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+/* 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): Pawel Dlotko
+ *
+ * Copyright (C) 2015 Inria
+ *
+ * Modification(s):
+ * - YYYY/MM Author: Description of the modification
+ */
+
+#ifndef BITMAP_CUBICAL_COMPLEX_PERIODIC_BOUNDARY_CONDITIONS_BASE_H_
+#define BITMAP_CUBICAL_COMPLEX_PERIODIC_BOUNDARY_CONDITIONS_BASE_H_
+
+#include <gudhi/Bitmap_cubical_complex_base.h>
+
+#include <cmath>
+#include <limits> // for numeric_limits<>
+#include <vector>
+#include <stdexcept>
+#include <cstddef>
+
+namespace Gudhi {
+
+namespace cubical_complex {
+
+// in this class, we are storing all the elements which are in normal bitmap (i.e. the bitmap without the periodic
+// boundary conditions). But, we set up the iterators and the procedures to compute boundary and coboundary in the way
+// that it is all right. We assume here that all the cells that are on the left / bottom and so on remains, while all
+// the cells on the right / top are not in the Bitmap_cubical_complex_periodic_boundary_conditions_base
+
+/**
+ * @brief Cubical complex with periodic boundary conditions represented as a bitmap.
+ * @ingroup cubical_complex
+ * @details This is a class implementing a bitmap data structure with periodic boundary conditions. Most of the
+ * functions are
+ * identical to the functions from Bitmap_cubical_complex_base.
+ * The ones that needed to be updated are the constructors and get_boundary_of_a_cell and get_coboundary_of_a_cell.
+ */
+template <typename T>
+class Bitmap_cubical_complex_periodic_boundary_conditions_base : public Bitmap_cubical_complex_base<T> {
+ public:
+ // constructors that take an extra parameter:
+
+ /**
+ * Default constructor of Bitmap_cubical_complex_periodic_boundary_conditions_base class.
+ */
+ Bitmap_cubical_complex_periodic_boundary_conditions_base() {}
+ /**
+ * A constructor of Bitmap_cubical_complex_periodic_boundary_conditions_base class that takes the following
+ * parameters: (1) vector with numbers of top dimensional cells in all dimensions and (2) vector of booleans. If
+ * at i-th position of this vector there is true value, that means that periodic boundary conditions are to be
+ * imposed in this direction. In case of false, the periodic boundary conditions will not be imposed in the direction
+ * i.
+ */
+ Bitmap_cubical_complex_periodic_boundary_conditions_base(
+ const std::vector<unsigned>& sizes,
+ const std::vector<bool>& directions_in_which_periodic_b_cond_are_to_be_imposed);
+ /**
+ * A constructor of Bitmap_cubical_complex_periodic_boundary_conditions_base class that takes the name of Perseus
+ * style file as an input. Please consult the documentation about the specification of the file.
+ */
+ Bitmap_cubical_complex_periodic_boundary_conditions_base(const char* perseusStyleFile);
+ /**
+ * A constructor of Bitmap_cubical_complex_periodic_boundary_conditions_base class that takes the following
+ * parameters: (1) vector with numbers of top dimensional cells in all dimensions and (2) vector of top dimensional
+ * cells (ordered lexicographically) and (3) vector of booleans. If at i-th position of this vector there is true
+ * value, that means that periodic boundary conditions are to be imposed in this direction. In case of false, the
+ * periodic boundary conditions will not be imposed in the direction i.
+ */
+ Bitmap_cubical_complex_periodic_boundary_conditions_base(
+ const std::vector<unsigned>& dimensions, const std::vector<T>& topDimensionalCells,
+ const std::vector<bool>& directions_in_which_periodic_b_cond_are_to_be_imposed);
+
+ /**
+ * Destructor of the Bitmap_cubical_complex_periodic_boundary_conditions_base class.
+ **/
+ virtual ~Bitmap_cubical_complex_periodic_boundary_conditions_base() {}
+
+ // overwritten methods co compute boundary and coboundary
+ /**
+ * A version of a function that return boundary of a given cell for an object of
+ * Bitmap_cubical_complex_periodic_boundary_conditions_base class.
+ * The boundary elements are guaranteed to be returned so that the
+ * incidence coefficients are alternating.
+ */
+ virtual std::vector<std::size_t> get_boundary_of_a_cell(std::size_t cell) const;
+
+ /**
+ * A version of a function that return coboundary of a given cell for an object of
+ * Bitmap_cubical_complex_periodic_boundary_conditions_base class.
+ * Note that unlike in the case of boundary, over here the elements are
+ * not guaranteed to be returned with alternating incidence numbers.
+ * To compute incidence between cells use compute_incidence_between_cells
+ * procedure
+ */
+ virtual std::vector<std::size_t> get_coboundary_of_a_cell(std::size_t cell) const;
+
+ /**
+ * This procedure compute incidence numbers between cubes. For a cube \f$A\f$ of
+ * dimension n and a cube \f$B \subset A\f$ of dimension n-1, an incidence
+ * between \f$A\f$ and \f$B\f$ is the integer with which \f$B\f$ appears in the boundary of \f$A\f$.
+ * Note that first parameter is a cube of dimension n,
+ * and the second parameter is an adjusted cube in dimension n-1.
+ * Given \f$A = [b_1,e_1] \times \ldots \ [b_{j-1},e_{j-1}] \times [b_{j},e_{j}] \times [b_{j+1},e_{j+1}] \times \ldots
+ *\times [b_{n},e_{n}] \f$
+ * such that \f$ b_{j} \neq e_{j} \f$
+ * and \f$B = [b_1,e_1] \times \ldots \ [b_{j-1},e_{j-1}] \times [a,a] \times [b_{j+1},e_{j+1}] \times \ldots \times
+ *[b_{n},e_{n}]s \f$
+ * where \f$ a = b_{j}\f$ or \f$ a = e_{j}\f$, the incidence between \f$A\f$ and \f$B\f$
+ * computed by this procedure is given by formula:
+ * \f$ c\ (-1)^{\sum_{i=1}^{j-1} dim [b_{i},e_{i}]} \f$
+ * Where \f$ dim [b_{i},e_{i}] = 0 \f$ if \f$ b_{i}=e_{i} \f$ and 1 in other case.
+ * c is -1 if \f$ a = b_{j}\f$ and 1 if \f$ a = e_{j}\f$.
+ * @exception std::logic_error In case when the cube \f$B\f$ is not n-1
+ * dimensional face of a cube \f$A\f$.
+ **/
+ virtual int compute_incidence_between_cells(std::size_t coface, std::size_t face) {
+ // first get the counters for coface and face:
+ std::vector<unsigned> coface_counter = this->compute_counter_for_given_cell(coface);
+ std::vector<unsigned> face_counter = this->compute_counter_for_given_cell(face);
+
+ // coface_counter and face_counter should agree at all positions except from one:
+ int number_of_position_in_which_counters_do_not_agree = -1;
+ std::size_t number_of_full_faces_that_comes_before = 0;
+ for (std::size_t i = 0; i != coface_counter.size(); ++i) {
+ if ((coface_counter[i] % 2 == 1) && (number_of_position_in_which_counters_do_not_agree == -1)) {
+ ++number_of_full_faces_that_comes_before;
+ }
+ if (coface_counter[i] != face_counter[i]) {
+ if (number_of_position_in_which_counters_do_not_agree != -1) {
+ std::cout << "Cells given to compute_incidence_between_cells procedure do not form a pair of coface-face.\n";
+ throw std::logic_error(
+ "Cells given to compute_incidence_between_cells procedure do not form a pair of coface-face.");
+ }
+ number_of_position_in_which_counters_do_not_agree = i;
+ }
+ }
+
+ int incidence = 1;
+ if (number_of_full_faces_that_comes_before % 2) incidence = -1;
+ // if the face cell is on the right from coface cell:
+ if ((coface_counter[number_of_position_in_which_counters_do_not_agree] + 1 ==
+ face_counter[number_of_position_in_which_counters_do_not_agree]) ||
+ ((coface_counter[number_of_position_in_which_counters_do_not_agree] != 1) &&
+ (face_counter[number_of_position_in_which_counters_do_not_agree] == 0))) {
+ incidence *= -1;
+ }
+
+ return incidence;
+ }
+
+ protected:
+ std::vector<bool> directions_in_which_periodic_b_cond_are_to_be_imposed;
+
+ void set_up_containers(const std::vector<unsigned>& sizes) {
+ unsigned multiplier = 1;
+ for (std::size_t i = 0; i != sizes.size(); ++i) {
+ this->sizes.push_back(sizes[i]);
+ this->multipliers.push_back(multiplier);
+
+ if (directions_in_which_periodic_b_cond_are_to_be_imposed[i]) {
+ multiplier *= 2 * sizes[i];
+ } else {
+ multiplier *= 2 * sizes[i] + 1;
+ }
+ }
+ // std::reverse( this->sizes.begin() , this->sizes.end() );
+ this->data = std::vector<T>(multiplier, std::numeric_limits<T>::infinity());
+ this->total_number_of_cells = multiplier;
+ }
+ Bitmap_cubical_complex_periodic_boundary_conditions_base(const std::vector<unsigned>& sizes);
+ Bitmap_cubical_complex_periodic_boundary_conditions_base(const std::vector<unsigned>& dimensions,
+ const std::vector<T>& topDimensionalCells);
+
+ /**
+ * A procedure used to construct the data structures in the class.
+ **/
+ void construct_complex_based_on_top_dimensional_cells(
+ const std::vector<unsigned>& dimensions, const std::vector<T>& topDimensionalCells,
+ const std::vector<bool>& directions_in_which_periodic_b_cond_are_to_be_imposed);
+};
+
+template <typename T>
+void Bitmap_cubical_complex_periodic_boundary_conditions_base<T>::construct_complex_based_on_top_dimensional_cells(
+ const std::vector<unsigned>& dimensions, const std::vector<T>& topDimensionalCells,
+ const std::vector<bool>& directions_in_which_periodic_b_cond_are_to_be_imposed) {
+ this->directions_in_which_periodic_b_cond_are_to_be_imposed = directions_in_which_periodic_b_cond_are_to_be_imposed;
+ this->set_up_containers(dimensions);
+
+ std::size_t i = 0;
+ for (auto it = this->top_dimensional_cells_iterator_begin(); it != this->top_dimensional_cells_iterator_end(); ++it) {
+ this->get_cell_data(*it) = topDimensionalCells[i];
+ ++i;
+ }
+ this->impose_lower_star_filtration();
+}
+
+template <typename T>
+Bitmap_cubical_complex_periodic_boundary_conditions_base<T>::Bitmap_cubical_complex_periodic_boundary_conditions_base(
+ const std::vector<unsigned>& sizes,
+ const std::vector<bool>& directions_in_which_periodic_b_cond_are_to_be_imposed) {
+ this->directions_in_which_periodic_b_cond_are_to_be_imposed(directions_in_which_periodic_b_cond_are_to_be_imposed);
+ this->set_up_containers(sizes);
+}
+
+template <typename T>
+Bitmap_cubical_complex_periodic_boundary_conditions_base<T>::Bitmap_cubical_complex_periodic_boundary_conditions_base(
+ const char* perseus_style_file) {
+ // for Perseus style files:
+ bool dbg = false;
+
+ std::ifstream inFiltration;
+ inFiltration.open(perseus_style_file);
+ unsigned dimensionOfData;
+ inFiltration >> dimensionOfData;
+
+ this->directions_in_which_periodic_b_cond_are_to_be_imposed = std::vector<bool>(dimensionOfData, false);
+
+ std::vector<unsigned> sizes;
+ sizes.reserve(dimensionOfData);
+ for (std::size_t i = 0; i != dimensionOfData; ++i) {
+ int size_in_this_dimension;
+ inFiltration >> size_in_this_dimension;
+ if (size_in_this_dimension < 0) {
+ this->directions_in_which_periodic_b_cond_are_to_be_imposed[i] = true;
+ }
+ sizes.push_back(abs(size_in_this_dimension));
+ }
+ this->set_up_containers(sizes);
+
+ typename Bitmap_cubical_complex_periodic_boundary_conditions_base<T>::Top_dimensional_cells_iterator it(*this);
+ it = this->top_dimensional_cells_iterator_begin();
+
+ while (!inFiltration.eof()) {
+ double filtrationLevel;
+ inFiltration >> filtrationLevel;
+ if (inFiltration.eof()) break;
+
+ if (dbg) {
+ std::cerr << "Cell of an index : " << it.compute_index_in_bitmap()
+ << " and dimension: " << this->get_dimension_of_a_cell(it.compute_index_in_bitmap())
+ << " get the value : " << filtrationLevel << std::endl;
+ }
+ this->get_cell_data(*it) = filtrationLevel;
+ ++it;
+ }
+ inFiltration.close();
+ this->impose_lower_star_filtration();
+}
+
+template <typename T>
+Bitmap_cubical_complex_periodic_boundary_conditions_base<T>::Bitmap_cubical_complex_periodic_boundary_conditions_base(
+ const std::vector<unsigned>& sizes) {
+ this->directions_in_which_periodic_b_cond_are_to_be_imposed = std::vector<bool>(sizes.size(), false);
+ this->set_up_containers(sizes);
+}
+
+template <typename T>
+Bitmap_cubical_complex_periodic_boundary_conditions_base<T>::Bitmap_cubical_complex_periodic_boundary_conditions_base(
+ const std::vector<unsigned>& dimensions, const std::vector<T>& topDimensionalCells) {
+ std::vector<bool> directions_in_which_periodic_b_cond_are_to_be_imposed = std::vector<bool>(dimensions.size(), false);
+ this->construct_complex_based_on_top_dimensional_cells(dimensions, topDimensionalCells,
+ directions_in_which_periodic_b_cond_are_to_be_imposed);
+}
+
+template <typename T>
+Bitmap_cubical_complex_periodic_boundary_conditions_base<T>::Bitmap_cubical_complex_periodic_boundary_conditions_base(
+ const std::vector<unsigned>& dimensions, const std::vector<T>& topDimensionalCells,
+ const std::vector<bool>& directions_in_which_periodic_b_cond_are_to_be_imposed) {
+ this->construct_complex_based_on_top_dimensional_cells(dimensions, topDimensionalCells,
+ directions_in_which_periodic_b_cond_are_to_be_imposed);
+}
+
+// ***********************Methods************************ //
+
+template <typename T>
+std::vector<std::size_t> Bitmap_cubical_complex_periodic_boundary_conditions_base<T>::get_boundary_of_a_cell(
+ std::size_t cell) const {
+ bool dbg = false;
+ if (dbg) {
+ std::cerr << "Computations of boundary of a cell : " << cell << std::endl;
+ }
+
+ std::vector<std::size_t> boundary_elements;
+ boundary_elements.reserve(this->dimension() * 2);
+ std::size_t cell1 = cell;
+ std::size_t sum_of_dimensions = 0;
+
+ for (std::size_t i = this->multipliers.size(); i != 0; --i) {
+ unsigned position = cell1 / this->multipliers[i - 1];
+ // this cell have a nonzero length in this direction, therefore we can compute its boundary in this direction.
+ if (position % 2 == 1) {
+ // if there are no periodic boundary conditions in this direction, we do not have to do anything.
+ if (!directions_in_which_periodic_b_cond_are_to_be_imposed[i - 1]) {
+ // std::cerr << "A\n";
+ if (sum_of_dimensions % 2) {
+ boundary_elements.push_back(cell - this->multipliers[i - 1]);
+ boundary_elements.push_back(cell + this->multipliers[i - 1]);
+ } else {
+ boundary_elements.push_back(cell + this->multipliers[i - 1]);
+ boundary_elements.push_back(cell - this->multipliers[i - 1]);
+ }
+ if (dbg) {
+ std::cerr << cell - this->multipliers[i - 1] << " " << cell + this->multipliers[i - 1] << " ";
+ }
+ } else {
+ // in this direction we have to do boundary conditions. Therefore, we need to check if we are not at the end.
+ if (position != 2 * this->sizes[i - 1] - 1) {
+ // std::cerr << "B\n";
+ if (sum_of_dimensions % 2) {
+ boundary_elements.push_back(cell - this->multipliers[i - 1]);
+ boundary_elements.push_back(cell + this->multipliers[i - 1]);
+ } else {
+ boundary_elements.push_back(cell + this->multipliers[i - 1]);
+ boundary_elements.push_back(cell - this->multipliers[i - 1]);
+ }
+ if (dbg) {
+ std::cerr << cell - this->multipliers[i - 1] << " " << cell + this->multipliers[i - 1] << " ";
+ }
+ } else {
+ // std::cerr << "C\n";
+ if (sum_of_dimensions % 2) {
+ boundary_elements.push_back(cell - this->multipliers[i - 1]);
+ boundary_elements.push_back(cell - (2 * this->sizes[i - 1] - 1) * this->multipliers[i - 1]);
+ } else {
+ boundary_elements.push_back(cell - (2 * this->sizes[i - 1] - 1) * this->multipliers[i - 1]);
+ boundary_elements.push_back(cell - this->multipliers[i - 1]);
+ }
+ if (dbg) {
+ std::cerr << cell - this->multipliers[i - 1] << " "
+ << cell - (2 * this->sizes[i - 1] - 1) * this->multipliers[i - 1] << " ";
+ }
+ }
+ }
+ ++sum_of_dimensions;
+ }
+ cell1 = cell1 % this->multipliers[i - 1];
+ }
+ return boundary_elements;
+}
+
+template <typename T>
+std::vector<std::size_t> Bitmap_cubical_complex_periodic_boundary_conditions_base<T>::get_coboundary_of_a_cell(
+ std::size_t cell) const {
+ std::vector<unsigned> counter = this->compute_counter_for_given_cell(cell);
+ std::vector<std::size_t> coboundary_elements;
+ std::size_t cell1 = cell;
+ for (std::size_t i = this->multipliers.size(); i != 0; --i) {
+ unsigned position = cell1 / this->multipliers[i - 1];
+ // if the cell has zero length in this direction, then it will have cbd in this direction.
+ if (position % 2 == 0) {
+ if (!this->directions_in_which_periodic_b_cond_are_to_be_imposed[i - 1]) {
+ // no periodic boundary conditions in this direction
+ if ((counter[i - 1] != 0) && (cell > this->multipliers[i - 1])) {
+ coboundary_elements.push_back(cell - this->multipliers[i - 1]);
+ }
+ if ((counter[i - 1] != 2 * this->sizes[i - 1]) && (cell + this->multipliers[i - 1] < this->data.size())) {
+ coboundary_elements.push_back(cell + this->multipliers[i - 1]);
+ }
+ } else {
+ // we want to have periodic boundary conditions in this direction
+ if (counter[i - 1] != 0) {
+ coboundary_elements.push_back(cell - this->multipliers[i - 1]);
+ coboundary_elements.push_back(cell + this->multipliers[i - 1]);
+ } else {
+ // in this case counter[i-1] == 0.
+ coboundary_elements.push_back(cell + this->multipliers[i - 1]);
+ coboundary_elements.push_back(cell + (2 * this->sizes[i - 1] - 1) * this->multipliers[i - 1]);
+ }
+ }
+ }
+
+ cell1 = cell1 % this->multipliers[i - 1];
+ }
+ return coboundary_elements;
+}
+
+} // namespace cubical_complex
+
+namespace Cubical_complex = cubical_complex;
+
+} // namespace Gudhi
+
+#endif // BITMAP_CUBICAL_COMPLEX_PERIODIC_BOUNDARY_CONDITIONS_BASE_H_