factorize unordered_set and vector columns

src/Persistence_matrix/include/gudhi/Persistence_matrix/chain_matrix.h

@@ -86,7 +86,7 @@ class Chain_matrix
 	bool is_zero_column(index columnIndex) const;	//just for sanity checks as a valid chain matrix never has an empty column.
 
 	index get_column_with_pivot(index simplexIndex) const;
-	index get_pivot(index columnIndex) const;
+	index get_pivot(index columnIndex);
 
 	Chain_matrix& operator=(const Chain_matrix& other);
 	friend void swap(Chain_matrix& matrix1,
@@ -559,7 +559,7 @@ inline typename Chain_matrix<Master_matrix>::index Chain_matrix<Master_matrix>::
 }
 
 template<class Master_matrix>
-inline typename Chain_matrix<Master_matrix>::index Chain_matrix<Master_matrix>::get_pivot(index columnIndex) const
+inline typename Chain_matrix<Master_matrix>::index Chain_matrix<Master_matrix>::get_pivot(index columnIndex)
 {
 	if constexpr (Master_matrix::Option_list::has_removable_columns){
 		return matrix_.at(columnIndex).get_pivot();

src/Persistence_matrix/include/gudhi/Persistence_matrix/chain_vine_swap.h

@@ -222,7 +222,7 @@ class Chain_vine_swap : public std::conditional<
 	BirthCompFuncPointer birthComp_;	// for F x F & H x H
 	DeathCompFuncPointer deathComp_;	// for G x G
 
-	bool _is_negative_in_pair(index columnIndex) const;
+	bool _is_negative_in_pair(index columnIndex);
 
 	index _positive_vine_swap(index columnIndex1, index columnIndex2);
 	index _positive_negative_vine_swap(index columnIndex1, index columnIndex2);
@@ -363,7 +363,7 @@ inline Chain_vine_swap<Master_matrix> &Chain_vine_swap<Master_matrix>::operator=
 }
 
 template<class Master_matrix>
-inline bool Chain_vine_swap<Master_matrix>::_is_negative_in_pair(index columnIndex) const
+inline bool Chain_vine_swap<Master_matrix>::_is_negative_in_pair(index columnIndex)
 {
 	if constexpr (Master_matrix::Option_list::has_column_pairings){
 		return CP::is_negative_in_pair(_matrix()->get_pivot(columnIndex));

src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/intrusive_list_column.h

@@ -65,6 +65,7 @@ class Intrusive_list_column : public Master_matrix::Row_access_option,
 	std::vector<Field_element_type> get_content(int columnLength = -1) const;
 	bool is_non_zero(index rowIndex) const;
 	bool is_empty() const;
+	std::size_t size() const;
 
 	//****************
 	//only for base and boundary
@@ -377,6 +378,9 @@ Intrusive_list_column<Master_matrix>::get_content(int columnLength) const
 template<class Master_matrix>
 inline bool Intrusive_list_column<Master_matrix>::is_non_zero(index rowIndex) const
 {
+	//could be changed to dichotomic search as column is ordered by row index, 
+	//but I am not sure if it is really worth it as there is no random access
+	//and the columns should not be that long anyway.
 	for (const Cell& cell : column_)
 		if (cell.get_row_index() == rowIndex) return true;
 
@@ -389,6 +393,11 @@ inline bool Intrusive_list_column<Master_matrix>::is_empty() const
 	return column_.empty();
 }
 
+template<class Master_matrix>
+inline std::size_t Intrusive_list_column<Master_matrix>::size() const{
+	return column_.size();
+}
+
 template<class Master_matrix>
 template<class Map_type>
 inline void Intrusive_list_column<Master_matrix>::reorder(const Map_type &valueMap)

src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/intrusive_set_column.h

@@ -66,6 +66,7 @@ class Intrusive_set_column : public Master_matrix::Row_access_option,
 	std::vector<Field_element_type> get_content(int columnLength = -1) const;
 	bool is_non_zero(index rowIndex) const;
 	bool is_empty() const;
+	std::size_t size() const;
 
 	//****************
 	//only for base and boundary
@@ -387,6 +388,11 @@ inline bool Intrusive_set_column<Master_matrix>::is_empty() const
 	return column_.empty();
 }
 
+template<class Master_matrix>
+inline std::size_t Intrusive_set_column<Master_matrix>::size() const{
+	return column_.size();
+}
+
 template<class Master_matrix>
 template<class Map_type>
 inline void Intrusive_set_column<Master_matrix>::reorder(const Map_type &valueMap)
@@ -417,14 +423,15 @@ inline void Intrusive_set_column<Master_matrix>::reorder(const Map_type &valueMa
 			}
 		}
 	} else {
-		for (auto it = column_.begin(); it != column_.end(); ++it) {
+		for (auto it = column_.begin(); it != column_.end(); ) {
 			Cell *new_cell;
 			if constexpr (Master_matrix::Option_list::is_z2){
 				new_cell = cellPool_.construct(valueMap.at(it->get_row_index()));
 			} else {
 				new_cell = cellPool_.construct(it->get_element(), valueMap.at(it->get_row_index()));
 			}
 			newSet.insert(newSet.end(), *new_cell);
+			_delete_cell(it);	//increases it
 		}
 	}
 

src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/list_column.h

@@ -62,6 +62,7 @@ class List_column : public Master_matrix::Row_access_option,
 	std::vector<Field_element_type> get_content(int columnLength = -1) const;
 	bool is_non_zero(index rowIndex) const;
 	bool is_empty() const;
+	std::size_t size() const;
 
 	//****************
 	//only for base and boundary
@@ -370,6 +371,9 @@ List_column<Master_matrix>::get_content(int columnLength) const
 template<class Master_matrix>
 inline bool List_column<Master_matrix>::is_non_zero(index rowIndex) const
 {
+	//could be changed to dichotomic search as column is ordered by row index, 
+	//but I am not sure if it is really worth it as there is no random access
+	//and the columns should not be that long anyway.
 	for (const Cell* cell : column_)
 		if (cell->get_row_index() == rowIndex) return true;
 
@@ -382,6 +386,11 @@ inline bool List_column<Master_matrix>::is_empty() const
 	return column_.empty();
 }
 
+template<class Master_matrix>
+inline std::size_t List_column<Master_matrix>::size() const{
+	return column_.size();
+}
+
 template<class Master_matrix>
 template<class Map_type>
 inline void List_column<Master_matrix>::reorder(const Map_type &valueMap)
@@ -779,7 +788,7 @@ inline bool List_column<Master_matrix>::_add(const Cell_range &column)
 {
 	if (column.begin() == column.end()) return false;
 	if (column_.empty()){	//chain should never enter here.
-		column_.resize(column.column_.size());
+		column_.resize(column.size());
 		auto it = column_.begin();
 		for (const Cell& cell : column){
 			if constexpr (Master_matrix::Option_list::is_z2){