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Diffstat (limited to 'src/Persistence_representations/include/gudhi/PSSK.h')
| -rw-r--r-- | src/Persistence_representations/include/gudhi/PSSK.h | 257 |
1 files changed, 120 insertions, 137 deletions
diff --git a/src/Persistence_representations/include/gudhi/PSSK.h b/src/Persistence_representations/include/gudhi/PSSK.h index 42baa8ec..ece7e323 100644 --- a/src/Persistence_representations/include/gudhi/PSSK.h +++ b/src/Persistence_representations/include/gudhi/PSSK.h @@ -23,158 +23,141 @@ #ifndef PSSK_H_ #define PSSK_H_ -//gudhi include +// gudhi include #include <gudhi/Persistence_heat_maps.h> - -namespace Gudhi -{ -namespace Persistence_representations -{ +namespace Gudhi { +namespace Persistence_representations { /** * This is a version of a representation presented in https://arxiv.org/abs/1412.6821 -* In that paper the authors are using the representation just to compute kernel. Over here, we extend the usability by far. +* In that paper the authors are using the representation just to compute kernel. Over here, we extend the usability by +*far. * Note that the version presented here is not exact, since we are discretizing the kernel. -* The only difference with respect to the original class is the method of creation. We have full (square) image, and for every point (p,q), we add a kernel at (p,q) and the negative kernel +* The only difference with respect to the original class is the method of creation. We have full (square) image, and for +*every point (p,q), we add a kernel at (p,q) and the negative kernel * at (q,p) **/ -class PSSK : public Persistence_heat_maps<constant_scaling_function> -{ -public: - PSSK():Persistence_heat_maps(){} - - PSSK(const std::vector< std::pair< double,double > > & interval , std::vector< std::vector<double> > filter = create_Gaussian_filter(5,1) , size_t number_of_pixels = 1000 , double min_ = -1 , double max_ = -1 ) - :Persistence_heat_maps() - { - this->construct( interval , filter , number_of_pixels , min_ , max_ ); - } - - - PSSK( const char* filename , std::vector< std::vector<double> > filter = create_Gaussian_filter(5,1) , size_t number_of_pixels = 1000 , double min_ = -1 , double max_ = -1 , unsigned dimension = std::numeric_limits<unsigned>::max() ): - Persistence_heat_maps() - { - std::vector< std::pair< double , double > > intervals_; - if ( dimension == std::numeric_limits<unsigned>::max() ) - { - intervals_ = read_persistence_intervals_in_one_dimension_from_file( filename ); - } - else - { - intervals_ = read_persistence_intervals_in_one_dimension_from_file( filename , dimension ); - } - this->construct( intervals_ , filter , number_of_pixels , min_ , max_ ); - } - -protected: - void construct( const std::vector< std::pair<double,double> >& intervals_ , - std::vector< std::vector<double> > filter = create_Gaussian_filter(5,1), - size_t number_of_pixels = 1000 , double min_ = -1 , double max_ = -1 ); -}; - -//if min_ == max_, then the program is requested to set up the values itself based on persistence intervals -void PSSK::construct( const std::vector< std::pair<double,double> >& intervals_ , - std::vector< std::vector<double> > filter, - size_t number_of_pixels , double min_ , double max_ ) -{ - bool dbg = false; - if ( dbg ){std::cerr << "Entering construct procedure \n";getchar();} - - if ( min_ == max_ ) - { - //in this case, we want the program to set up the min_ and max_ values by itself. - min_ = std::numeric_limits<int>::max(); - max_ = -std::numeric_limits<int>::max(); - - - for ( size_t i = 0 ; i != intervals_.size() ; ++i ) - { - if ( intervals_[i].first < min_ )min_ = intervals_[i].first; - if ( intervals_[i].second > max_ )max_ = intervals_[i].second; - } - //now we have the structure filled in, and moreover we know min_ and max_ values of the interval, so we know the range. - - //add some more space: - min_ -= fabs(max_ - min_)/100; - max_ += fabs(max_ - min_)/100; +class PSSK : public Persistence_heat_maps<constant_scaling_function> { + public: + PSSK() : Persistence_heat_maps() {} + + PSSK(const std::vector<std::pair<double, double> >& interval, + std::vector<std::vector<double> > filter = create_Gaussian_filter(5, 1), size_t number_of_pixels = 1000, + double min_ = -1, double max_ = -1) + : Persistence_heat_maps() { + this->construct(interval, filter, number_of_pixels, min_, max_); + } + + PSSK(const char* filename, std::vector<std::vector<double> > filter = create_Gaussian_filter(5, 1), + size_t number_of_pixels = 1000, double min_ = -1, double max_ = -1, + unsigned dimension = std::numeric_limits<unsigned>::max()) + : Persistence_heat_maps() { + std::vector<std::pair<double, double> > intervals_; + if (dimension == std::numeric_limits<unsigned>::max()) { + intervals_ = read_persistence_intervals_in_one_dimension_from_file(filename); + } else { + intervals_ = read_persistence_intervals_in_one_dimension_from_file(filename, dimension); } + this->construct(intervals_, filter, number_of_pixels, min_, max_); + } - if ( dbg ) - { - std::cerr << "min_ : " << min_ << std::endl; - std::cerr << "max_ : " << max_ << std::endl; - std::cerr << "number_of_pixels : " << number_of_pixels << std::endl; - getchar(); - } - - this->min_ = min_; - this->max_ = max_; + protected: + void construct(const std::vector<std::pair<double, double> >& intervals_, + std::vector<std::vector<double> > filter = create_Gaussian_filter(5, 1), + size_t number_of_pixels = 1000, double min_ = -1, double max_ = -1); +}; +// if min_ == max_, then the program is requested to set up the values itself based on persistence intervals +void PSSK::construct(const std::vector<std::pair<double, double> >& intervals_, + std::vector<std::vector<double> > filter, size_t number_of_pixels, double min_, double max_) { + bool dbg = false; + if (dbg) { + std::cerr << "Entering construct procedure \n"; + getchar(); + } + + if (min_ == max_) { + // in this case, we want the program to set up the min_ and max_ values by itself. + min_ = std::numeric_limits<int>::max(); + max_ = -std::numeric_limits<int>::max(); + + for (size_t i = 0; i != intervals_.size(); ++i) { + if (intervals_[i].first < min_) min_ = intervals_[i].first; + if (intervals_[i].second > max_) max_ = intervals_[i].second; + } + // now we have the structure filled in, and moreover we know min_ and max_ values of the interval, so we know the + // range. + + // add some more space: + min_ -= fabs(max_ - min_) / 100; + max_ += fabs(max_ - min_) / 100; + } + + if (dbg) { + std::cerr << "min_ : " << min_ << std::endl; + std::cerr << "max_ : " << max_ << std::endl; + std::cerr << "number_of_pixels : " << number_of_pixels << std::endl; + getchar(); + } + + this->min_ = min_; + this->max_ = max_; + + // initialization of the structure heat_map + std::vector<std::vector<double> > heat_map_; + for (size_t i = 0; i != number_of_pixels; ++i) { + std::vector<double> v(number_of_pixels, 0); + heat_map_.push_back(v); + } + this->heat_map = heat_map_; + + if (dbg) std::cerr << "Done creating of the heat map, now we will fill in the structure \n"; + + for (size_t pt_nr = 0; pt_nr != intervals_.size(); ++pt_nr) { + // compute the value of intervals_[pt_nr] in the grid: + int x_grid = (int)((intervals_[pt_nr].first - this->min_) / (this->max_ - this->min_) * number_of_pixels); + int y_grid = (int)((intervals_[pt_nr].second - this->min_) / (this->max_ - this->min_) * number_of_pixels); + + if (dbg) { + std::cerr << "point : " << intervals_[pt_nr].first << " , " << intervals_[pt_nr].second << std::endl; + std::cerr << "x_grid : " << x_grid << std::endl; + std::cerr << "y_grid : " << y_grid << std::endl; + } + // x_grid and y_grid gives a center of the kernel. We want to have its lower left corner. To get this, we need to + // shift x_grid and y_grid by a grid diameter. + x_grid -= filter.size() / 2; + y_grid -= filter.size() / 2; + // note that the numbers x_grid and y_grid may be negative. + + if (dbg) { + std::cerr << "After shift : \n"; + ; + std::cerr << "x_grid : " << x_grid << std::endl; + std::cerr << "y_grid : " << y_grid << std::endl; + std::cerr << "filter.size() : " << filter.size() << std::endl; + getchar(); + } - //initialization of the structure heat_map - std::vector< std::vector<double> > heat_map_; - for ( size_t i = 0 ; i != number_of_pixels ; ++i ) - { - std::vector<double> v( number_of_pixels , 0 ); - heat_map_.push_back( v ); + for (size_t i = 0; i != filter.size(); ++i) { + for (size_t j = 0; j != filter.size(); ++j) { + // if the point (x_grid+i,y_grid+j) is the correct point in the grid. + if (((x_grid + i) >= 0) && (x_grid + i < this->heat_map.size()) && ((y_grid + j) >= 0) && + (y_grid + j < this->heat_map.size())) { + if (dbg) { + std::cerr << y_grid + j << " " << x_grid + i << std::endl; + } + this->heat_map[y_grid + j][x_grid + i] += filter[i][j]; + this->heat_map[x_grid + i][y_grid + j] += -filter[i][j]; + } + } } - this->heat_map = heat_map_; - - if (dbg)std::cerr << "Done creating of the heat map, now we will fill in the structure \n"; - - for ( size_t pt_nr = 0 ; pt_nr != intervals_.size() ; ++pt_nr ) - { - //compute the value of intervals_[pt_nr] in the grid: - int x_grid = (int)((intervals_[pt_nr].first - this->min_)/( this->max_-this->min_ )*number_of_pixels); - int y_grid = (int)((intervals_[pt_nr].second - this->min_)/( this->max_-this->min_ )*number_of_pixels); - - if ( dbg ) - { - std::cerr << "point : " << intervals_[pt_nr].first << " , " << intervals_[pt_nr].second << std::endl; - std::cerr << "x_grid : " << x_grid << std::endl; - std::cerr << "y_grid : " << y_grid << std::endl; - } - - //x_grid and y_grid gives a center of the kernel. We want to have its lower left corner. To get this, we need to shift x_grid and y_grid by a grid diameter. - x_grid -= filter.size()/2; - y_grid -= filter.size()/2; - //note that the numbers x_grid and y_grid may be negative. - - if ( dbg ) - { - std::cerr << "After shift : \n";; - std::cerr << "x_grid : " << x_grid << std::endl; - std::cerr << "y_grid : " << y_grid << std::endl; - std::cerr << "filter.size() : " << filter.size() << std::endl; - getchar(); - } - - - for ( size_t i = 0 ; i != filter.size() ; ++i ) - { - for ( size_t j = 0 ; j != filter.size() ; ++j ) - { - //if the point (x_grid+i,y_grid+j) is the correct point in the grid. - if ( - ((x_grid+i)>=0) && (x_grid+i<this->heat_map.size()) - && - ((y_grid+j)>=0) && (y_grid+j<this->heat_map.size()) - ) - { - if ( dbg ){std::cerr << y_grid+j << " " << x_grid+i << std::endl;} - this->heat_map[ y_grid+j ][ x_grid+i ] += filter[i][j]; - this->heat_map[ x_grid+i ][ y_grid+j ] += -filter[i][j]; - } - } - } - - } -}//construct - -} //namespace Persistence_representations -} //namespace Gudhi + } +} // construct +} // namespace Persistence_representations +} // namespace Gudhi #endif // PSSK_H_ |