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Diffstat (limited to 'src/Bitmap_cubical_complex/include/gudhi/Compute_persistence_with_phat.h')
| -rw-r--r-- | src/Bitmap_cubical_complex/include/gudhi/Compute_persistence_with_phat.h | 242 |
1 files changed, 0 insertions, 242 deletions
diff --git a/src/Bitmap_cubical_complex/include/gudhi/Compute_persistence_with_phat.h b/src/Bitmap_cubical_complex/include/gudhi/Compute_persistence_with_phat.h deleted file mode 100644 index 9f4ada45..00000000 --- a/src/Bitmap_cubical_complex/include/gudhi/Compute_persistence_with_phat.h +++ /dev/null @@ -1,242 +0,0 @@ -/* 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 Sophia-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/>. - */ -
-#pragma once
-
-
-#include "phat/compute_persistence_pairs.h"
-#include "phat/representations/vector_vector.h"
-#include "phat/algorithms/standard_reduction.h"
-#include "phat/algorithms/chunk_reduction.h"
-#include "phat/algorithms/row_reduction.h"
-#include "phat/algorithms/twist_reduction.h"
-
-
-namespace Gudhi -{ -
-
-//the only aim of this class is to have a ability to compute persistence with phat.
-template <typename K>
-void writeBettiNumbersAndPersistenceIntervalsToFile( char* prefix , std::pair< std::vector<std::vector< K > > , std::vector< std::vector< std::pair<K,K> > > > resutsFromPhat )
-{
- std::ostringstream filenameStr;
- filenameStr << prefix << "_bettiNumbers";
- std::string str = filenameStr.str();
- const char* filename = str.c_str();
- ofstream out;
- out.open( filename );
- for ( size_t dim = 0 ; dim != resutsFromPhat.first.size() ; ++dim )
- {
- out << "Dimension : " << dim << endl;
- for ( size_t i = 0 ; i != resutsFromPhat.first[dim].size() ; ++i )
- {
- out << resutsFromPhat.first[dim][i] << endl;
- }
- out << endl;
- }
- out.close();
-
-
- cerr << "Write persistence to file \n";
- for ( size_t dim = 0 ; dim != resutsFromPhat.second.size() ; ++dim )
- {
- cerr << "resutsFromPhat.second[dim].size() : " << resutsFromPhat.second[dim].size() << endl;
- if ( resutsFromPhat.second[dim].size() == 0 )continue;
- std::ostringstream filenameStr;
- filenameStr << prefix << "_persistence_" << dim;
- std::string str = filenameStr.str();
- const char* filename = str.c_str();
- ofstream out1;
- out1.open( filename );
- for ( size_t i = 0 ; i != resutsFromPhat.second[dim].size() ; ++i )
- {
- out1 << resutsFromPhat.second[dim][i].first << " " << resutsFromPhat.second[dim][i].second << endl;
- }
- out1.close();
- }
-}//writeBettiNumbersAndPersistenceIntervalsToFile
-
-
-template <typename T , typename K>
-class Compute_persistence_with_phat
-{
-public:
- Compute_persistence_with_phat( T* data_structure_ );
- std::pair< std::vector< std::vector<K> > , std::vector< std::vector< std::pair<K,K> > > > get_the_intervals( phat::persistence_pairs pairs );
-
- phat::persistence_pairs compute_persistence_pairs_dualized_chunk_reduction();
- phat::persistence_pairs compute_persistence_pairs_twist_reduction();
- phat::persistence_pairs compute_persistence_pairs_standard_reduction();
- //phat::persistence_pairs compute_persistence_pairs_spectral_sequence_reduction();
-private:
- void print_bd_matrix();
- phat::boundary_matrix< phat::vector_vector > boundary_matrix;
- T* data_structure;
-};
-
-template <typename T , typename K>
-void Compute_persistence_with_phat<T,K>::print_bd_matrix()
-{
- std::cout << "The boundary matrix has " << this->boundary_matrix.get_num_cols() << " columns: " << std::endl;
- for( phat::index col_idx = 0; col_idx < this->boundary_matrix.get_num_cols(); col_idx++ ) {
- std::cout << "Colum " << col_idx << " represents a cell of dimension " << (int)this->boundary_matrix.get_dim( col_idx ) << ". ";
- if( !this->boundary_matrix.is_empty( col_idx ) ) {
- std::vector< phat::index > temp_col;
- this->boundary_matrix.get_col( col_idx, temp_col );
- std::cout << "Its boundary consists of the cells";
- for( phat::index idx = 0; idx < (phat::index)temp_col.size(); idx++ )
- std::cout << " " << temp_col[ idx ];
- }
- std::cout << std::endl;
- }
-}
-
-template <typename T , typename K>
-phat::persistence_pairs Compute_persistence_with_phat<T,K>::compute_persistence_pairs_dualized_chunk_reduction()
-{
- phat::persistence_pairs pairs;
- phat::compute_persistence_pairs_dualized< phat::chunk_reduction >( pairs, this->boundary_matrix );
- return pairs;
-}
-
-template <typename T , typename K>
-phat::persistence_pairs Compute_persistence_with_phat<T,K>::compute_persistence_pairs_twist_reduction()
-{
- phat::persistence_pairs pairs;
- phat::compute_persistence_pairs< phat::twist_reduction >( pairs, this->boundary_matrix );
- return pairs;
-}
-
-template <typename T , typename K>
-phat::persistence_pairs Compute_persistence_with_phat<T,K>::compute_persistence_pairs_standard_reduction()
-{
- phat::persistence_pairs pairs;
- phat::compute_persistence_pairs< phat::standard_reduction >( pairs, this->boundary_matrix );
- return pairs;
-}
-
-//template <typename T , typename K>
-//phat::persistence_pairs Compute_persistence_with_phat<T,K>::compute_persistence_pairs_spectral_sequence_reduction()
-//{
-// phat::persistence_pairs pairs;
-// phat::compute_persistence_pairs< phat::spectral_sequence_reduction >( pairs, this->boundary_matrix );
-// return pairs;
-//}
-
-template <typename T , typename K>
-Compute_persistence_with_phat<T,K>::Compute_persistence_with_phat( T* data_structure_ ):data_structure( data_structure_ )
-{
- bool dbg = false;
- this->boundary_matrix.set_num_cols( this->data_structure->num_simplices() );
-
- //setting up the dimensions of cells:
- for ( size_t i = 0 ; i != this->data_structure->num_simplices() ; ++i )
- {
- this->boundary_matrix.set_dim( i, this->data_structure->dimension( this->data_structure->simplex(i) ) );
- }
-
-
- //now it is time to set up the boundary matrix:
- typename T::Filtration_simplex_range range = this->data_structure->filtration_simplex_range();
- std::vector< phat::index > temp_col;
- for ( typename T::Filtration_simplex_iterator it = range.begin() ; it != range.end() ; ++it )
- {
- typename T::Boundary_simplex_range boundary_range = this->data_structure->boundary_simplex_range( *it );
- for ( typename T::Boundary_simplex_iterator bd = boundary_range.begin() ; bd != boundary_range.end() ; ++bd )
- {
- temp_col.push_back( this->data_structure->key( *bd ) );
- }
- //we do not know if the boundary elements are sorted according to filtration, that is why I am enforcing it here:
- this->boundary_matrix.set_col( this->data_structure->key( *it ) , temp_col );
- temp_col.clear();
- }
-}
-
-template <typename T , typename K>
-std::pair< std::vector< std::vector<K> > , std::vector< std::vector< std::pair<K,K> > > > Compute_persistence_with_phat<T,K>::get_the_intervals( phat::persistence_pairs pairs )
-{
- bool dbg = false;
- //in order to find the birth times of the infinite homology classes, we need to know which elements are not paired. To search for them, we will use this vector:
- std::vector<bool> isTheElementPaired( this->data_structure->num_simplices() , false );
-
- //now it is time to recover the finite persistence pairs and the Betti numbers:
- std::vector< std::vector< std::pair<K,K> > > finitePersistencePairs( this->data_structure->dimension() );
- for( phat::index idx = 0; idx < pairs.get_num_pairs(); idx++ )
- {
- typename T::Simplex_key positionOfBeginOfInterval = pairs.get_pair( idx ).first;
- typename T::Simplex_key positionOfEndOfInterval = pairs.get_pair( idx ).second;
-
- typename T::Simplex_handle first_simplex = this->data_structure->simplex(positionOfBeginOfInterval);
- typename T::Simplex_handle second_simplex = this->data_structure->simplex(positionOfEndOfInterval);
-
- typename T::Filtration_value valueFirst = this->data_structure->filtration( first_simplex );
- typename T::Filtration_value valueSecond = this->data_structure->filtration( second_simplex );
-
- if ( valueFirst > valueSecond ){std::swap( valueFirst , valueSecond );}
-
- unsigned dimFirst = this->data_structure->dimension(first_simplex);
- unsigned dimSecond = this->data_structure->dimension(second_simplex);
- unsigned dim = std::min( dimFirst , dimSecond );
-
-
- //we are ignoring trivial barcodes
- if ( valueFirst != valueSecond )
- {
- finitePersistencePairs[ dim ].push_back( std::make_pair(valueFirst , valueSecond) );
- if ( dbg ){cerr << "Adding barcode : " << valueFirst << "," << valueSecond << endl;}
- }
-
- //isTheElementPaired[ positionOfBeginOfIntervalInBitmap ] = true;
- //isTheElementPaired[ positionOfEndOfIntervalInBitmap ] = true;
- isTheElementPaired[ pairs.get_pair( idx ).first ] = true;
- isTheElementPaired[ pairs.get_pair( idx ).second ] = true;
- }
-
-
- std::vector< std::vector<K> > birthTimesOfInfinitePersistnceClasses(this->data_structure->dimension()+1 );
- for ( size_t i = 0 ; i != this->data_structure->dimension()+1 ; ++i )
- {
- std::vector<K> v;
- birthTimesOfInfinitePersistnceClasses[i] = v;
- }
- for ( size_t i = 0 ; i != isTheElementPaired.size() ; ++i )
- {
- if ( isTheElementPaired[i] == false )
- {
- //i-th element is not paired, therefore it gives an infinite class
- typename T::Simplex_handle simplex = this->data_structure->simplex(i);
- birthTimesOfInfinitePersistnceClasses[ this->data_structure->dimension( simplex ) ].push_back( this->data_structure->filtration(simplex) );
- }
- }
-
- //sorting finite persistence pairs:
- for ( size_t dim = 0 ; dim != finitePersistencePairs.size() ; ++dim )
- {
- std::sort( finitePersistencePairs[dim].begin() , finitePersistencePairs[dim].end() );
- }
- return std::make_pair( birthTimesOfInfinitePersistnceClasses , finitePersistencePairs );
-}//Compute_persistence_with_phat
-
-
-
-}//namespace Gudhi
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