex);
-
-    if (it == deathToBar_.end()) {  // birth
-      barcode_.pop_back();          // sorted by birth and columnIndex has to be the highest one
-    } else {                        // death
-      barcode_[it->second].death = -1;
-      deathToBar_.erase(it);
-    };
-  }
-
-  auto it = PIDM::map_.find(columnIndex);
-  if (it != PIDM::map_.end()){
-    idToPosition_.erase(it->second);
-    PIDM::map_.erase(it);
-  }
-}
-
-}  // namespace persistence_matrix
-}  // namespace Gudhi
-
-#endif  // PM_BASE_PAIRING_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) 2022-24 Inria
+ *
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
+ */
+
+/**
+ * @file base_pairing.h
+ * @author Hannah Schreiber
+ * @brief Contains the @ref Gudhi::persistence_matrix::Base_pairing class and
+ * @ref Gudhi::persistence_matrix::Dummy_base_pairing structure.
+ */
+
+#ifndef PM_BASE_PAIRING_H
+#define PM_BASE_PAIRING_H
+
+#include <utility>  //std::swap & std::move
+#include <unordered_map>
+#include <algorithm>
+#include <vector>
+
+#include "boundary_cell_position_to_id_mapper.h"
+
+namespace Gudhi {
+namespace persistence_matrix {
+
+/**
+ * @ingroup persistence_matrix
+ *
+ * @brief Empty structure.
+ * Inherited instead of @ref Base_pairing, when the computation of the barcode was not enabled or if the pairing
+ * is already managed by the vine update classes.
+ */
+struct Dummy_base_pairing {
+  friend void swap([[maybe_unused]] Dummy_base_pairing& d1, [[maybe_unused]] Dummy_base_pairing& d2) {}
+};
+
+/**
+ * @class Base_pairing base_pairing.h gudhi/Persistence_matrix/base_pairing.h
+ * @ingroup persistence_matrix
+ *
+ * @brief Class managing the barcode for @ref Boundary_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 Base_pairing : public std::conditional<
+                       Master_matrix::Option_list::has_removable_columns,
+                       Cell_position_to_ID_mapper<typename Master_matrix::ID_index, typename Master_matrix::Pos_index>,
+                       Dummy_pos_mapper
+                    >::type
+{
+ public:
+  using Bar = typename Master_matrix::Bar;                            /**< Bar type. */
+  using Barcode = typename Master_matrix::Barcode;                    /**< Barcode type. */
+  using Column_container = typename Master_matrix::Column_container;  /**< Column container type. */
+  using Index = typename Master_matrix::Index;                        /**< Container index type. */
+  using Dimension = typename Master_matrix::Dimension;                /**< Dimension value type. */
+
+  /**
+   * @brief Default constructor.
+   */
+  Base_pairing();
+
+  /**
+   * @brief Reduces the matrix stored in @ref Boundary_matrix and computes the corresponding barcode.
+   *
+   * @warning The barcode will not be recomputed if the matrix is modified later after calling this method
+   * for the first time. So call it only once the matrix is finalized. This behaviour could be changed in the future,
+   * if the need is mentioned.
+   * 
+   * @return Const reference to the barcode.
+   */
+  const Barcode& get_current_barcode();
+
+  /**
+   * @brief Swap operator.
+   */
+  friend void swap(Base_pairing& pairing1, Base_pairing& pairing2) {
+    if constexpr (Master_matrix::Option_list::has_removable_columns) {
+      swap(static_cast<Cell_position_to_ID_mapper<ID_index, Pos_index>&>(pairing1),
+           static_cast<Cell_position_to_ID_mapper<ID_index, Pos_index>&>(pairing2));
+    }
+    pairing1.barcode_.swap(pairing2.barcode_);
+    pairing1.deathToBar_.swap(pairing2.deathToBar_);
+    pairing1.idToPosition_.swap(pairing2.idToPosition_);
+    std::swap(pairing1.isReduced_, pairing2.isReduced_);
+  }
+
+ protected:
+  using Pos_index = typename Master_matrix::Pos_index;
+  using ID_index = typename Master_matrix::ID_index;
+  using Dictionary = typename Master_matrix::Bar_dictionary;
+  using Base_matrix = typename Master_matrix::Master_boundary_matrix;
+  //PIDM = Position to ID Map
+  using PIDM = typename std::conditional<Master_matrix::Option_list::has_removable_columns,
+                                         Cell_position_to_ID_mapper<ID_index, Pos_index>,
+                                         Dummy_pos_mapper
+                                        >::type;
+
+  Barcode barcode_;       /**< Bar container. */
+  Dictionary deathToBar_; /**< Map from death 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
+  bool isReduced_;        /**< True if `_reduce()` was called. */
+
+  void _reduce();
+  void _remove_last(Pos_index columnIndex);
+
+  //access to inheriting Boundary_matrix class
+  constexpr Base_matrix* _matrix() { return static_cast<Base_matrix*>(this); }
+  constexpr const Base_matrix* _matrix() const { return static_cast<const Base_matrix*>(this); }
+};
+
+template <class Master_matrix>
+inline Base_pairing<Master_matrix>::Base_pairing() : PIDM(), isReduced_(false) 
+{}
+
+template <class Master_matrix>
+inline const typename Base_pairing<Master_matrix>::Barcode& Base_pairing<Master_matrix>::get_current_barcode() 
+{
+  if (!isReduced_) _reduce();
+  return barcode_;
+}
+
+template <class Master_matrix>
+inline void Base_pairing<Master_matrix>::_reduce() 
+{
+  std::unordered_map<Index, Index> negativeColumns(_matrix()->get_number_of_columns());
+
+  auto dim = _matrix()->get_max_dimension();
+  std::vector<std::vector<Index> > columnsByDim(dim + 1);
+  for (unsigned int i = 0; i < _matrix()->get_number_of_columns(); i++) {
+    columnsByDim[dim - _matrix()->get_column_dimension(i)].push_back(i);
+  }
+
+  for (const auto& cols : columnsByDim) {
+    for (Index i : cols) {
+      auto& curr = _matrix()->get_column(i);
+      if (curr.is_empty()) {
+        if (negativeColumns.find(i) == negativeColumns.end()) {
+          barcode_.emplace_back(i, -1, dim);
+        }
+      } else {
+        ID_index pivot = curr.get_pivot();
+        auto it = idToPosition_.find(pivot);
+        Index pivotColumnNumber = it == idToPosition_.end() ? pivot : it->second;
+        auto itNeg = negativeColumns.find(pivotColumnNumber);
+        Index pivotKiller = itNeg == negativeColumns.end() ? -1 : itNeg->second;
+
+        while (pivot != static_cast<ID_index>(-1) && pivotKiller != static_cast<Index>(-1)) {
+          if constexpr (Master_matrix::Option_list::is_z2) {
+            curr += _matrix()->get_column(pivotKiller);
+          } else {
+            auto& toadd = _matrix()->get_column(pivotKiller);
+            typename Master_matrix::Element coef = toadd.get_pivot_value();
+            auto& operators = _matrix()->colSettings_->operators;
+            coef = operators.get_inverse(coef);
+            operators.multiply_inplace(coef, operators.get_characteristic() - curr.get_pivot_value());
+            curr.multiply_source_and_add(toadd, coef);
+          }
+
+          pivot = curr.get_pivot();
+          it = idToPosition_.find(pivot);
+          pivotColumnNumber = it == idToPosition_.end() ? pivot : it->second;
+          itNeg = negativeColumns.find(pivotColumnNumber);
+          pivotKiller = itNeg == negativeColumns.end() ? -1 : itNeg->second;
+        }
+
+        if (pivot != static_cast<ID_index>(-1)) {
+          negativeColumns.emplace(pivotColumnNumber, i);
+          _matrix()->get_column(pivotColumnNumber).clear();
+          barcode_.emplace_back(pivotColumnNumber, i, dim - 1);
+        } else {
+          curr.clear();
+          barcode_.emplace_back(i, -1, dim);
+        }
+      }
+    }
+    --dim;
+  }
+
+  if constexpr (Master_matrix::Option_list::has_removable_columns) {
+    // sort barcode by birth such that a removal is trivial
+    std::sort(barcode_.begin(), barcode_.end(), [](const Bar& b1, const Bar& b2) { return b1.birth < b2.birth; });
+    // map can only be constructed once barcode is sorted
+    for (Index i = 0; i < barcode_.size(); ++i) {
+      auto d = barcode_[i].death;
+      if (d != static_cast<Pos_index>(-1)) {
+        deathToBar_.emplace(d, i);
+      }
+    }
+  }
+
+  isReduced_ = true;
+}
+
+template <class Master_matrix>
+inline void Base_pairing<Master_matrix>::_remove_last(Pos_index columnIndex) 
+{
+  static_assert(Master_matrix::Option_list::has_removable_columns, "remove_last not available.");
+
+  if (isReduced_) {
+    auto it = deathToBar_.find(columnIndex);
+
+    if (it == deathToBar_.end()) {  // birth
+      barcode_.pop_back();          // sorted by birth and columnIndex has to be the highest one
+    } else {                        // death
+      barcode_[it->second].death = -1;
+      deathToBar_.erase(it);
+    };
+  }
+
+  auto it = PIDM::map_.find(columnIndex);
+  if (it != PIDM::map_.end()){
+    idToPosition_.erase(it->second);
+    PIDM::map_.erase(it);
+  }
+}
+
+}  // namespace persistence_matrix
+}  // namespace Gudhi
+
+#endif  // PM_BASE_PAIRING_H