diff options
Diffstat (limited to 'src/Persistent_cohomology/include')
4 files changed, 45 insertions, 52 deletions
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h index c6593cc4..d096792f 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h @@ -20,17 +20,17 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#ifndef SRC_PERSISTENT_COHOMOLOGY_INCLUDE_GUDHI_PERSISTENT_COHOMOLOGY_H_ -#define SRC_PERSISTENT_COHOMOLOGY_INCLUDE_GUDHI_PERSISTENT_COHOMOLOGY_H_ +#ifndef PERSISTENT_COHOMOLOGY_H_ +#define PERSISTENT_COHOMOLOGY_H_ #include <gudhi/Persistent_cohomology/Persistent_cohomology_column.h> #include <gudhi/Persistent_cohomology/Field_Zp.h> +#include <gudhi/Simple_object_pool.h> #include <boost/tuple/tuple.hpp> #include <boost/intrusive/set.hpp> #include <boost/pending/disjoint_sets.hpp> #include <boost/intrusive/list.hpp> -#include <boost/pool/object_pool.hpp> #include <map> #include <utility> @@ -38,6 +38,10 @@ #include <vector> #include <set> #include <fstream> // std::ofstream +#include <limits> // for numeric_limits<> +#include <tuple> +#include <algorithm> +#include <string> namespace Gudhi { @@ -266,13 +270,10 @@ class Persistent_cohomology { } ~Persistent_cohomology() { -// Clean the remaining columns in the matrix. - for (auto & cam_ref : cam_) { - cam_ref.col_.clear(); - } -// Clean the transversal lists + // Clean the transversal lists for (auto & transverse_ref : transverse_idx_) { - transverse_ref.second.row_->clear(); + // Destruct all the cells + transverse_ref.second.row_->clear_and_dispose([&](Cell*p){p->~Cell();}); delete transverse_ref.second.row_; } } @@ -527,8 +528,8 @@ class Persistent_cohomology { Arith_element charac) { Simplex_key key = cpx_->key(sigma); // Create a column containing only one cell, - Column * new_col = column_pool_.construct(Column(key)); - Cell * new_cell = cell_pool_.construct(Cell(key, x, new_col)); + Column * new_col = column_pool_.construct(key); + Cell * new_cell = cell_pool_.construct(key, x, new_col); new_col->col_.push_back(*new_cell); // and insert it in the matrix, in constant time thanks to the hint cam_.end(). // Indeed *new_col has the biggest lexicographic value because key is the @@ -572,9 +573,8 @@ class Persistent_cohomology { Column * curr_col = row_cell_it->self_col_; ++row_cell_it; // Disconnect the column from the rows in the CAM. - for (auto col_cell_it = curr_col->col_.begin(); - col_cell_it != curr_col->col_.end(); ++col_cell_it) { - col_cell_it->base_hook_cam_h::unlink(); + for (auto& col_cell : curr_col->col_) { + col_cell.base_hook_cam_h::unlink(); } // Remove the column from the CAM before modifying its value @@ -589,9 +589,9 @@ class Persistent_cohomology { // Find whether the column obtained is already in the CAM result_insert_cam = cam_.insert(*curr_col); if (result_insert_cam.second) { // If it was not in the CAM before: insertion has succeeded - for (auto col_cell_it = curr_col->col_.begin(); col_cell_it != curr_col->col_.end(); ++col_cell_it) { + for (auto& col_cell : curr_col->col_) { // re-establish the row links - transverse_idx_[col_cell_it->key_].row_->push_front(*col_cell_it); + transverse_idx_[col_cell.key_].row_->push_front(col_cell); } } else { // There is already an identical column in the CAM: // merge two disjoint sets. @@ -601,6 +601,8 @@ class Persistent_cohomology { Simplex_key key_tmp = dsets_.find_set(curr_col->class_key_); ds_repr_[key_tmp] = &(*(result_insert_cam.first)); result_insert_cam.first->class_key_ = key_tmp; + // intrusive containers don't own their elements, we have to release them manually + curr_col->col_.clear_and_dispose([&](Cell*p){cell_pool_.destroy(p);}); column_pool_.destroy(curr_col); // delete curr_col; } } @@ -711,13 +713,11 @@ class Persistent_cohomology { } } - void write_output_diagram(std::string diagram_name) - { - std::ofstream diagram_out(diagram_name.c_str()); - cmp_intervals_by_length cmp( cpx_ ); + void write_output_diagram(std::string diagram_name) { + std::ofstream diagram_out(diagram_name.c_str()); + cmp_intervals_by_length cmp(cpx_); std::sort(std::begin(persistent_pairs_), std::end(persistent_pairs_), cmp); - for(auto pair : persistent_pairs_) - { + for (auto pair : persistent_pairs_) { diagram_out << cpx_->dimension(get<0>(pair)) << " " << cpx_->filtration(get<0>(pair)) << " " << cpx_->filtration(get<1>(pair)) << std::endl; @@ -766,8 +766,8 @@ class Persistent_cohomology { std::vector<Persistent_interval> persistent_pairs_; length_interval interval_length_policy; - boost::object_pool<Column> column_pool_; - boost::object_pool<Cell> cell_pool_; + Simple_object_pool<Column> column_pool_; + Simple_object_pool<Cell> cell_pool_; }; /** @} */ // end defgroup persistent_cohomology @@ -776,4 +776,4 @@ class Persistent_cohomology { } // namespace Gudhi -#endif // SRC_PERSISTENT_COHOMOLOGY_INCLUDE_GUDHI_PERSISTENT_COHOMOLOGY_H_ +#endif // PERSISTENT_COHOMOLOGY_H_ diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h index a12019f8..6db16e69 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h @@ -20,8 +20,8 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#ifndef SRC_PERSISTENT_COHOMOLOGY_INCLUDE_GUDHI_PERSISTENT_COHOMOLOGY_FIELD_ZP_H_ -#define SRC_PERSISTENT_COHOMOLOGY_INCLUDE_GUDHI_PERSISTENT_COHOMOLOGY_FIELD_ZP_H_ +#ifndef PERSISTENT_COHOMOLOGY_FIELD_ZP_H_ +#define PERSISTENT_COHOMOLOGY_FIELD_ZP_H_ #include <utility> #include <vector> @@ -113,4 +113,4 @@ class Field_Zp { } // namespace Gudhi -#endif // SRC_PERSISTENT_COHOMOLOGY_INCLUDE_GUDHI_PERSISTENT_COHOMOLOGY_FIELD_ZP_H_ +#endif // PERSISTENT_COHOMOLOGY_FIELD_ZP_H_ diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h index 555d696f..0591fc95 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h @@ -20,8 +20,8 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#ifndef SRC_PERSISTENT_COHOMOLOGY_INCLUDE_GUDHI_PERSISTENT_COHOMOLOGY_MULTI_FIELD_H_ -#define SRC_PERSISTENT_COHOMOLOGY_INCLUDE_GUDHI_PERSISTENT_COHOMOLOGY_MULTI_FIELD_H_ +#ifndef PERSISTENT_COHOMOLOGY_MULTI_FIELD_H_ +#define PERSISTENT_COHOMOLOGY_MULTI_FIELD_H_ #include <gmpxx.h> @@ -183,4 +183,4 @@ class Multi_field { } // namespace Gudhi -#endif // SRC_PERSISTENT_COHOMOLOGY_INCLUDE_GUDHI_PERSISTENT_COHOMOLOGY_MULTI_FIELD_H_ +#endif // PERSISTENT_COHOMOLOGY_MULTI_FIELD_H_ diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Persistent_cohomology_column.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Persistent_cohomology_column.h index fcec819a..612658e6 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Persistent_cohomology_column.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Persistent_cohomology_column.h @@ -20,14 +20,14 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#ifndef SRC_PERSISTENT_COHOMOLOGY_INCLUDE_GUDHI_PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_ -#define SRC_PERSISTENT_COHOMOLOGY_INCLUDE_GUDHI_PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_ +#ifndef PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_ +#define PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_ -#include <list> +#include <boost/tuple/tuple.hpp> +#include <boost/intrusive/set.hpp> +#include <boost/intrusive/list.hpp> -#include "boost/tuple/tuple.hpp" -#include "boost/intrusive/set.hpp" -#include "boost/intrusive/list.hpp" +#include <list> namespace Gudhi { @@ -80,40 +80,33 @@ class Persistent_cohomology_cell : public base_hook_cam_h, * The non-zero coefficients of the column are stored in a * boost::intrusive::list. Contains a hook to be stored in a * boost::intrusive::set. + * + * Movable but not Copyable. */ template<typename SimplexKey, typename ArithmeticElement> class Persistent_cohomology_column : public boost::intrusive::set_base_hook< boost::intrusive::link_mode<boost::intrusive::normal_link> > { - private: template<class T1, class T2> friend class Persistent_cohomology; + public: typedef Persistent_cohomology_cell<SimplexKey, ArithmeticElement> Cell; typedef boost::intrusive::list<Cell, boost::intrusive::constant_time_size<false>, boost::intrusive::base_hook<base_hook_cam_v> > Col_type; /** \brief Creates an empty column.*/ - explicit Persistent_cohomology_column(SimplexKey key) { - class_key_ = key; - col_ = Col_type(); - } - public: - /** Copy constructor.*/ - Persistent_cohomology_column(Persistent_cohomology_column const &other) + explicit Persistent_cohomology_column(SimplexKey key) : col_(), - class_key_(other.class_key_) { - if (!other.col_.empty()) - std::cerr << "Copying a non-empty column.\n"; - } + class_key_(key) {} /** \brief Returns true iff the column is null.*/ - bool is_null() { + bool is_null() const { return col_.empty(); } /** \brief Returns the key of the representative simplex of * the set of simplices having this column as annotation vector * in the compressed annotation matrix.*/ - SimplexKey class_key() { + SimplexKey class_key() const { return class_key_; } @@ -145,4 +138,4 @@ class Persistent_cohomology_column : public boost::intrusive::set_base_hook< } // namespace Gudhi -#endif // SRC_PERSISTENT_COHOMOLOGY_INCLUDE_GUDHI_PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_ +#endif // PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_ |