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diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h new file mode 100644 index 00000000..0d6299d2 --- /dev/null +++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h @@ -0,0 +1,857 @@ +/* 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_BASE_H_ +#define BITMAP_CUBICAL_COMPLEX_BASE_H_ + +#include <gudhi/Bitmap_cubical_complex/counter.h> + +#include <iostream> +#include <vector> +#include <string> +#include <fstream> +#include <algorithm> +#include <iterator> +#include <limits> +#include <utility> +#include <stdexcept> +#include <cstddef> + +namespace Gudhi { + +namespace cubical_complex { + +/** + * @brief Cubical complex represented as a bitmap, class with basic implementation. + * @ingroup cubical_complex + * @details This is a class implementing a basic bitmap data structure to store cubical complexes. + * It implements only the most basic subroutines. + * The idea of the bitmap is the following. Our aim is to have a memory efficient + * data structure to store d-dimensional cubical complex + * C being a cubical decomposition + * of a rectangular region of a space. This is achieved by storing C as a + * vector of bits (this is where the name 'bitmap' came from). + * Each cell is represented by a single + * bit (in case of black and white bitmaps, or by a single element of a type T + * (here T is a filtration type of a bitmap, typically a double). + * All the informations needed for homology and + * persistent homology computations (like dimension of a cell, boundary and + * coboundary elements of a cell, are then obtained from the + * position of the element in C. + * The default filtration used in this implementation is the lower star filtration. + */ +template <typename T> +class Bitmap_cubical_complex_base { + public: + typedef T filtration_type; + + /** + *Default constructor + **/ + Bitmap_cubical_complex_base() : total_number_of_cells(0) {} + /** + * There are a few constructors of a Bitmap_cubical_complex_base class. + * First one, that takes vector<unsigned>, creates an empty bitmap of a dimension equal + * the number of elements in the + * input vector and size in the i-th dimension equal the number in the position i-of the input vector. + */ + Bitmap_cubical_complex_base(const std::vector<unsigned>& sizes); + /** + * The second constructor takes as a input a Perseus style file. For more details, + * please consult the documentations of + * Perseus software as well as examples attached to this + * implementation. + **/ + Bitmap_cubical_complex_base(const char* perseus_style_file); + /** + * The last constructor of a Bitmap_cubical_complex_base class accepts vector of dimensions (as the first one) + * together with vector of filtration values of top dimensional cells. + **/ + Bitmap_cubical_complex_base(const std::vector<unsigned>& dimensions, const std::vector<T>& top_dimensional_cells); + + /** + * Destructor of the Bitmap_cubical_complex_base class. + **/ + virtual ~Bitmap_cubical_complex_base() {} + + /** + * The functions get_boundary_of_a_cell, get_coboundary_of_a_cell, get_dimension_of_a_cell + * and get_cell_data are the basic + * functions that compute boundary / coboundary / dimension and the filtration + * value form a position of a cell in the structure of a bitmap. The input parameter of all of those function is a + * non-negative integer, indicating a position of a cube in the data structure. + * In the case of functions that compute (co)boundary, the output is a vector if non-negative integers pointing to + * the positions of (co)boundary element of the input cell. + * The boundary elements are guaranteed to be returned so that the + * incidence coefficients of boundary elements are alternating. + */ + virtual inline std::vector<std::size_t> get_boundary_of_a_cell(std::size_t cell) const; + /** + * The functions get_coboundary_of_a_cell, get_coboundary_of_a_cell, + * get_dimension_of_a_cell and get_cell_data are the basic + * functions that compute boundary / coboundary / dimension and the filtration + * value form a position of a cell in the structure of a bitmap. + * The input parameter of all of those function is a non-negative integer, + * indicating a position of a cube in the data structure. + * In the case of functions that compute (co)boundary, the output is a vector if + * non-negative integers pointing to the + * positions of (co)boundary element of the input cell. + * Note that unlike in the case of boundary, over here the elements are + * not guaranteed to be returned with alternating incidence numbers. + * + **/ + virtual inline 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$B = [b_1,e_1] \times \ldots \ [b_{j-1},e_{j-1}] \times [a,a] \times [b_{j+1},e_{j+1}] \times \ldots \times + *[b_{n},e_{n}] \f$ + * 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) const { + // 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]) { + incidence *= -1; + } + + return incidence; + } + + /** +* In the case of get_dimension_of_a_cell function, the output is a non-negative integer +* indicating the dimension of a cell. +* 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 +**/ + inline unsigned get_dimension_of_a_cell(std::size_t cell) const; + + /** + * In the case of get_cell_data, the output parameter is a reference to the value of a cube in a given position. + * This allows reading and changing the value of filtration. Note that if the value of a filtration is changed, the + * code do not check if we have a filtration or not. i.e. it do not check if the value of a filtration of a cell is + * not smaller than the value of a filtration of its boundary and not greater than the value of its coboundary. + **/ + inline T& get_cell_data(std::size_t cell); + + /** + * Typical input used to construct a baseBitmap class is a filtration given at the top dimensional cells. + * Then, there are a few ways one can pick the filtration of lower dimensional + * cells. The most typical one is by so called lower star filtration. This function is always called by any + * constructor which takes the top dimensional cells. If you use such a constructor, + * then there is no need to call this function. Call it only if you are putting the filtration + * of the cells by your own (for instance by using Top_dimensional_cells_iterator). + **/ + void impose_lower_star_filtration(); // assume that top dimensional cells are already set. + + /** + * Returns dimension of a complex. + **/ + inline unsigned dimension() const { return sizes.size(); } + + /** + * Returns number of all cubes in the data structure. + **/ + inline unsigned size() const { return this->data.size(); } + + /** + * Writing to stream operator. By using it we get the values T of cells in order in which they are stored in the + * structure. This procedure is used for debugging purposes. + **/ + template <typename K> + friend std::ostream& operator<<(std::ostream& os, const Bitmap_cubical_complex_base<K>& b); + + /** + * Function that put the input data to bins. By putting data to bins we mean rounding them to a sequence of values + * equally distributed in the range of data. + * Sometimes if most of the cells have different birth-death times, the performance of the algorithms to compute + * persistence gets worst. When dealing with this type of data, one may want to put different values on cells to + * some number of bins. The function put_data_to_bins( std::size_t number_of_bins ) is designed for that purpose. + * The parameter of the function is the number of bins (distinct values) we want to have in the cubical complex. + **/ + void put_data_to_bins(std::size_t number_of_bins); + + /** + * Function that put the input data to bins. By putting data to bins we mean rounding them to a sequence of values + * equally distributed in the range of data. + * Sometimes if most of the cells have different birth-death times, the performance of the algorithms to compute + * persistence gets worst. When dealing with this type of data, one may want to put different values on cells to + * some number of bins. The function put_data_to_bins( T diameter_of_bin ) is designed for that purpose. + * The parameter of it is the diameter of each bin. Note that the bottleneck distance between the persistence + * diagram of the cubical complex before and after using such a function will be bounded by the parameter + * diameter_of_bin. + **/ + void put_data_to_bins(T diameter_of_bin); + + /** + * Functions to find min and max values of filtration. + **/ + std::pair<T, T> min_max_filtration(); + + // ITERATORS + + /** + * @brief Iterator through all cells in the complex (in order they appear in the structure -- i.e. + * in lexicographical order). + **/ + class All_cells_iterator : std::iterator<std::input_iterator_tag, T> { + public: + All_cells_iterator() { this->counter = 0; } + + All_cells_iterator operator++() { + // first find first element of the counter that can be increased: + ++this->counter; + return *this; + } + + All_cells_iterator operator++(int) { + All_cells_iterator result = *this; + ++(*this); + return result; + } + + All_cells_iterator& operator=(const All_cells_iterator& rhs) { + this->counter = rhs.counter; + return *this; + } + + bool operator==(const All_cells_iterator& rhs) const { + if (this->counter != rhs.counter) return false; + return true; + } + + bool operator!=(const All_cells_iterator& rhs) const { return !(*this == rhs); } + + /* + * The operator * returns position of a cube in the structure of cubical complex. This position can be then used as + * an argument of the following functions: + * get_boundary_of_a_cell, get_coboundary_of_a_cell, get_dimension_of_a_cell to get information about the cell + * boundary and coboundary and dimension + * and in function get_cell_data to get a filtration of a cell. + */ + std::size_t operator*() { return this->counter; } + friend class Bitmap_cubical_complex_base; + + protected: + std::size_t counter; + }; + + /** + * Function returning a All_cells_iterator to the first cell of the bitmap. + **/ + All_cells_iterator all_cells_iterator_begin() { + All_cells_iterator a; + return a; + } + + /** + * Function returning a All_cells_iterator to the last cell of the bitmap. + **/ + All_cells_iterator all_cells_iterator_end() { + All_cells_iterator a; + a.counter = this->data.size(); + return a; + } + + /** + * @brief All_cells_range class provides ranges for All_cells_iterator + **/ + class All_cells_range { + public: + All_cells_range(Bitmap_cubical_complex_base* b) : b(b) {} + + All_cells_iterator begin() { return b->all_cells_iterator_begin(); } + + All_cells_iterator end() { return b->all_cells_iterator_end(); } + + private: + Bitmap_cubical_complex_base<T>* b; + }; + + All_cells_range all_cells_range() { return All_cells_range(this); } + + /** + * Boundary_range class provides ranges for boundary iterators. + **/ + typedef typename std::vector<std::size_t>::const_iterator Boundary_iterator; + typedef typename std::vector<std::size_t> Boundary_range; + + /** + * boundary_simplex_range creates an object of a Boundary_simplex_range class + * that provides ranges for the Boundary_simplex_iterator. + **/ + Boundary_range boundary_range(std::size_t sh) { return this->get_boundary_of_a_cell(sh); } + + /** + * Coboundary_range class provides ranges for boundary iterators. + **/ + typedef typename std::vector<std::size_t>::const_iterator Coboundary_iterator; + typedef typename std::vector<std::size_t> Coboundary_range; + + /** + * boundary_simplex_range creates an object of a Boundary_simplex_range class + * that provides ranges for the Boundary_simplex_iterator. + **/ + Coboundary_range coboundary_range(std::size_t sh) { return this->get_coboundary_of_a_cell(sh); } + + /** + * @brief Iterator through top dimensional cells of the complex. The cells appear in order they are stored + * in the structure (i.e. in lexicographical order) + **/ + class Top_dimensional_cells_iterator : std::iterator<std::input_iterator_tag, T> { + public: + Top_dimensional_cells_iterator(Bitmap_cubical_complex_base& b) : b(b) { + this->counter = std::vector<std::size_t>(b.dimension()); + // std::fill( this->counter.begin() , this->counter.end() , 0 ); + } + + Top_dimensional_cells_iterator operator++() { + // first find first element of the counter that can be increased: + std::size_t dim = 0; + while ((dim != this->b.dimension()) && (this->counter[dim] == this->b.sizes[dim] - 1)) ++dim; + + if (dim != this->b.dimension()) { + ++this->counter[dim]; + for (std::size_t i = 0; i != dim; ++i) { + this->counter[i] = 0; + } + } else { + ++this->counter[0]; + } + return *this; + } + + Top_dimensional_cells_iterator operator++(int) { + Top_dimensional_cells_iterator result = *this; + ++(*this); + return result; + } + + Top_dimensional_cells_iterator& operator=(const Top_dimensional_cells_iterator& rhs) { + this->counter = rhs.counter; + this->b = rhs.b; + return *this; + } + + bool operator==(const Top_dimensional_cells_iterator& rhs) const { + if (&this->b != &rhs.b) return false; + if (this->counter.size() != rhs.counter.size()) return false; + for (std::size_t i = 0; i != this->counter.size(); ++i) { + if (this->counter[i] != rhs.counter[i]) return false; + } + return true; + } + + bool operator!=(const Top_dimensional_cells_iterator& rhs) const { return !(*this == rhs); } + + /* + * The operator * returns position of a cube in the structure of cubical complex. This position can be then used as + * an argument of the following functions: + * get_boundary_of_a_cell, get_coboundary_of_a_cell, get_dimension_of_a_cell to get information about the cell + * boundary and coboundary and dimension + * and in function get_cell_data to get a filtration of a cell. + */ + std::size_t operator*() { return this->compute_index_in_bitmap(); } + + std::size_t compute_index_in_bitmap() const { + std::size_t index = 0; + for (std::size_t i = 0; i != this->counter.size(); ++i) { + index += (2 * this->counter[i] + 1) * this->b.multipliers[i]; + } + return index; + } + + void print_counter() const { + for (std::size_t i = 0; i != this->counter.size(); ++i) { + std::cout << this->counter[i] << " "; + } + } + friend class Bitmap_cubical_complex_base; + + protected: + std::vector<std::size_t> counter; + Bitmap_cubical_complex_base& b; + }; + + /** + * Function returning a Top_dimensional_cells_iterator to the first top dimensional cell of the bitmap. + **/ + Top_dimensional_cells_iterator top_dimensional_cells_iterator_begin() { + Top_dimensional_cells_iterator a(*this); + return a; + } + + /** + * Function returning a Top_dimensional_cells_iterator to the last top dimensional cell of the bitmap. + **/ + Top_dimensional_cells_iterator top_dimensional_cells_iterator_end() { + Top_dimensional_cells_iterator a(*this); + for (std::size_t i = 0; i != this->dimension(); ++i) { + a.counter[i] = this->sizes[i] - 1; + } + a.counter[0]++; + return a; + } + + /** + * @brief Top_dimensional_cells_iterator_range class provides ranges for Top_dimensional_cells_iterator_range + **/ + class Top_dimensional_cells_range { + public: + Top_dimensional_cells_range(Bitmap_cubical_complex_base* b) : b(b) {} + + Top_dimensional_cells_iterator begin() { return b->top_dimensional_cells_iterator_begin(); } + + Top_dimensional_cells_iterator end() { return b->top_dimensional_cells_iterator_end(); } + + private: + Bitmap_cubical_complex_base<T>* b; + }; + + Top_dimensional_cells_range top_dimensional_cells_range() { return Top_dimensional_cells_range(this); } + + //****************************************************************************************************************// + //****************************************************************************************************************// + //****************************************************************************************************************// + //****************************************************************************************************************// + + inline std::size_t number_cells() const { return this->total_number_of_cells; } + + //****************************************************************************************************************// + //****************************************************************************************************************// + //****************************************************************************************************************// + //****************************************************************************************************************// + + protected: + std::vector<unsigned> sizes; + std::vector<unsigned> multipliers; + std::vector<T> data; + std::size_t total_number_of_cells; + + 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); + multiplier *= 2 * sizes[i] + 1; + } + this->data = std::vector<T>(multiplier, std::numeric_limits<T>::infinity()); + this->total_number_of_cells = multiplier; + } + + std::size_t compute_position_in_bitmap(const std::vector<unsigned>& counter) { + std::size_t position = 0; + for (std::size_t i = 0; i != this->multipliers.size(); ++i) { + position += this->multipliers[i] * counter[i]; + } + return position; + } + + std::vector<unsigned> compute_counter_for_given_cell(std::size_t cell) const { + std::vector<unsigned> counter; + counter.reserve(this->sizes.size()); + for (std::size_t dim = this->sizes.size(); dim != 0; --dim) { + counter.push_back(cell / this->multipliers[dim - 1]); + cell = cell % this->multipliers[dim - 1]; + } + std::reverse(counter.begin(), counter.end()); + return counter; + } + void read_perseus_style_file(const char* perseus_style_file); + void setup_bitmap_based_on_top_dimensional_cells_list(const std::vector<unsigned>& sizes_in_following_directions, + const std::vector<T>& top_dimensional_cells); + Bitmap_cubical_complex_base(const char* perseus_style_file, std::vector<bool> directions); + Bitmap_cubical_complex_base(const std::vector<unsigned>& sizes, std::vector<bool> directions); + Bitmap_cubical_complex_base(const std::vector<unsigned>& dimensions, const std::vector<T>& top_dimensional_cells, + std::vector<bool> directions); +}; + +template <typename T> +void Bitmap_cubical_complex_base<T>::put_data_to_bins(std::size_t number_of_bins) { + bool dbg = false; + + std::pair<T, T> min_max = this->min_max_filtration(); + T dx = (min_max.second - min_max.first) / (T)number_of_bins; + + // now put the data into the appropriate bins: + for (std::size_t i = 0; i != this->data.size(); ++i) { + if (dbg) { + std::cerr << "Before binning : " << this->data[i] << std::endl; + } + this->data[i] = min_max.first + dx * (this->data[i] - min_max.first) / number_of_bins; + if (dbg) { + std::cerr << "After binning : " << this->data[i] << std::endl; + } + } +} + +template <typename T> +void Bitmap_cubical_complex_base<T>::put_data_to_bins(T diameter_of_bin) { + bool dbg = false; + std::pair<T, T> min_max = this->min_max_filtration(); + + std::size_t number_of_bins = (min_max.second - min_max.first) / diameter_of_bin; + // now put the data into the appropriate bins: + for (std::size_t i = 0; i != this->data.size(); ++i) { + if (dbg) { + std::cerr << "Before binning : " << this->data[i] << std::endl; + } + this->data[i] = min_max.first + diameter_of_bin * (this->data[i] - min_max.first) / number_of_bins; + if (dbg) { + std::cerr << "After binning : " << this->data[i] << std::endl; + } + } +} + +template <typename T> +std::pair<T, T> Bitmap_cubical_complex_base<T>::min_max_filtration() { + std::pair<T, T> min_max(std::numeric_limits<T>::infinity(), -std::numeric_limits<T>::infinity()); + for (std::size_t i = 0; i != this->data.size(); ++i) { + if (this->data[i] < min_max.first) min_max.first = this->data[i]; + if (this->data[i] > min_max.second) min_max.second = this->data[i]; + } + return min_max; +} + +template <typename K> +std::ostream& operator<<(std::ostream& out, const Bitmap_cubical_complex_base<K>& b) { + for (typename Bitmap_cubical_complex_base<K>::all_cells_const_iterator it = b.all_cells_const_begin(); + it != b.all_cells_const_end(); ++it) { + out << *it << " "; + } + return out; +} + +template <typename T> +Bitmap_cubical_complex_base<T>::Bitmap_cubical_complex_base(const std::vector<unsigned>& sizes) { + this->set_up_containers(sizes); +} + +template <typename T> +void Bitmap_cubical_complex_base<T>::setup_bitmap_based_on_top_dimensional_cells_list( + const std::vector<unsigned>& sizes_in_following_directions, const std::vector<T>& top_dimensional_cells) { + this->set_up_containers(sizes_in_following_directions); + + std::size_t number_of_top_dimensional_elements = 1; + for (std::size_t i = 0; i != sizes_in_following_directions.size(); ++i) { + number_of_top_dimensional_elements *= sizes_in_following_directions[i]; + } + if (number_of_top_dimensional_elements != top_dimensional_cells.size()) { + std::cerr << "Error in constructor Bitmap_cubical_complex_base ( std::vector<std::size_t> " + << "sizes_in_following_directions, std::vector<T> top_dimensional_cells ). Number of top dimensional " + << "elements that follow from sizes_in_following_directions vector is different than the size of " + << "top_dimensional_cells vector." + << std::endl; + throw( + "Error in constructor Bitmap_cubical_complex_base( std::vector<std::size_t> sizes_in_following_directions," + "std::vector<T> top_dimensional_cells ). Number of top dimensional elements that follow from " + "sizes_in_following_directions vector is different than the size of top_dimensional_cells vector."); + } + + Bitmap_cubical_complex_base<T>::Top_dimensional_cells_iterator it(*this); + std::size_t index = 0; + for (it = this->top_dimensional_cells_iterator_begin(); it != this->top_dimensional_cells_iterator_end(); ++it) { + this->get_cell_data(*it) = top_dimensional_cells[index]; + ++index; + } + this->impose_lower_star_filtration(); +} + +template <typename T> +Bitmap_cubical_complex_base<T>::Bitmap_cubical_complex_base(const std::vector<unsigned>& sizes_in_following_directions, + const std::vector<T>& top_dimensional_cells) { + this->setup_bitmap_based_on_top_dimensional_cells_list(sizes_in_following_directions, top_dimensional_cells); +} + +template <typename T> +void Bitmap_cubical_complex_base<T>::read_perseus_style_file(const char* perseus_style_file) { + bool dbg = false; + std::ifstream inFiltration; + inFiltration.open(perseus_style_file); + unsigned dimensionOfData; + inFiltration >> dimensionOfData; + + if (dbg) { + std::cerr << "dimensionOfData : " << dimensionOfData << std::endl; + } + + std::vector<unsigned> sizes; + sizes.reserve(dimensionOfData); + // all dimensions multiplied + std::size_t dimensions = 1; + for (std::size_t i = 0; i != dimensionOfData; ++i) { + unsigned size_in_this_dimension; + inFiltration >> size_in_this_dimension; + sizes.push_back(size_in_this_dimension); + dimensions *= size_in_this_dimension; + if (dbg) { + std::cerr << "size_in_this_dimension : " << size_in_this_dimension << std::endl; + } + } + this->set_up_containers(sizes); + + Bitmap_cubical_complex_base<T>::Top_dimensional_cells_iterator it(*this); + it = this->top_dimensional_cells_iterator_begin(); + + T filtrationLevel = 0.; + std::size_t filtration_counter = 0; + while (!inFiltration.eof()) { + std::string line; + getline(inFiltration, line); + if (line.length() != 0) { + int n = sscanf(line.c_str(), "%lf", &filtrationLevel); + if (n != 1) { + std::string perseus_error("Bad Perseus file format. This line is incorrect : " + line); + throw std::ios_base::failure(perseus_error.c_str()); + } + + 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; + ++filtration_counter; + } + } + + if (filtration_counter != dimensions) { + std::string perseus_error("Bad Perseus file format. Read " + std::to_string(filtration_counter) + " expected " + \ + std::to_string(dimensions) + " values"); + throw std::ios_base::failure(perseus_error.c_str()); + } + + inFiltration.close(); + this->impose_lower_star_filtration(); +} + +template <typename T> +Bitmap_cubical_complex_base<T>::Bitmap_cubical_complex_base(const char* perseus_style_file, + std::vector<bool> directions) { + // this constructor is here just for compatibility with a class that creates cubical complexes with periodic boundary + // conditions. + // It ignores the last parameter of the function. + this->read_perseus_style_file(perseus_style_file); +} + +template <typename T> +Bitmap_cubical_complex_base<T>::Bitmap_cubical_complex_base(const std::vector<unsigned>& sizes, + std::vector<bool> directions) { + // this constructor is here just for compatibility with a class that creates cubical complexes with periodic boundary + // conditions. + // It ignores the last parameter of the function. + this->set_up_containers(sizes); +} + +template <typename T> +Bitmap_cubical_complex_base<T>::Bitmap_cubical_complex_base(const std::vector<unsigned>& dimensions, + const std::vector<T>& top_dimensional_cells, + std::vector<bool> directions) { + // this constructor is here just for compatibility with a class that creates cubical complexes with periodic boundary + // conditions. + // It ignores the last parameter of the function. + this->setup_bitmap_based_on_top_dimensional_cells_list(dimensions, top_dimensional_cells); +} + +template <typename T> +Bitmap_cubical_complex_base<T>::Bitmap_cubical_complex_base(const char* perseus_style_file) { + this->read_perseus_style_file(perseus_style_file); +} + +template <typename T> +std::vector<std::size_t> Bitmap_cubical_complex_base<T>::get_boundary_of_a_cell(std::size_t cell) const { + std::vector<std::size_t> boundary_elements; + + // Speed traded of for memory. Check if it is better in practice. + boundary_elements.reserve(this->dimension() * 2); + + std::size_t sum_of_dimensions = 0; + std::size_t cell1 = cell; + for (std::size_t i = this->multipliers.size(); i != 0; --i) { + unsigned position = cell1 / this->multipliers[i - 1]; + if (position % 2 == 1) { + 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]); + } + ++sum_of_dimensions; + } + cell1 = cell1 % this->multipliers[i - 1]; + } + + return boundary_elements; +} + +template <typename T> +std::vector<std::size_t> Bitmap_cubical_complex_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 (position % 2 == 0) { + if ((cell > this->multipliers[i - 1]) && (counter[i - 1] != 0)) { + coboundary_elements.push_back(cell - this->multipliers[i - 1]); + } + if ((cell + this->multipliers[i - 1] < this->data.size()) && (counter[i - 1] != 2 * this->sizes[i - 1])) { + coboundary_elements.push_back(cell + this->multipliers[i - 1]); + } + } + cell1 = cell1 % this->multipliers[i - 1]; + } + return coboundary_elements; +} + +template <typename T> +unsigned Bitmap_cubical_complex_base<T>::get_dimension_of_a_cell(std::size_t cell) const { + bool dbg = false; + if (dbg) std::cerr << "\n\n\n Computing position o a cell of an index : " << cell << std::endl; + unsigned dimension = 0; + for (std::size_t i = this->multipliers.size(); i != 0; --i) { + unsigned position = cell / this->multipliers[i - 1]; + + if (dbg) { + std::cerr << "i-1 :" << i - 1 << std::endl; + std::cerr << "cell : " << cell << std::endl; + std::cerr << "position : " << position << std::endl; + std::cerr << "multipliers[" << i - 1 << "] = " << this->multipliers[i - 1] << std::endl; + } + + if (position % 2 == 1) { + if (dbg) std::cerr << "Nonzero length in this direction \n"; + dimension++; + } + cell = cell % this->multipliers[i - 1]; + } + return dimension; +} + +template <typename T> +inline T& Bitmap_cubical_complex_base<T>::get_cell_data(std::size_t cell) { + return this->data[cell]; +} + +template <typename T> +void Bitmap_cubical_complex_base<T>::impose_lower_star_filtration() { + bool dbg = false; + + // this vector will be used to check which elements have already been taken care of in imposing lower star filtration + std::vector<bool> is_this_cell_considered(this->data.size(), false); + + std::size_t size_to_reserve = 1; + for (std::size_t i = 0; i != this->multipliers.size(); ++i) { + size_to_reserve *= (std::size_t)((this->multipliers[i] - 1) / 2); + } + + std::vector<std::size_t> indices_to_consider; + indices_to_consider.reserve(size_to_reserve); + // we assume here that we already have a filtration on the top dimensional cells and + // we have to extend it to lower ones. + typename Bitmap_cubical_complex_base<T>::Top_dimensional_cells_iterator it(*this); + for (it = this->top_dimensional_cells_iterator_begin(); it != this->top_dimensional_cells_iterator_end(); ++it) { + indices_to_consider.push_back(it.compute_index_in_bitmap()); + } + + while (indices_to_consider.size()) { + if (dbg) { + std::cerr << "indices_to_consider in this iteration \n"; + for (std::size_t i = 0; i != indices_to_consider.size(); ++i) { + std::cout << indices_to_consider[i] << " "; + } + } + std::vector<std::size_t> new_indices_to_consider; + for (std::size_t i = 0; i != indices_to_consider.size(); ++i) { + std::vector<std::size_t> bd = this->get_boundary_of_a_cell(indices_to_consider[i]); + for (std::size_t boundaryIt = 0; boundaryIt != bd.size(); ++boundaryIt) { + if (dbg) { + std::cerr << "filtration of a cell : " << bd[boundaryIt] << " is : " << this->data[bd[boundaryIt]] + << " while of a cell: " << indices_to_consider[i] << " is: " << this->data[indices_to_consider[i]] + << std::endl; + } + if (this->data[bd[boundaryIt]] > this->data[indices_to_consider[i]]) { + this->data[bd[boundaryIt]] = this->data[indices_to_consider[i]]; + if (dbg) { + std::cerr << "Setting the value of a cell : " << bd[boundaryIt] + << " to : " << this->data[indices_to_consider[i]] << std::endl; + } + } + if (is_this_cell_considered[bd[boundaryIt]] == false) { + new_indices_to_consider.push_back(bd[boundaryIt]); + is_this_cell_considered[bd[boundaryIt]] = true; + } + } + } + indices_to_consider.swap(new_indices_to_consider); + } +} + +template <typename T> +bool compareFirstElementsOfTuples(const std::pair<std::pair<T, std::size_t>, char>& first, + const std::pair<std::pair<T, std::size_t>, char>& second) { + if (first.first.first < second.first.first) { + return true; + } else { + if (first.first.first > second.first.first) { + return false; + } + // in this case first.first.first == second.first.first, so we need to compare dimensions + return first.second < second.second; + } +} + +} // namespace cubical_complex + +namespace Cubical_complex = cubical_complex; + +} // namespace Gudhi + +#endif // BITMAP_CUBICAL_COMPLEX_BASE_H_ |