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/* 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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