diff options
author | pdlotko <pdlotko@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2016-03-14 12:59:53 +0000 |
---|---|---|
committer | pdlotko <pdlotko@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2016-03-14 12:59:53 +0000 |
commit | 5389d8969d8386bb4c74dbef4b7c7992e9130f13 (patch) | |
tree | 25864562808aa410483b482b1944efcbcb6e43b7 /src/Bitmap_cubical_complex | |
parent | ff41ff166c9ea66fcc1187056053e43bf7d7be8f (diff) |
Answers to Marc's comments.
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bitmap@1042 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 481841d609bae68df85a93527e6d3cc20f1b06e2
Diffstat (limited to 'src/Bitmap_cubical_complex')
5 files changed, 288 insertions, 235 deletions
diff --git a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp index 39a55f24..4c30ee85 100644 --- a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp +++ b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp @@ -1,73 +1,73 @@ - /* This file is part of the Gudhi Library. The Gudhi library
- * (Geometric Understanding in Higher Dimensions) is a generic C++
- * library for computational topology.
- *
- * Author(s): Pawel Dlotko
- *
- * Copyright (C) 2015 INRIA Saclay (France)
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-
-
-#include <gudhi/reader_utils.h>
-#include <gudhi/Bitmap_cubical_complex.h>
-#include <gudhi/Persistent_cohomology.h>
-
-
-using namespace Gudhi;
-using namespace Gudhi::Cubical_complex;
-using namespace Gudhi::persistent_cohomology;
-
-//standard stuff
-#include <iostream>
-#include <sstream>
-#include <vector>
-
-using namespace std;
-
-
-int main( int argc , char** argv )
-{
- cout << "This program computes persistent homology, by using bitmap_cubical_complex class, of cubical complexes provided in text files in Perseus style (the only numbered in \
-the first line is a dimension D of a bitmap. In the lines I between 2 and D+1 there are numbers of top dimensional cells in the direction I. Let N denote product \
-of the numbers in the lines between 2 and D. In the lines D+2 to D+2+N there are filtrations of top dimensional cells. We assume that the cells are in the \
-lexicographical order. See CubicalOneSphere.txt or CubicalTwoSphere.txt for example." << endl;
-
- int p = 2;
- double min_persistence = 0;
-
- if ( argc != 2 )
- {
- cout << "Wrong number of parameters. Please provide the name of a file with a Perseus style bitmap at the input. The program will now terminate.\n";
- return 1;
- }
-
- Bitmap_cubical_complex< Bitmap_cubical_complex_base<double> > b( argv[1] );
-
-
- // Compute the persistence diagram of the complex
- persistent_cohomology::Persistent_cohomology< Bitmap_cubical_complex< Bitmap_cubical_complex_base<double> >, Field_Zp > pcoh(b);
- pcoh.init_coefficients( p ); //initilizes the coefficient field for homology
- pcoh.compute_persistent_cohomology( min_persistence );
-
-
- stringstream ss;
- ss << argv[1] << "_persistence";
- std::ofstream out((char*)ss.str().c_str());
- pcoh.output_diagram(out);
- out.close();
-
- return 0;
-}
+ /* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2015 INRIA Saclay (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + + +#include <gudhi/reader_utils.h> +#include <gudhi/Bitmap_cubical_complex_base.h> +#include <gudhi/Bitmap_cubical_complex.h> +#include <gudhi/Persistent_cohomology.h> + + +using namespace Gudhi; +using namespace Gudhi::Cubical_complex; +using namespace Gudhi::persistent_cohomology; + +//standard stuff +#include <iostream> +#include <sstream> +#include <vector> + +using namespace std; + + +int main( int argc , char** argv ) +{ + cout << "This program computes persistent homology, by using bitmap_cubical_complex class, of cubical complexes provided in text files in Perseus style (the only numbered in \ +the first line is a dimension D of a bitmap. In the lines I between 2 and D+1 there are numbers of top dimensional cells in the direction I. Let N denote product \ +of the numbers in the lines between 2 and D. In the lines D+2 to D+2+N there are filtrations of top dimensional cells. We assume that the cells are in the \ +lexicographical order. See CubicalOneSphere.txt or CubicalTwoSphere.txt for example." << endl; + + int p = 2; + double min_persistence = 0; + + if ( argc != 2 ) + { + cout << "Wrong number of parameters. Please provide the name of a file with a Perseus style bitmap at the input. The program will now terminate.\n"; + return 1; + } + + Bitmap_cubical_complex< Bitmap_cubical_complex_base<double> > b( argv[1] ); + + // Compute the persistence diagram of the complex + persistent_cohomology::Persistent_cohomology< Bitmap_cubical_complex< Bitmap_cubical_complex_base<double> >, Field_Zp > pcoh(b); + pcoh.init_coefficients( p ); //initilizes the coefficient field for homology + + pcoh.compute_persistent_cohomology( min_persistence ); + + stringstream ss; + ss << argv[1] << "_persistence"; + std::ofstream out((char*)ss.str().c_str()); + pcoh.output_diagram(out); + out.close(); + + return 0; +} diff --git a/src/Bitmap_cubical_complex/example/CMakeLists.txt b/src/Bitmap_cubical_complex/example/CMakeLists.txt index fbd1b28b..14c94e8e 100644 --- a/src/Bitmap_cubical_complex/example/CMakeLists.txt +++ b/src/Bitmap_cubical_complex/example/CMakeLists.txt @@ -13,5 +13,5 @@ add_test(Random_bitmap_cubical_complex ${CMAKE_CURRENT_BINARY_DIR}/Random_bitmap add_executable ( Bitmap_cubical_complex_periodic_boundary_conditions Bitmap_cubical_complex_periodic_boundary_conditions.cpp ) target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${Boost_SYSTEM_LIBRARY}) -add_executable ( Compute_persistence_with_phat Compute_persistence_with_phat.cpp ) -target_link_libraries(Compute_persistence_with_phat ${Boost_SYSTEM_LIBRARY})
\ No newline at end of file +#add_executable ( Compute_persistence_with_phat Compute_persistence_with_phat.cpp ) +#target_link_libraries(Compute_persistence_with_phat ${Boost_SYSTEM_LIBRARY})
\ No newline at end of file diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h index 70f19e03..4dd295e7 100644 --- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h +++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h @@ -23,6 +23,7 @@ #pragma once #include <limits> +#include <numeric>
#include "Bitmap_cubical_complex_base.h" #include "Bitmap_cubical_complex_periodic_boundary_conditions_base.h" @@ -127,7 +128,12 @@ public: //If the user decide to change some elements of the bitmap, then this procedure need //to be called again. this->initialize_simplex_associated_to_key(); - } + }
+
+ /** + * Destructor of the Bitmap_cubical_complex class. + **/
+ virtual ~Bitmap_cubical_complex(){} //*********************************************// 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 index 22b703a9..807be335 100644 --- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h +++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h @@ -23,13 +23,14 @@ #pragma once #include <iostream> +#include <numeric> #include <string> #include <vector> #include <string> #include <fstream> #include <algorithm> #include <iterator> -#include <limits>
+#include <limits> #include <ctime> #include "Bitmap_cubical_complex/counter.h" @@ -43,7 +44,11 @@ namespace Cubical_complex { - +/** + *@class Bitmap_cubical_complex_base + *@brief Cubical complex represented as a bitmap, class with basic implementation. + *@ingroup cubical_complex + */ /** * This is a class implementing a basic bitmap data structure to store cubical complexes. * It implements only the most basic subroutines. @@ -64,13 +69,13 @@ namespace Cubical_complex template <typename T> class Bitmap_cubical_complex_base { -public:
- typedef T filtration_type;
- /**
- *Default constructor
- **/
- Bitmap_cubical_complex_base()
- {
+public: + typedef T filtration_type; + /** + *Default constructor + **/ + Bitmap_cubical_complex_base() + { } /** * There are a few constructors of a Bitmap_cubical_complex_base class. @@ -93,6 +98,11 @@ public: 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 @@ -152,18 +162,27 @@ public: * Writing to stream operator. **/ template <typename K> - friend ostream& operator << ( ostream & os , const Bitmap_cubical_complex_base<K>& b );
-
-
+ friend ostream& operator << ( ostream & os , const Bitmap_cubical_complex_base<K>& b ); + + /** - * Functions that put the input data to bins. + * Function that put the input data to bins. 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_toBins( size_t number_of_bins ) + * ais 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_toBins( size_t number_of_bins ); - void put_data_toBins( T diameter_of_bin );
-
+ + /** + * Function that put the input data to bins. 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_toBins( 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_toBins( T diameter_of_bin ); + /** * Functions to find min and max values of filtration. - **/
+ **/ std::pair< T ,T > min_max_filtration(); //ITERATORS @@ -172,42 +191,60 @@ public: * Iterator through all cells in the complex (in order they appear in the structure -- i.e. * in lexicographical order). **/ - typedef typename std::vector< T >::iterator all_cells_iterator;
-
+ typedef typename std::vector< T >::iterator all_cells_iterator; + + /** - * Function returning an iterator to the first cell of the bitmap. + * Constant iterator through all cells in the complex (in order they appear in the structure -- i.e. + * in lexicographical order). **/ - all_cells_iterator all_cells_begin() + typedef typename std::vector< T >::const_iterator all_cells_const_iterator; + + /** + * Function returning a constant iterator to the first cell of the bitmap. + **/ + all_cells_const_iterator all_cells_const_begin()const { return this->data.begin(); - }
-
- /** - * Function returning an iterator to the last cell of the bitmap. + } + + + /** + * Function returning a constant iterator to the last cell of the bitmap. **/ - all_cells_iterator all_cells_end()const + all_cells_const_iterator all_cells_const_end()const { return this->data.end(); } /** - * Constant iterator through all cells in the complex (in order they appear in the structure -- i.e. - * in lexicographical order). + * Function returning an iterator to the first cell of the bitmap. **/ - typedef typename std::vector< T >::const_iterator all_cells_const_iterator;
-
+ all_cells_iterator all_cells_begin() + { + return this->data.begin(); + } + /** * Function returning a constant iterator to the first cell of the bitmap. **/ - all_cells_const_iterator all_cells_const_begin()const + all_cells_const_iterator all_cells_begin() const { return this->data.begin(); - }
-
+ } + + /** + * Function returning an iterator to the last cell of the bitmap. + **/ + all_cells_iterator all_cells_end() + { + return this->data.end(); + } + /** * Function returning a constant iterator to the last cell of the bitmap. **/ - all_cells_const_iterator all_cells_const_end()const + all_cells_const_iterator all_cells_end() const { return this->data.end(); } @@ -303,8 +340,8 @@ public: protected: std::vector< size_t > counter; Bitmap_cubical_complex_base& b; - };
-
+ }; + /** * Function returning a Top_dimensional_cells_iterator to the first top dimensional cell cell of the bitmap. **/ @@ -312,8 +349,8 @@ public: { Top_dimensional_cells_iterator a(*this); return a; - }
-
+ } + /** * Function returning a Top_dimensional_cells_iterator to the last top dimensional cell cell of the bitmap. **/ @@ -333,11 +370,11 @@ public: //****************************************************************************************************************// //****************************************************************************************************************// //****************************************************************************************************************// -
-
-inline size_t number_cells()const
-{
- return this->total_number_of_cells;
+ + +inline size_t number_cells()const +{ + return this->total_number_of_cells; } //****************************************************************************************************************// @@ -375,7 +412,7 @@ protected: std::vector<unsigned> compute_counter_for_given_cell( size_t cell )const { - std::vector<unsigned> counter;
+ std::vector<unsigned> counter; counter.reserve( this->sizes.size() ); for ( size_t dim = this->sizes.size() ; dim != 0 ; --dim ) { @@ -384,59 +421,59 @@ protected: } 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 );
+ } + 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_toBins( size_t number_of_bins )
-{
- bool bdg = 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 ( size_t i = 0 ; i != this->data.size() ; ++i )
- {
- if ( bdg ){cerr << "Before binning : " << this->data[i] << endl;}
- this->data[i] = min_max.first + dx*(this->data[i]-min_max.first)/number_of_bins;
- if ( bdg ){cerr << "After binning : " << this->data[i] << endl;getchar();}
- }
-}
-
template <typename T> -void Bitmap_cubical_complex_base<T>::put_data_toBins( T diameter_of_bin )
-{
- bool bdg = false;
- std::pair< T ,T > min_max = this->min_max_filtration();
-
- size_t number_of_bins = (min_max.second - min_max.first)/diameter_of_bin;
- //now put the data into the appropriate bins:
- for ( size_t i = 0 ; i != this->data.size() ; ++i )
- {
- if ( bdg ){cerr << "Before binning : " << this->data[i] << endl;}
- this->data[i] = min_max.first + diameter_of_bin*(this->data[i]-min_max.first)/number_of_bins;
- if ( bdg ){cerr << "After binning : " << this->data[i] << endl;getchar();}
- }
-}
-
-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>::max() , std::numeric_limits<T>::min() );
- for ( 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;
-}
+void Bitmap_cubical_complex_base<T>::put_data_toBins( size_t number_of_bins ) +{ + bool bdg = 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 ( size_t i = 0 ; i != this->data.size() ; ++i ) + { + if ( bdg ){cerr << "Before binning : " << this->data[i] << endl;} + this->data[i] = min_max.first + dx*(this->data[i]-min_max.first)/number_of_bins; + if ( bdg ){cerr << "After binning : " << this->data[i] << endl;getchar();} + } +} + +template <typename T> +void Bitmap_cubical_complex_base<T>::put_data_toBins( T diameter_of_bin ) +{ + bool bdg = false; + std::pair< T ,T > min_max = this->min_max_filtration(); + + size_t number_of_bins = (min_max.second - min_max.first)/diameter_of_bin; + //now put the data into the appropriate bins: + for ( size_t i = 0 ; i != this->data.size() ; ++i ) + { + if ( bdg ){cerr << "Before binning : " << this->data[i] << endl;} + this->data[i] = min_max.first + diameter_of_bin*(this->data[i]-min_max.first)/number_of_bins; + if ( bdg ){cerr << "After binning : " << this->data[i] << endl;getchar();} + } +} + +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>::max() , std::numeric_limits<T>::min() ); + for ( 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> @@ -457,10 +494,10 @@ Bitmap_cubical_complex_base<T>::Bitmap_cubical_complex_base { 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)
-{
+ +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 ); size_t number_of_top_dimensional_elements = 1; @@ -489,19 +526,19 @@ void Bitmap_cubical_complex_base<T>::setup_bitmap_based_on_top_dimensional_cells (*it) = top_dimensional_cells[index]; ++index; } - this->impose_lower_star_filtration();
-}
+ 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 )
-{
+} + +template <typename T> +void Bitmap_cubical_complex_base<T>::read_perseus_style_file( const char* perseus_style_file ) +{ bool dbg = false; ifstream inFiltration, inIds; inFiltration.open( perseus_style_file ); @@ -510,7 +547,7 @@ void Bitmap_cubical_complex_base<T>::read_perseus_style_file( const char* perseu if (dbg){cerr << "dimensionOfData : " << dimensionOfData << endl;getchar();} - std::vector<unsigned> sizes;
+ std::vector<unsigned> sizes; sizes.reserve( dimensionOfData ); for ( size_t i = 0 ; i != dimensionOfData ; ++i ) { @@ -541,31 +578,31 @@ void Bitmap_cubical_complex_base<T>::read_perseus_style_file( const char* perseu ++it; } 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 bundary 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 bundary conditions.
- //It ignores the last parameter of the function.
- this->set_up_containers( sizes );
-}
-
-template <typename T>
+ 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 bundary 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 bundary 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 bundary conditions.
- //It ignores the last parameter of the function.
- this->setup_bitmap_based_on_top_dimensional_cells_list( dimensions , top_dimensional_cells );
+{ + //this constructor is here just for compatibility with a class that creates cubical complexes with periodic bundary 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> @@ -578,29 +615,29 @@ Bitmap_cubical_complex_base<T>::Bitmap_cubical_complex_base( const char* perseus template <typename T> std::vector< size_t > Bitmap_cubical_complex_base<T>::get_boundary_of_a_cell( size_t cell )const { - std::vector< size_t > boundary_elements;
-
- //Speed traded of for memory. Check if it is better in practice.
- boundary_elements.reserve( this->dimension()*2 );
+ std::vector< size_t > boundary_elements; + + //Speed traded of for memory. Check if it is better in practice. + boundary_elements.reserve( this->dimension()*2 ); size_t cell1 = cell; for ( size_t i = this->multipliers.size() ; i != 0 ; --i ) { unsigned position = cell1/this->multipliers[i-1]; if ( position%2 == 1 ) - {
- boundary_elements.push_back( cell - this->multipliers[ i-1 ] );
+ { + boundary_elements.push_back( cell - this->multipliers[ i-1 ] ); boundary_elements.push_back( cell + this->multipliers[ i-1 ] ); } cell1 = cell1%this->multipliers[i-1]; } return boundary_elements; -}
+} + + + -
-
-
template <typename T> std::vector< size_t > Bitmap_cubical_complex_base<T>::get_coboundary_of_a_cell( size_t cell )const { @@ -625,8 +662,8 @@ std::vector< size_t > Bitmap_cubical_complex_base<T>::get_coboundary_of_a_cell( cell1 = cell1%this->multipliers[i-1]; } return coboundary_elements; -}
-
+} + @@ -675,14 +712,14 @@ void Bitmap_cubical_complex_base<T>::impose_lower_star_filtration() //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 ); -
- size_t size_to_reserve = 1;
- for ( size_t i = 0 ; i != this->multipliers.size() ; ++i )
- {
- size_to_reserve *= (size_t)((this->multipliers[i]-1)/2);
- }
- - std::vector<size_t> indices_to_consider;
+ + size_t size_to_reserve = 1; + for ( size_t i = 0 ; i != this->multipliers.size() ; ++i ) + { + size_to_reserve *= (size_t)((this->multipliers[i]-1)/2); + } + + std::vector<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. @@ -708,20 +745,20 @@ void Bitmap_cubical_complex_base<T>::impose_lower_star_filtration() { std::vector<size_t> bd = this->get_boundary_of_a_cell( indices_to_consider[i] ); for ( size_t boundaryIt = 0 ; boundaryIt != bd.size() ; ++boundaryIt ) - {
- if ( dbg )
- {
- 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] ] << endl;
- getchar();
-
+ { + if ( dbg ) + { + 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] ] << endl; + getchar(); + } if ( this->data[ bd[boundaryIt] ] > this->data[ indices_to_consider[i] ] ) { - this->data[ bd[boundaryIt] ] = this->data[ indices_to_consider[i] ];
- if ( dbg )
- {
- cerr << "Setting the value of a cell : " << bd[boundaryIt] << " to : " << this->data[ indices_to_consider[i] ] << endl;
- getchar();
+ this->data[ bd[boundaryIt] ] = this->data[ indices_to_consider[i] ]; + if ( dbg ) + { + cerr << "Setting the value of a cell : " << bd[boundaryIt] << " to : " << this->data[ indices_to_consider[i] ] << endl; + getchar(); } } if ( is_this_cell_considered[ bd[boundaryIt] ] == false ) @@ -760,4 +797,4 @@ bool compareFirstElementsOfTuples( const std::pair< std::pair< T , size_t > , ch } -}
+} diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h index f0fd785f..8c1254db 100644 --- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h +++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h @@ -38,6 +38,11 @@ namespace Cubical_complex /** + *@class Bitmap_cubical_complex_periodic_boundary_conditions_base + *@brief Cubical complex with periodic boundary conditions represented as a bitmap. + *@ingroup cubical_complex + */
+/** * 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. */
@@ -64,6 +69,11 @@ public: */
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. |