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[Persistence matrix] renaming matrix cells as matrix entries #1134

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Sep 25, 2024
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[Persistence matrix] renaming matrix cells as matrix entries #1134

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7dd5177
renaming matrix cell as matrix entry
hschreiber Sep 23, 2024
fdaeb01
renaming matrix cell as matrix entry
hschreiber Sep 24, 2024
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134 changes: 71 additions & 63 deletions src/Persistence_matrix/concept/PersistenceMatrixColumn.h
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6 changes: 3 additions & 3 deletions src/Persistence_matrix/concept/PersistenceMatrixOptions.h
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Original file line number Diff line number Diff line change
Expand Up @@ -74,7 +74,7 @@ struct PersistenceMatrixOptions
* Note that some methods of the @ref basematrix "base matrix" are not available when true:
* - @ref Matrix::insert_column(const Container&, Index) "insert_column(const Container&, Index)",
* - @ref Matrix::zero_column(Index) "zero_column(Index)",
* - @ref Matrix::zero_cell(Index, Index) "zero_cell(Index, ID_index)",
* - @ref Matrix::zero_entry(Index, Index) "zero_entry(Index, ID_index)",
* - @ref Matrix::swap_columns(Index, Index) "swap_columns(Index, Index)",
* - @ref Matrix::swap_rows(Index, Index) "swap_rows(Index, Index)",
* - @ref Matrix::remove_column(Index) "remove_column(Index)",
Expand Down Expand Up @@ -111,8 +111,8 @@ struct PersistenceMatrixOptions
static const bool has_row_access;
/**
* @brief Only enabled if @ref has_row_access is true, ignored otherwise.
* If set to true, the underlying container representing a row is an boost::intrusive::list<Cell>.
* If set to false, the container is a std::set<Cell>. It is usually recommended to set it to true.
* If set to true, the underlying container representing a row is an boost::intrusive::list<Entry>.
* If set to false, the container is a std::set<Entry>. It is usually recommended to set it to true.
*/
static const bool has_intrusive_rows;
/**
Expand Down
249 changes: 125 additions & 124 deletions src/Persistence_matrix/include/gudhi/Matrix.h
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126 changes: 64 additions & 62 deletions src/Persistence_matrix/include/gudhi/Persistence_matrix/Base_matrix.h
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101 changes: 51 additions & 50 deletions ...Persistence_matrix/include/gudhi/Persistence_matrix/Base_matrix_with_column_compression.h
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Original file line number Diff line number Diff line change
Expand Up @@ -45,18 +45,18 @@ template <class Master_matrix>
class Base_matrix_with_column_compression : protected Master_matrix::Matrix_row_access_option
{
public:
using Index = typename Master_matrix::Index; /**< Container index type. */
using Dimension = typename Master_matrix::Dimension; /**< Dimension value type. */
using Index = typename Master_matrix::Index; /**< Container index type. */
using Dimension = typename Master_matrix::Dimension; /**< Dimension value type. */
/**
* @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; /**< Field element value type. */
using Row = typename Master_matrix::Row; /**< Row type,
only necessary with row access option. */
using Cell_constructor = typename Master_matrix::Cell_constructor; /**< Factory of @ref Cell classes. */
using Column_settings = typename Master_matrix::Column_settings; /**< Structure giving access to the columns to
necessary external classes. */
using Field_element = typename Master_matrix::Element; /**< Field element value 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. */

/**
* @brief Type for columns. Only one for each "column class" is explicitly constructed.
Expand Down Expand Up @@ -119,9 +119,9 @@ class Base_matrix_with_column_compression : protected Master_matrix::Matrix_row_
* If no identical column already existed, a copy of the column is stored. If an identical one existed, no new
* column is constructed and the relationship between the two is registered in an union-find structure.
*
* @tparam Container Range type for @ref Matrix::Cell_representative ranges.
* @tparam Container Range type for @ref Matrix::Entry_representative ranges.
* Assumed to have a begin(), end() and size() method.
* @param columns A vector of @ref Matrix::Cell_representative ranges to construct the columns from.
* @param columns A vector of @ref Matrix::Entry_representative ranges to construct the columns from.
* The content of the ranges are assumed to be sorted by increasing ID value.
* @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.
Expand Down Expand Up @@ -162,20 +162,21 @@ class Base_matrix_with_column_compression : protected Master_matrix::Matrix_row_

/**
* @brief Inserts a new ordered column at the end of the matrix by copying the given range of
* @ref Matrix::Cell_representative. The content of the range is assumed to be sorted by increasing ID value.
* @ref Matrix::Entry_representative. The content of the range is assumed to be sorted by increasing ID value.
*
* @tparam Container Range of @ref Matrix::Cell_representative. Assumed to have a begin(), end() and size() method.
* @param column Range of @ref Matrix::Cell_representative from which the column has to be constructed. Assumed to be
* @tparam Container Range of @ref Matrix::Entry_representative. Assumed to have a begin(), end() and size() method.
* @param column Range of @ref Matrix::Entry_representative from which the column has to be constructed. Assumed to be
* ordered by increasing ID value.
*/
template <class Container>
void insert_column(const Container& column);
/**
* @brief Same as @ref insert_column, only for interface purposes. The given dimension is ignored and not stored.
*
* @tparam Boundary_range Range of @ref Matrix::Cell_representative. Assumed to have a begin(), end() and size() method.
* @param boundary Range of @ref Matrix::Cell_representative from which the column has to be constructed. Assumed to be
* ordered by increasing ID value.
* @tparam Boundary_range Range of @ref Matrix::Entry_representative. Assumed to have a begin(), end() and size()
* method.
* @param boundary Range of @ref Matrix::Entry_representative from which the column has to be constructed. Assumed to
* be ordered by increasing ID value.
* @param dim Ignored.
*/
template <class Boundary_range>
Expand Down Expand Up @@ -205,11 +206,11 @@ class Base_matrix_with_column_compression : protected Master_matrix::Matrix_row_
* @brief If @ref PersistenceMatrixOptions::has_row_access and @ref PersistenceMatrixOptions::has_removable_rows
* are true: assumes that the row is empty and removes it. Otherwise, does nothing.
*
* @warning The removed rows are always assumed to be empty. If it is not the case, the deleted row cells are not
* @warning The removed rows are always assumed to be empty. 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 cells are destroyed later. The row access is just meant as a "read only" access to the rows and the
* 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 cell removal, what can be
* 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.
Expand All @@ -229,28 +230,28 @@ class Base_matrix_with_column_compression : protected Master_matrix::Matrix_row_
* The representatives of redundant columns are summed together, which means that
* all column compressed together with the target column are affected by the change, not only the target.
*
* @tparam Cell_range_or_column_index Either a range of @ref Cell with a begin() and end() method,
* @tparam Entry_range_or_column_index Either a range of @ref Entry with a begin() and end() method,
* or any integer type.
* @param sourceColumn Either a cell range or the @ref MatIdx index of the column to add.
* @param sourceColumn Either an entry range or the @ref MatIdx index of the column to add.
* @param targetColumnIndex @ref MatIdx index of the target column.
*/
template <class Cell_range_or_column_index>
void add_to(const Cell_range_or_column_index& sourceColumn, Index targetColumnIndex);
template <class Entry_range_or_column_index>
void add_to(const Entry_range_or_column_index& sourceColumn, Index targetColumnIndex);
/**
* @brief Multiplies the target column with the coefficient and then adds the source column to it.
* That is: `targetColumn = (targetColumn * coefficient) + sourceColumn`.
*
* The representatives of redundant columns are summed together, which means that
* all column compressed together with the target column are affected by the change, not only the target.
*
* @tparam Cell_range_or_column_index Either a range of @ref Cell with a begin() and end() method,
* @tparam Entry_range_or_column_index Either a range of @ref Entry with a begin() and end() method,
* or any integer type.
* @param sourceColumn Either a @ref Cell range or the @ref MatIdx index of the column to add.
* @param sourceColumn Either a @ref Entry range or the @ref MatIdx index of the column to add.
* @param coefficient Value to multiply.
* @param targetColumnIndex @ref MatIdx index of the target column.
*/
template <class Cell_range_or_column_index>
void multiply_target_and_add_to(const Cell_range_or_column_index& sourceColumn,
template <class Entry_range_or_column_index>
void multiply_target_and_add_to(const Entry_range_or_column_index& sourceColumn,
const Field_element& coefficient,
Index targetColumnIndex);
/**
Expand All @@ -260,26 +261,26 @@ class Base_matrix_with_column_compression : protected Master_matrix::Matrix_row_
* The representatives of redundant columns are summed together, which means that
* all column compressed together with the target column are affected by the change, not only the target.
*
* @tparam Cell_range_or_column_index Either a range of @ref Cell with a begin() and end() method,
* @tparam Entry_range_or_column_index Either a range of @ref Entry with a begin() and end() method,
* or any integer type.
* @param coefficient Value to multiply.
* @param sourceColumn Either a @ref Cell range or the @ref MatIdx index of the column to add.
* @param sourceColumn Either a @ref Entry range or the @ref MatIdx index of the column to add.
* @param targetColumnIndex @ref MatIdx index of the target column.
*/
template <class Cell_range_or_column_index>
template <class Entry_range_or_column_index>
void multiply_source_and_add_to(const Field_element& coefficient,
const Cell_range_or_column_index& sourceColumn,
const Entry_range_or_column_index& sourceColumn,
Index targetColumnIndex);

/**
* @brief Indicates if the cell at given coordinates has value zero.
* @brief Indicates if the entry at given coordinates has value zero.
*
* @param columnIndex @ref MatIdx index of the column of the cell.
* @param rowIndex @ref rowindex "Row index" of the row of the cell.
* @return true If the cell has value zero.
* @param columnIndex @ref MatIdx index of the column of the entry.
* @param rowIndex @ref rowindex "Row index" of the row of the entry.
* @return true If the entry has value zero.
* @return false Otherwise.
*/
bool is_zero_cell(Index columnIndex, Index rowIndex);
bool is_zero_entry(Index columnIndex, Index rowIndex);
/**
* @brief Indicates if the column at given index has value zero.
*
Expand All @@ -292,7 +293,7 @@ class Base_matrix_with_column_compression : protected Master_matrix::Matrix_row_
/**
* @brief Resets the matrix to an empty matrix.
*
* @param colSettings Pointer to the cell factory.
* @param colSettings Pointer to the entry factory.
*/
void reset(Column_settings* colSettings) {
columnToRep_.clear_and_dispose(Delete_disposer(this));
Expand Down Expand Up @@ -346,7 +347,7 @@ class Base_matrix_with_column_compression : protected Master_matrix::Matrix_row_
std::vector<Column*> repToColumn_; /**< Map from the representative index to
the representative Column. */
Index nextColumnIndex_; /**< Next unused column index. */
Column_settings* colSettings_; /**< Cell factory. */
Column_settings* colSettings_; /**< Entry factory. */
/**
* @brief Column factory. Has to be a pointer as Simple_object_pool is not swappable, so their addresses have to be
* exchanged instead.
Expand Down Expand Up @@ -519,15 +520,15 @@ Base_matrix_with_column_compression<Master_matrix>::get_number_of_columns() cons
}

template <class Master_matrix>
template <class Cell_range_or_column_index>
inline void Base_matrix_with_column_compression<Master_matrix>::add_to(const Cell_range_or_column_index& sourceColumn,
template <class Entry_range_or_column_index>
inline void Base_matrix_with_column_compression<Master_matrix>::add_to(const Entry_range_or_column_index& sourceColumn,
Index targetColumnIndex)
{
// handle case where targetRep == sourceRep?
Index targetRep = columnClasses_.find_set(targetColumnIndex);
Column& target = *repToColumn_[targetRep];
columnToRep_.erase(target);
if constexpr (std::is_integral_v<Cell_range_or_column_index>) {
if constexpr (std::is_integral_v<Entry_range_or_column_index>) {
target += get_column(sourceColumn);
} else {
target += sourceColumn;
Expand All @@ -536,15 +537,15 @@ inline void Base_matrix_with_column_compression<Master_matrix>::add_to(const Cel
}

template <class Master_matrix>
template <class Cell_range_or_column_index>
template <class Entry_range_or_column_index>
inline void Base_matrix_with_column_compression<Master_matrix>::multiply_target_and_add_to(
const Cell_range_or_column_index& sourceColumn, const Field_element& coefficient, Index targetColumnIndex)
const Entry_range_or_column_index& sourceColumn, const Field_element& coefficient, Index targetColumnIndex)
{
// handle case where targetRep == sourceRep?
Index targetRep = columnClasses_.find_set(targetColumnIndex);
Column& target = *repToColumn_[targetRep];
columnToRep_.erase(target);
if constexpr (std::is_integral_v<Cell_range_or_column_index>) {
if constexpr (std::is_integral_v<Entry_range_or_column_index>) {
target.multiply_target_and_add(coefficient, get_column(sourceColumn));
} else {
target.multiply_target_and_add(coefficient, sourceColumn);
Expand All @@ -553,15 +554,15 @@ inline void Base_matrix_with_column_compression<Master_matrix>::multiply_target_
}

template <class Master_matrix>
template <class Cell_range_or_column_index>
template <class Entry_range_or_column_index>
inline void Base_matrix_with_column_compression<Master_matrix>::multiply_source_and_add_to(
const Field_element& coefficient, const Cell_range_or_column_index& sourceColumn, Index targetColumnIndex)
const Field_element& coefficient, const Entry_range_or_column_index& sourceColumn, Index targetColumnIndex)
{
// handle case where targetRep == sourceRep?
Index targetRep = columnClasses_.find_set(targetColumnIndex);
Column& target = *repToColumn_[targetRep];
columnToRep_.erase(target);
if constexpr (std::is_integral_v<Cell_range_or_column_index>) {
if constexpr (std::is_integral_v<Entry_range_or_column_index>) {
target.multiply_source_and_add(get_column(sourceColumn), coefficient);
} else {
target.multiply_source_and_add(sourceColumn, coefficient);
Expand All @@ -570,7 +571,7 @@ inline void Base_matrix_with_column_compression<Master_matrix>::multiply_source_
}

template <class Master_matrix>
inline bool Base_matrix_with_column_compression<Master_matrix>::is_zero_cell(Index columnIndex, Index rowIndex)
inline bool Base_matrix_with_column_compression<Master_matrix>::is_zero_entry(Index columnIndex, Index rowIndex)
{
auto col = repToColumn_[columnClasses_.find_set(columnIndex)];
if (col == nullptr) return true;
Expand Down Expand Up @@ -636,8 +637,8 @@ inline void Base_matrix_with_column_compression<Master_matrix>::print()
std::cout << "Row Matrix:\n";
for (Index i = 0; i < RA_opt::rows_->size(); ++i) {
const Row& row = RA_opt::rows_[i];
for (const auto& cell : row) {
std::cout << cell.get_column_index() << " ";
for (const auto& entry : row) {
std::cout << entry.get_column_index() << " ";
}
std::cout << "(" << i << ")\n";
}
Expand Down
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