diff options
Diffstat (limited to 'src/Persistence_representations/include')
9 files changed, 228 insertions, 535 deletions
diff --git a/src/Persistence_representations/include/gudhi/PSSK.h b/src/Persistence_representations/include/gudhi/PSSK.h index bd142c02..42baa8ec 100644 --- a/src/Persistence_representations/include/gudhi/PSSK.h +++ b/src/Persistence_representations/include/gudhi/PSSK.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2017 INRIA (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 @@ -20,9 +20,8 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#pragma once -#ifndef PSSK_H -#define PSSK_H +#ifndef PSSK_H_ +#define PSSK_H_ //gudhi include #include <gudhi/Persistence_heat_maps.h> @@ -138,7 +137,7 @@ void PSSK::construct( const std::vector< std::pair<double,double> >& intervals_ 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 cordner. To get this, we need to shift x_grid and y_grid by a grid diameter. + //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. @@ -174,8 +173,8 @@ void PSSK::construct( const std::vector< std::pair<double,double> >& intervals_ } }//construct +} //namespace Persistence_representations +} //namespace Gudhi -#endif -}//namespace Gudhi_stat -}//namespace Gudhi +#endif // PSSK_H_ diff --git a/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h b/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h index 59e58e41..a20702ff 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h +++ b/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2017 INRIA (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 @@ -20,8 +20,8 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#ifndef Persistence_heat_maps_H -#define Persistence_heat_maps_H +#ifndef PERSISTENCE_HEAT_MAPS_H_ +#define PERSISTENCE_HEAT_MAPS_H_ //standard include #include <vector> @@ -69,7 +69,7 @@ std::vector< std::vector<double> > create_Gaussian_filter( size_t pixel_radius , if ( dbg ) { - std::cerr << "Kernel initalize \n"; + std::cerr << "Kernel initialize \n"; std::cerr << "pixel_radius : " << pixel_radius << std::endl; std::cerr << "kernel.size() : " << kernel.size() << std::endl; getchar(); @@ -114,7 +114,7 @@ std::vector< std::vector<double> > create_Gaussian_filter( size_t pixel_radius , /* -* There are various options to scale the poits depending on their location. One can for instance: +* There are various options to scale the points depending on their location. One can for instance: * (1) do nothing (scale all of them with the weight 1), as in the function constant_function * (2) Scale them by the distance to the diagonal. This is implemented in function * (3) Scale them with the square of their distance to diagonal. This is implemented in function @@ -123,8 +123,8 @@ std::vector< std::vector<double> > create_Gaussian_filter( size_t pixel_radius , /** - * This is one of a scaling functions used to weight poits depending on their persistence and/or location in the diagram. - * This particular functiona is a finction which always assign value 1 to a point in the diagram. + * This is one of a scaling functions used to weight points depending on their persistence and/or location in the diagram. + * This particular functionality is a function which always assign value 1 to a point in the diagram. **/ class constant_scaling_function { @@ -137,7 +137,7 @@ public: /** - * This is one of a scaling functions used to weight poits depending on their persistence and/or location in the diagram. + * This is one of a scaling functions used to weight points depending on their persistence and/or location in the diagram. * The scaling given by this function to a point (b,d) is Euclidean distance of (b,d) from diagonal. **/ class distance_from_diagonal_scaling @@ -151,7 +151,7 @@ public: }; /** - * This is one of a scaling functions used to weight poits depending on their persistence and/or location in the diagram. + * This is one of a scaling functions used to weight points depending on their persistence and/or location in the diagram. * The scaling given by this function to a point (b,d) is a square of Euclidean distance of (b,d) from diagonal. **/ class squared_distance_from_diagonal_scaling @@ -164,7 +164,7 @@ public: }; /** - * This is one of a scaling functions used to weight poits depending on their persistence and/or location in the diagram. + * This is one of a scaling functions used to weight points depending on their persistence and/or location in the diagram. * The scaling given by this function to a point (b,d) is an arctan of a persistence of a point (i.e. arctan( b-d ). **/ class arc_tan_of_persistence_of_point @@ -177,7 +177,7 @@ public: }; /** - * This is one of a scaling functions used to weight poits depending on their persistence and/or location in the diagram. + * This is one of a scaling functions used to weight points depending on their persistence and/or location in the diagram. * This scaling function do not only depend on a point (p,d) in the diagram, but it depends on the whole diagram. * The longest persistence pair get a scaling 1. Any other pair get a scaling belong to [0,1], which is proportional * to the persistence of that pair. @@ -196,14 +196,19 @@ private: /** - * This class implements the following concepts: Vectorized_topological_data, Topological_data_with_distances, Real_valued_topological_data, Topological_data_with_averages, Topological_data_with_scalar_product -**/ + * \class Persistence_heat_maps Persistence_heat_maps.h gudhi/Persistence_heat_maps.h + * \brief A class implementing persistence heat maps. + * + * \ingroup Persistence_representations +**/ + +// This class implements the following concepts: Vectorized_topological_data, Topological_data_with_distances, Real_valued_topological_data, Topological_data_with_averages, Topological_data_with_scalar_product template <typename Scalling_of_kernels = constant_scaling_function> class Persistence_heat_maps { public: /** - * The default constructor. A scaling function from the diagonal is set up to a constant function. The image is not erased below the diagonal. The gaussian have diameter 5. + * The default constructor. A scaling function from the diagonal is set up to a constant function. The image is not erased below the diagonal. The Gaussian have diameter 5. **/ Persistence_heat_maps() { @@ -217,7 +222,7 @@ public: /** * Construction that takes at the input the following parameters: * (1) A vector of pairs of doubles (representing persistence intervals). All other parameters are optional. They are: - * (2) a Gausian filter generated by create_Gaussian_filter filter (the default value of this vaiable is a Gaussian filter of a radius 5), + * (2) a Gaussian filter generated by create_Gaussian_filter filter (the default value of this variable is a Gaussian filter of a radius 5), * (3) a boolean value which determines if the area of image below diagonal should, or should not be erased (it will be erased by default). * (4) a number of pixels in each direction (set to 1000 by default). * (5) a min x and y value of points that are to be taken into account. By default it is set to std::numeric_limits<double>::max(), in which case the program compute the values based on the data, @@ -226,12 +231,12 @@ public: Persistence_heat_maps( const std::vector< std::pair< double,double > > & interval , std::vector< std::vector<double> > filter = create_Gaussian_filter(5,1) , bool erase_below_diagonal = false , size_t number_of_pixels = 1000 , double min_ = std::numeric_limits<double>::max() , double max_ = std::numeric_limits<double>::max() ); /** - * Construction that takes at the input a name of a file with persistence intervals, a filter (radius 5 by default), a scaling function (constant by default), a boolean value which determines if the area of image below diagonal should, or should not be erased (should by default). The next parameter is the number of pixels in each direction (set to 1000 by default). and min and max values of images (both set to std::numeric_limits<double>::max() by defaulet. If this is the case, the program will pick the right values based on the data). + * Construction that takes at the input a name of a file with persistence intervals, a filter (radius 5 by default), a scaling function (constant by default), a boolean value which determines if the area of image below diagonal should, or should not be erased (should by default). The next parameter is the number of pixels in each direction (set to 1000 by default) and min and max values of images (both set to std::numeric_limits<double>::max() by default. If this is the case, the program will pick the right values based on the data). **/ /** * Construction that takes at the input the following parameters: - * (1) A a name of a file with persistence intervals. The file shold be readable by the function read_persistence_intervals_in_one_dimension_from_file. All other parameters are optional. They are: - * (2) a Gausian filter generated by create_Gaussian_filter filter (the default value of this vaiable is a Gaussian filter of a radius 5), + * (1) A name of a file with persistence intervals. The file should be readable by the function read_persistence_intervals_in_one_dimension_from_file. All other parameters are optional. They are: + * (2) a Gaussian filter generated by create_Gaussian_filter filter (the default value of this variable is a Gaussian filter of a radius 5), * (3) a boolean value which determines if the area of image below diagonal should, or should not be erased (it will be erased by default). * (4) a number of pixels in each direction (set to 1000 by default). * (5) a min x and y value of points that are to be taken into account. By default it is set to std::numeric_limits<double>::max(), in which case the program compute the values based on the data, @@ -259,14 +264,14 @@ public: //put to file subroutine /** - * The function outputs the perssitence image to a text file. The format as follow: + * The function outputs the persistence image to a text file. The format as follow: * In the first line, the values min and max of the image are stored * In the next lines, we have the persistence images in a form of a bitmap image. **/ void print_to_file( const char* filename )const; /** - * A function that load a heat map from file to the current object (and arase qhatever was stored in the current object before). + * A function that load a heat map from file to the current object (and erase whatever was stored in the current object before). **/ void load_from_file( const char* filename ); @@ -347,7 +352,7 @@ public: /** - * A function to generate a gnuplot script to vizualize the persistent image. + * A function to generate a gnuplot script to visualize the persistent image. **/ void plot( const char* filename )const; @@ -474,7 +479,7 @@ public: //Implementations of functions for various concepts. /** - * This function produce a vector of doubles based on a persisence heat map. It is required in a concept Vectorized_topological_data + * This function produce a vector of doubles based on a persistence heat map. It is required in a concept Vectorized_topological_data */ std::vector<double> vectorize( int number_of_function )const; /** @@ -486,9 +491,9 @@ public: } /** - * This function is required by the Real_valued_topological_data concept. It returns various projections od the persistence heat map to a real line. - * At the moment this function is not tested, since it is quite likelly to be changed in the future. Given this, when using it, keep in mind that it - * will be most likelly changed in the next versions. + * This function is required by the Real_valued_topological_data concept. It returns various projections on the persistence heat map to a real line. + * At the moment this function is not tested, since it is quite likely to be changed in the future. Given this, when using it, keep in mind that it + * will be most likely changed in the next versions. **/ double project_to_R( int number_of_function )const; /** @@ -515,7 +520,7 @@ public: /** * A function to compute scalar product of persistence heat maps. - * The parameter of this functionis a const reference to an object of a class Persistence_heat_maps. + * The parameter of this function is a const reference to an object of a class Persistence_heat_maps. * This function is required in Topological_data_with_scalar_product concept. **/ double compute_scalar_product( const Persistence_heat_maps& second_ )const; @@ -559,7 +564,6 @@ protected: } //data - //double (*scalling_function_with_respect_to_distance_from_diagonal)( const std::pair< double , double >& point_in_diagram ); Scalling_of_kernels f; bool erase_below_diagonal; double min_; @@ -583,7 +587,7 @@ void Persistence_heat_maps<Scalling_of_kernels>::construct( const std::vector< s if ( min_ == max_ ) { - if (dbg)std::cerr << "min and max parameters will be etermined based on intervals \n"; + if (dbg)std::cerr << "min and max parameters will be determined based on intervals \n"; //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(); @@ -636,7 +640,7 @@ void Persistence_heat_maps<Scalling_of_kernels>::construct( const std::vector< s 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 cordner. To get this, we need to shift x_grid and y_grid by a grid diameter. + //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. @@ -711,11 +715,6 @@ Persistence_heat_maps<Scalling_of_kernels>::Persistence_heat_maps( const char* f { intervals_ = read_persistence_intervals_in_one_dimension_from_file( filename , dimension ); } - //std::cerr << "intervals_.size() : " << intervals_.size() << std::endl; - //for ( size_t i = 0 ; i != intervals_.size() ; ++i ) - //{ - // std::cerr << intervals_[i].first << " " << intervals_[i].second << std::endl; - //} this->construct( intervals_ , filter, erase_below_diagonal , number_of_pixels , min_ , max_ ); this->set_up_parameters_for_basic_classes(); } @@ -956,11 +955,11 @@ double Persistence_heat_maps<Scalling_of_kernels>::distance( const Persistence_h //first we need to check if (*this) and second are defined on the same domain and have the same dimensions: if ( !this->check_if_the_same(second) ) { - std::cerr << "The persistence images are of noncompatible sizes. We cannot therefore compute distance between them. The program will now terminate"; - throw "The persistence images are of noncompatible sizes. We cannot therefore compute distance between them. The program will now terminate"; + std::cerr << "The persistence images are of non compatible sizes. We cannot therefore compute distance between them. The program will now terminate"; + throw "The persistence images are of non compatible sizes. We cannot therefore compute distance between them. The program will now terminate"; } - //if we are here, we know that the two persistence iomages are defined on the same domain, so we can start computing their distances: + //if we are here, we know that the two persistence images are defined on the same domain, so we can start computing their distances: double distance = 0; if ( power < std::numeric_limits<double>::max() ) @@ -1016,11 +1015,11 @@ double Persistence_heat_maps<Scalling_of_kernels>::compute_scalar_product( const //first we need to check if (*this) and second are defined on the same domain and have the same dimensions: if ( !this->check_if_the_same(second) ) { - std::cerr << "The persistence images are of noncompatible sizes. We cannot therefore compute distance between them. The program will now terminate"; - throw "The persistence images are of noncompatible sizes. We cannot therefore compute distance between them. The program will now terminate"; + std::cerr << "The persistence images are of non compatible sizes. We cannot therefore compute distance between them. The program will now terminate"; + throw "The persistence images are of non compatible sizes. We cannot therefore compute distance between them. The program will now terminate"; } - //if we are here, we know that the two persistence iomages are defined on the same domain, so we can start computing their scalar product: + //if we are here, we know that the two persistence images are defined on the same domain, so we can start computing their scalar product: double scalar_prod = 0; for ( size_t i = 0 ; i != this->heat_map.size() ; ++i ) { @@ -1035,8 +1034,8 @@ double Persistence_heat_maps<Scalling_of_kernels>::compute_scalar_product( const -}//namespace Gudhi_stat -}//namespace Gudhi +} // namespace Persistence_representations +} // namespace Gudhi -#endif +#endif // PERSISTENCE_HEAT_MAPS_H_ diff --git a/src/Persistence_representations/include/gudhi/Persistence_intervals.h b/src/Persistence_representations/include/gudhi/Persistence_intervals.h index 792c0a28..40c24670 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_intervals.h +++ b/src/Persistence_representations/include/gudhi/Persistence_intervals.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2017 INRIA (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 @@ -20,8 +20,8 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#ifndef Persistence_intervals_H_ -#define Persistence_intervals_H_ +#ifndef PERSISTENCE_INTERVALS_H_ +#define PERSISTENCE_INTERVALS_H_ //gudhi include #include <gudhi/read_persistence_from_file.h> @@ -48,14 +48,14 @@ class Persistence_intervals { public: /** - * This is a constructor of a class Persistence_intervals from a text file. Each line of the input file is supposed to contain two numbers of a type doube (or convertable to double) + * This is a constructor of a class Persistence_intervals from a text file. Each line of the input file is supposed to contain two numbers of a type double (or convertible to double) * representing the birth and the death of the persistence interval. If the pairs are not sorted so that birth <= death, then the constructor will sort then that way. - * * The second parameter of a constructor is a dimension of intervals to be read from a file. If your file contains only birt-death pairs, use the default value. + * * The second parameter of a constructor is a dimension of intervals to be read from a file. If your file contains only birth-death pairs, use the default value. **/ Persistence_intervals( const char* filename , unsigned dimension = std::numeric_limits<unsigned>::max() ); /** - * This is a constructor of a class Persistence_intervals from a vector of pairs. Each pair is assumed to represent a persistence interval. We assume that the first elemnets of pairs + * This is a constructor of a class Persistence_intervals from a vector of pairs. Each pair is assumed to represent a persistence interval. We assume that the first elements of pairs * are smaller or equal the second elements of pairs. **/ Persistence_intervals( const std::vector< std::pair< double,double > >& intervals ); @@ -102,15 +102,15 @@ public: std::vector< std::pair<double,double> > dominant_intervals( size_t where_to_cut = 100 )const; /** - * Procedure to compute a histogram of interva's length. A histogram is a block plot. The number of blocks is determined by the first parameter of the function (set by default to 10). + * Procedure to compute a histogram of interval's length. A histogram is a block plot. The number of blocks is determined by the first parameter of the function (set by default to 10). * For the sake of argument let us assume that the length of the longest interval is 1 and the number of bins is 10. In this case the i-th block correspond to a range between i-1/10 and i10. * The vale of a block supported at the interval is the number of persistence intervals of a length between x_0 and x_1. **/ std::vector< size_t > histogram_of_lengths( size_t number_of_bins = 10 )const; /** - * Based on a histogram of intervals lengts computed by the function histogram_of_lengths H the procedure below computes the cumulative histogram. The i-th position of the resulting histogram - * is the sume of values of H for the positions from 0 to i. + * Based on a histogram of intervals lengths computed by the function histogram_of_lengths H the procedure below computes the cumulative histogram. The i-th position of the resulting histogram + * is the sum of values of H for the positions from 0 to i. **/ std::vector< size_t > cumulative_histogram_of_lengths( size_t number_of_bins = 10 )const; @@ -127,13 +127,13 @@ public: std::vector< double > cumulative_characteristic_function_of_diagram( double x_min , double x_max , size_t number_of_bins = 10 )const; /** - * Compute the funtion of persistence Betti numbers. The returned value is a vector of pair. First element of each pair is a place where persistence Betti numbers change. + * Compute the function of persistence Betti numbers. The returned value is a vector of pair. First element of each pair is a place where persistence Betti numbers change. * Second element of each pair is the value of Persistence Betti numbers at that point. **/ std::vector< std::pair< double , size_t > > compute_persistent_betti_numbers()const; /** - *This is a non optimal procedure that compute vector of distances from each point of diagram to its k-th nearest neighbor (k is a parameted of the program). The resulting vector is by default truncated to 10 + *This is a non optimal procedure that compute vector of distances from each point of diagram to its k-th nearest neighbor (k is a parameter of the program). The resulting vector is by default truncated to 10 *elements (this value can be changed by using the second parameter of the program). The points are returned in order from the ones which are farthest away from their k-th nearest neighbors. **/ std::vector< double > k_n_n( size_t k , size_t where_to_cut = 10 )const; @@ -188,12 +188,9 @@ public: std::cout << "Gnuplot script to visualize persistence diagram written to the file: " << nameStr << ". Type load '" << nameStr << "' in gnuplot to visualize." << std::endl; } - - - /** - * Retun numbr of points in the diagram. + * Return number of points in the diagram. **/ size_t size()const{return this->intervals.size();} @@ -207,25 +204,12 @@ public: } - - - - - - - - - - - - - //Implementations of functions for various concepts. /** - * This is a simple function projectig the persistence intervals to a real number. The function we use here is a sum of squared lendgths of intervals. It can be naturally interpreted as + * This is a simple function projecting the persistence intervals to a real number. The function we use here is a sum of squared lengths of intervals. It can be naturally interpreted as * sum of step function, where the step hight it equal to the length of the interval. - * At the moment this function is not tested, since it is quite likelly to be changed in the future. Given this, when using it, keep in mind that it - * will be most likelly changed in the next versions. + * At the moment this function is not tested, since it is quite likely to be changed in the future. Given this, when using it, keep in mind that it + * will be most likely changed in the next versions. **/ double project_to_R( int number_of_function )const; /** @@ -237,14 +221,14 @@ public: } /** - * Return a familly of vectors obtained from the persistence diagram. The i-th vector consist of the lenfth of i dominant persistence intervals. + * Return a family of vectors obtained from the persistence diagram. The i-th vector consist of the length of i dominant persistence intervals. **/ std::vector<double> vectorize( int number_of_function )const { return this->length_of_dominant_intervals( number_of_function ); } /** - * This function return the number of functions that allows vectorization of a persisence diagram. It is required in a concept Vectorized_topological_data. + * This function return the number of functions that allows vectorization of a persistence diagram. It is required in a concept Vectorized_topological_data. **/ size_t number_of_vectorize_functions()const { @@ -252,19 +236,7 @@ public: } //end of implementation of functions needed for concepts. - //end of implementation of functions needed for concepts. - - - - - - - - - - - - + //For visualization use output from vectorize and build histograms. std::vector< std::pair< double,double > > output_for_visualization() @@ -289,37 +261,6 @@ protected: Persistence_intervals::Persistence_intervals( const char* filename , unsigned dimension ) { - //bool dbg = false; - //ifstream in; - //in.open( filename ); - - //if ( !in.good() ) - //{ - // throw("File with the persistence diagram do not exist, the program will now terminate.\n"); - //} - - //while ( true ) - //{ - // double first; - // double second; - // in >> first >> second; - - // if ( first > second ) - // { - // double buf = first; - // first = second; - // second = buf; - // } - - // if ( in.eof() )break; - // this->intervals.push_back( std::make_pair( first,second ) ); - // if ( dbg ) - // { - // std::cerr << "Adding interval [ " << first << " , " << second << " ]\n"; - // getchar(); - // } - //} - //in.close(); if ( dimension == std::numeric_limits<unsigned>::max() ) { this->intervals = read_persistence_intervals_in_one_dimension_from_file( filename ); @@ -490,7 +431,6 @@ std::vector< double > Persistence_intervals::characteristic_function_of_diagram( { result[pos] += ( (x_max - x_min)/(double)number_of_bins ) * ( this->intervals[i].second - this->intervals[i].first ); } - //cerr << "x_max : " << x_max << " x_min : " << x_min << " , number_of_bins : " << number_of_bins << " this->intervals[i].second : " << this->intervals[i].second << " this->intervals[i].first : " << this->intervals[i].first << endl; if ( dbg ) { std::cerr << "Result at this stage \n"; @@ -499,7 +439,6 @@ std::vector< double > Persistence_intervals::characteristic_function_of_diagram( std::cerr << result[aa] << " "; } std::cerr << std::endl; - //getchar(); } } return result; @@ -599,8 +538,7 @@ std::vector< double > Persistence_intervals::k_n_n( size_t k , size_t where_to_c { distancesFromI.push_back( compute_euclidean_distance( this->intervals[i] , this->intervals[j] ) ); } - //distances.push_back( distancesFromI ); - //also add a distance from this guy to daigonal: + //also add a distance from this guy to diagonal: double distanceToDiagonal = compute_euclidean_distance( this->intervals[i] , std::make_pair( 0.5*(this->intervals[i].first + this->intervals[i].second) , 0.5*(this->intervals[i].first + this->intervals[i].second) ) ); distances_from_diagonal[i] = distanceToDiagonal; @@ -694,7 +632,7 @@ double Persistence_intervals::project_to_R( int number_of_function )const } -}//namespace gudhi stat -}//namespace gudhi +} // namespace Persistence_representations +} // namespace gudhi -#endif +#endif // PERSISTENCE_INTERVALS_H_ diff --git a/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h b/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h index 7ef711e9..0da58399 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h +++ b/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2017 INRIA (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 @@ -20,8 +20,8 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#ifndef Persistence_intervals_WITH_DISTANCES_H_ -#define Persistence_intervals_WITH_DISTANCES_H_ +#ifndef PERSISTENCE_INTERVALS_WITH_DISTANCES_H_ +#define PERSISTENCE_INTERVALS_WITH_DISTANCES_H_ #include <gudhi/Persistence_intervals.h> @@ -59,7 +59,7 @@ public: }; -}//namespace gudhi stat -}//namespace gudhi +} // namespace Persistence_representations +} // namespace gudhi -#endif +#endif // PERSISTENCE_INTERVALS_WITH_DISTANCES_H_ diff --git a/src/Persistence_representations/include/gudhi/Persistence_landscape.h b/src/Persistence_representations/include/gudhi/Persistence_landscape.h index 9a177b60..642bba84 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_landscape.h +++ b/src/Persistence_representations/include/gudhi/Persistence_landscape.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2017 INRIA (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 @@ -21,8 +21,8 @@ */ -#ifndef Persistence_landscapes_H -#define Persistence_landscapes_H +#ifndef PERSISTENCE_LANDSCAPE_H_ +#define PERSISTENCE_LANDSCAPE_H_ //standard include #include <cmath> @@ -48,7 +48,7 @@ namespace Persistence_representations -//predeclaration +// pre declaration class Persistence_landscape; template < typename operation > Persistence_landscape operation_on_pair_of_landscapes( const Persistence_landscape& land1 , const Persistence_landscape& land2 ); @@ -56,12 +56,25 @@ Persistence_landscape operation_on_pair_of_landscapes( const Persistence_landsca /** - * A clas implementing persistence landascpes data structures. For theroretical desciritpion, please consult a paper ''Statistical topological data analysis using persistence landscapes'' by Peter Bubenik. - * For details of algorithms, please consult ''A persistence landscapes toolbox for topological statistics'' by Peter Bubenik and Pawel Dlotko. - * Persistence landscapes allow vertorization, computations of distances, computations of projections to Real, computations of averages and scalar products. Therefore they implement suitable interfaces. - * It implements the following concepts: Vectorized_topological_data, Topological_data_with_distances, Real_valued_topological_data, Topological_data_with_averages, Topological_data_with_scalar_product - * Note that at the moment, due to roundoff errors during the construction of persistence landscapes, elements which are different by 0.000005 are considered the same. If the scale in your persistence diagrams - * is comparable to this value, please rescale them before use this code. + * \class Persistence_landscape Persistence_landscape.h gudhi/Persistence_landscape.h + * \brief A class implementing persistence landscapes data structures. + * + * \ingroup Persistence_representations + * + * \details + * For theoretical description, please consult <i>Statistical topological data analysis using persistence + * landscapes</i>\cite bubenik_landscapes_2015 , and for details of algorithms, + * <i>A persistence landscapes toolbox for topological statistics</i>\cite bubenik_dlotko_landscapes_2016. + * + * Persistence landscapes allow vectorization, computations of distances, computations of projections to Real, + * computations of averages and scalar products. Therefore they implement suitable interfaces. + * It implements the following concepts: Vectorized_topological_data, Topological_data_with_distances, + * Real_valued_topological_data, Topological_data_with_averages, Topological_data_with_scalar_product + * + * Note that at the moment, due to rounding errors during the construction of persistence landscapes, elements which + * are different by 0.000005 are considered the same. If the scale in your persistence diagrams is comparable to this + * value, please rescale them before use this code. + * **/ class Persistence_landscape { @@ -169,7 +182,7 @@ public: } /** - * An operator * that allows multipilication of a landscape by a real number. + * An operator * that allows multiplication of a landscape by a real number. **/ friend Persistence_landscape operator*( const Persistence_landscape& first , double con ) { @@ -177,7 +190,7 @@ public: } /** - * An operator * that allows multipilication of a landscape by a real number (order of parameters swapped). + * An operator * that allows multiplication of a landscape by a real number (order of parameters swapped). **/ friend Persistence_landscape operator*( double con , const Persistence_landscape& first ) { @@ -297,7 +310,6 @@ public: *\private Computations of \f$L^{\infty}\f$ distance between two landscapes. **/ friend double compute_max_norm_distance_of_landscapes( const Persistence_landscape& first, const Persistence_landscape& second ); - //friend double compute_max_norm_distance_of_landscapes( const Persistence_landscape& first, const Persistence_landscape& second , unsigned& nrOfLand , double&x , double& y1, double& y2 ); /** @@ -308,7 +320,7 @@ public: /** - * Function to compute absolute value of a PL function. The representation of persistence landscapes allow to store general PL-function. When computing distance betwen two landscapes, we compute difference between + * Function to compute absolute value of a PL function. The representation of persistence landscapes allow to store general PL-function. When computing distance between two landscapes, we compute difference between * them. In this case, a general PL-function with negative value can appear as a result. Then in order to compute distance, we need to take its absolute value. This is the purpose of this procedure. **/ Persistence_landscape abs(); @@ -319,7 +331,7 @@ public: size_t size()const{return this->land.size(); } /** - * Computate maximal value of lambda-level landscape. + * Compute maximal value of lambda-level landscape. **/ double find_max( unsigned lambda )const; @@ -328,27 +340,13 @@ public: **/ friend double compute_inner_product( const Persistence_landscape& l1 , const Persistence_landscape& l2 ); - - - - - - - - - - - - - - //Implementations of functions for various concepts. /** * The number of projections to R is defined to the number of nonzero landscape functions. I-th projection is an integral of i-th landscape function over whole R. * This function is required by the Real_valued_topological_data concept. - * At the moment this function is not tested, since it is quite likelly to be changed in the future. Given this, when using it, keep in mind that it - * will be most likelly changed in the next versions. + * At the moment this function is not tested, since it is quite likely to be changed in the future. Given this, when using it, keep in mind that it + * will be most likely changed in the next versions. **/ double project_to_R( int number_of_function )const { @@ -382,7 +380,7 @@ public: return v; } /** - * This function return the number of functions that allows vectorization of persistence laandscape. It is required in a concept Vectorized_topological_data. + * This function return the number of functions that allows vectorization of persistence landscape. It is required in a concept Vectorized_topological_data. **/ size_t number_of_vectorize_functions()const { @@ -404,8 +402,8 @@ public: { nextLevelMerge[i] = to_average[i]; } - bool is_this_first_level = true;//in the loop, we will create dynamically a unmber of intermediate complexes. We have to clean that up, but we cannot erase the initial andscapes we have - //to average. In this case, we simply check if the nextLevelMerge are the input landscapes or the ones created in that loop by usig this extra variable. + bool is_this_first_level = true;//in the loop, we will create dynamically a number of intermediate complexes. We have to clean that up, but we cannot erase the initial landscapes we have + //to average. In this case, we simply check if the nextLevelMerge are the input landscapes or the ones created in that loop by using this extra variable. while ( nextLevelMerge.size() != 1 ) { @@ -446,7 +444,7 @@ public: /** * A function to compute distance between persistence landscape. - * The parameter of this functionis a Persistence_landscape. + * The parameter of this function is a Persistence_landscape. * This function is required in Topological_data_with_distances concept. * For max norm distance, set power to std::numeric_limits<double>::max() **/ @@ -465,7 +463,7 @@ public: /** * A function to compute scalar product of persistence landscapes. - * The parameter of this functionis a Persistence_landscape. + * The parameter of this function is a Persistence_landscape. * This function is required in Topological_data_with_scalar_product concept. **/ double compute_scalar_product( const Persistence_landscape& second )const @@ -473,25 +471,6 @@ public: return compute_inner_product( (*this) , second ); } //end of implementation of functions needed for concepts. - - - // - // This procedure returns x-range of a given level persistence landscape. If a default value is used, the x-range - //of 0th level landscape is given (and this range contains the ranges of all other landscapes). - // - //std::pair< double , double > get_x_range( size_t level = 0 )const - //{ - // std::pair< double , double > result; - // if ( level < this->land.size() ) - // { - // result = std::make_pair( this->land[level][1].first , this->land[level][ this->land[level].size() - 2 ].first ); - // } - // else - // { - // result = std::make_pair( 0,0 ); - // } - // return result; - //} /** * This procedure returns y-range of a given level persistence landscape. If a default value is used, the y-range @@ -582,7 +561,6 @@ bool Persistence_landscape::operator == ( const Persistence_landscape& rhs )con { if ( !( almost_equal(this->land[level][i].first , rhs.land[level][i].first) && almost_equal(this->land[level][i].second , rhs.land[level][i].second) ) ) { - //std::cerr<< this->land[level][i].first << " , " << rhs.land[level][i].first << " and " << this->land[level][i].second << " , " << rhs.land[level][i].second << std::endl; if (operatorEqualDbg)std::cerr << "this->land[level][i] : " << this->land[level][i].first << " " << this->land[level][i].second << "\n"; if (operatorEqualDbg)std::cerr << "rhs.land[level][i] : " << rhs.land[level][i].first << " " << rhs.land[level][i].second << "\n"; if (operatorEqualDbg)std::cerr << "3\n"; @@ -768,7 +746,7 @@ double Persistence_landscape::compute_integral_of_landscape()const { for ( size_t nr = 2 ; nr != this->land[i].size()-1 ; ++nr ) { - //it suffices to compute every planar integral and then sum them ap for each lambda_n + //it suffices to compute every planar integral and then sum them up for each lambda_n result += 0.5*( this->land[i][nr].first - this->land[i][nr-1].first )*(this->land[i][nr].second + this->land[i][nr-1].second); } } @@ -780,7 +758,7 @@ double Persistence_landscape::compute_integral_of_a_level_of_a_landscape( size_t double result = 0; if ( level >= this->land.size() ) { - //this landscape function is constantly equal 0, so is the intergral. + //this landscape function is constantly equal 0, so is the integral. return result; } //also negative landscapes are assumed to be zero. @@ -788,7 +766,7 @@ double Persistence_landscape::compute_integral_of_a_level_of_a_landscape( size_t for ( size_t nr = 2 ; nr != this->land[ level ].size()-1 ; ++nr ) { - //it suffices to compute every planar integral and then sum them ap for each lambda_n + //it suffices to compute every planar integral and then sum them up for each lambda_n result += 0.5*( this->land[ level ][nr].first - this->land[ level ][nr-1].first )*(this->land[ level ][nr].second + this->land[ level ][nr-1].second); } @@ -826,7 +804,6 @@ double Persistence_landscape::compute_integral_of_landscape( double p )const std::cout << "result : " << result << std::endl; } } - //if (compute_integral_of_landscapeDbg) std::cin.ignore(); } return result; } @@ -953,7 +930,7 @@ Persistence_landscape Persistence_landscape::abs() for ( size_t i = 1 ; i != this->land[level].size() ; ++i ) { if ( AbsDbg ){std::cout << "this->land[" << level << "][" << i << "] : " << this->land[level][i].first << " " << this->land[level][i].second << std::endl;} - //if a line segment between this->land[level][i-1] and this->land[level][i] crosses the x-axis, then we have to add one landscape point t oresult + //if a line segment between this->land[level][i-1] and this->land[level][i] crosses the x-axis, then we have to add one landscape point t o result if ( (this->land[level][i-1].second)*(this->land[level][i].second) < 0 ) { double zero = find_zero_of_a_line_segment_between_those_two_points( this->land[level][i-1] , this->land[level][i] ); @@ -1025,7 +1002,7 @@ void Persistence_landscape::load_landscape_from_file( const char* filename ) this->land.clear(); - //this constructor reads persistence landscape form a file. This file have to be created by this software beforehead + //this constructor reads persistence landscape form a file. This file have to be created by this software before head std::ifstream in; in.open( filename ); if ( !in.good() ) @@ -1049,7 +1026,7 @@ void Persistence_landscape::load_landscape_from_file( const char* filename ) lineSS >> beginn; lineSS >> endd; landscapeAtThisLevel.push_back( std::make_pair( beginn , endd ) ); - if (dbg){std::cerr << "Reading a pont : " << beginn << " , " << endd << std::endl;} + if (dbg){std::cerr << "Reading a point : " << beginn << " , " << endd << std::endl;} } else { @@ -1117,7 +1094,6 @@ Persistence_landscape operation_on_pair_of_landscapes ( const Persistence_landsc std::cerr << "land2.land[" << i << "].size() : " << land2.land[i].size() << std::endl; std::cout << "land1.land[i][p].first : " << land1.land[i][p].first << "\n"; std::cout << "land2.land[i][q].first : " << land2.land[i][q].first << "\n"; - //getchar(); } if ( land1.land[i][p].first < land2.land[i][q].first ) @@ -1126,7 +1102,6 @@ Persistence_landscape operation_on_pair_of_landscapes ( const Persistence_landsc { std::cout << "first \n"; std::cout << " function_value(land2.land[i][q-1],land2.land[i][q],land1.land[i][p].first) : "<< function_value(land2.land[i][q-1],land2.land[i][q],land1.land[i][p].first) << "\n"; - //std::cout << "oper( " << land1.land[i][p].second <<"," << function_value(land2.land[i][q-1],land2.land[i][q],land1.land[i][p].first) << " : " << oper( land1.land[i][p].second , function_value(land2.land[i][q-1],land2.land[i][q],land1.land[i][p].first) ) << "\n"; } lambda_n.push_back( std::make_pair( @@ -1242,7 +1217,7 @@ double compute_maximal_distance_non_symmetric( const Persistence_landscape& pl1, } int p2Count = 0; - for ( size_t i = 1 ; i != pl1.land[level].size()-1 ; ++i ) //w tym przypadku nie rozwarzam punktow w nieskocznosci + for ( size_t i = 1 ; i != pl1.land[level].size()-1 ; ++i ) // In this case, I consider points at the infinity { while ( true ) { @@ -1488,11 +1463,8 @@ void Persistence_landscape::plot( const char* filename, double xRangeBegin , do std::cout << "Gnuplot script to visualize persistence diagram written to the file: " << nameStr << ". Type load '" << nameStr << "' in gnuplot to visualize." << std::endl; } +} // namespace Persistence_representations +} // namespace gudhi - -}//namespace gudhi stat -}//namespace gudhi - - -#endif +#endif // PERSISTENCE_LANDSCAPE_H_ diff --git a/src/Persistence_representations/include/gudhi/Persistence_landscape_on_grid.h b/src/Persistence_representations/include/gudhi/Persistence_landscape_on_grid.h index 5703163a..d663b543 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_landscape_on_grid.h +++ b/src/Persistence_representations/include/gudhi/Persistence_landscape_on_grid.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2017 INRIA (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 @@ -21,8 +21,8 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. **/ -#ifndef Persistence_landscape_on_grid_H_ -#define Persistence_landscape_on_grid_H_ +#ifndef PERSISTENCE_LANDSCAPE_ON_GRID_H_ +#define PERSISTENCE_LANDSCAPE_ON_GRID_H_ //standard include @@ -50,16 +50,25 @@ namespace Gudhi namespace Persistence_representations { -//predeclaration +// pre declaration class Persistence_landscape_on_grid; template < typename operation > Persistence_landscape_on_grid operation_on_pair_of_landscapes_on_grid( const Persistence_landscape_on_grid& land1 , const Persistence_landscape_on_grid& land2 ); /** - * A clas implementing persistence landascpes by approximating them on a collection of grid points. * Persistence landscapes on grid allow vertorization, computations of distances, computations - * of projections to Real, computations of averages and scalar products. Therefore they implement suitable interfaces. - * It implements the following concepts: Vectorized_topological_data, Topological_data_with_distances, Real_valued_topological_data, Topological_data_with_averages, Topological_data_with_scalar_product - * Note that at the moment, due to roundoff errors during the construction of persistence landscapes on a grid, elements which are different by 0.000005 are considered the same. If the scale in your persistence diagrams + * \class Persistence_landscape_on_grid Persistence_landscape_on_grid.h gudhi/Persistence_landscape_on_grid.h + * \brief A class implementing persistence landscapes by approximating them on a collection of grid points. + * + * \ingroup Persistence_representations + * + * \details + * Persistence landscapes on grid allows vectorization, computations of distances, computations of projections to Real, + * computations of averages and scalar products. Therefore they implement suitable interfaces. + * It implements the following concepts: Vectorized_topological_data, Topological_data_with_distances, + * Real_valued_topological_data, Topological_data_with_averages, Topological_data_with_scalar_product + * + * Note that at the moment, due to rounding errors during the construction of persistence landscapes on a grid, + * elements which are different by 0.000005 are considered the same. If the scale in your persistence diagrams * is comparable to this value, please rescale them before use this code. **/ @@ -89,14 +98,14 @@ public: /** * Constructor that reads persistence intervals from file and creates persistence landscape. The format of the input file is the following: in each line we put birth-death pair. Last line is assumed - * to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read. The additional parameters of this procedure are: ranges of grid, resoltion of a grid + * to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read. The additional parameters of this procedure are: ranges of grid, resolution of a grid * number of landscape functions to be created and the dimension of intervals that are need to be read from a file (in case of Gudhi format files). **/ Persistence_landscape_on_grid(const char* filename , double grid_min_, double grid_max_ , size_t number_of_points_ , unsigned number_of_levels_of_landscape , unsigned short dimension_ = std::numeric_limits<unsigned short>::max() ); /** * Constructor that reads persistence intervals from file and creates persistence landscape. The format of the input file is the following: in each line we put birth-death pair. Last line is assumed - * to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read. The additional parameters of this procedure are: ranges of grid, resoltion of a grid + * to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read. The additional parameters of this procedure are: ranges of grid, resolution of a grid * and the dimension of intervals that are need to be read from a file (in case of Gudhi format files). **/ Persistence_landscape_on_grid(const char* filename , double grid_min_, double grid_max_ , size_t number_of_points_ , unsigned short dimension_ = std::numeric_limits<unsigned short>::max() ); @@ -104,16 +113,16 @@ public: /** * Constructor that reads persistence intervals from file and creates persistence landscape. The format of the input file is the following: in each line we put birth-death pair. Last line is assumed - * to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read. The additional parameter is the resoution of a grid and the number of landscape - * functions to be created. The remaning parameters are calculated based on data. + * to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read. The additional parameter is the resolution of a grid and the number of landscape + * functions to be created. The remaining parameters are calculated based on data. **/ Persistence_landscape_on_grid(const char* filename , size_t number_of_points , unsigned number_of_levels_of_landscape , unsigned short dimension = std::numeric_limits<unsigned short>::max() ); /** * Constructor that reads persistence intervals from file and creates persistence landscape. The format of the input file is the following: in each line we put birth-death pair. Last line is assumed - * to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read. The additional parameter is the resoution of a grid. The last parameter is the dimension + * to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read. The additional parameter is the resolution of a grid. The last parameter is the dimension * of a persistence to read from the file. If your file contains only persistence pair in a single dimension, please set it up to std::numeric_limits<unsigned>::max(). - * The remaning parameters are calculated based on data. + * The remaining parameters are calculated based on data. **/ Persistence_landscape_on_grid(const char* filename , size_t number_of_points , unsigned short dimension = std::numeric_limits<unsigned short>::max() ); @@ -258,7 +267,7 @@ public: if ( dbg ) { std::cerr << "Increasing result by : " << value_to_add << std::endl; - std::cerr << "restult : " << result << std::endl; + std::cerr << "result : " << result << std::endl; getchar(); } previous_x = current_x; @@ -311,9 +320,9 @@ public: std::cerr << "This is a procedure compute_value_at_a_given_point \n"; std::cerr << "level : " << level << std::endl; std::cerr << "x : " << x << std::endl; - std::cerr << "psoition : " << position << std::endl; + std::cerr << "position : " << position << std::endl; } - //check if we are not exacly in the grid point: + //check if we are not exactly in the grid point: if ( almost_equal( position*dx+ this->grid_min , x) ) { if ( this->values_of_landscapes[position].size() < level ) @@ -389,7 +398,7 @@ public: } /** - * An operator * that allows multipilication of a landscape by a real number. + * An operator * that allows multiplication of a landscape by a real number. **/ friend Persistence_landscape_on_grid operator*( const Persistence_landscape_on_grid& first , double con ) { @@ -397,7 +406,7 @@ public: } /** - * An operator * that allows multipilication of a landscape by a real number (order of parameters swapped). + * An operator * that allows multiplication of a landscape by a real number (order of parameters swapped). **/ friend Persistence_landscape_on_grid operator*( double con , const Persistence_landscape_on_grid& first ) { @@ -413,7 +422,7 @@ public: } /** - * Operator +=. The second parameter is persistnece landwscape. + * Operator +=. The second parameter is persistence landscape. **/ Persistence_landscape_on_grid operator += ( const Persistence_landscape_on_grid& rhs ) { @@ -422,7 +431,7 @@ public: } /** - * Operator -=. The second parameter is persistnece landwscape. + * Operator -=. The second parameter is persistence landscape. **/ Persistence_landscape_on_grid operator -= ( const Persistence_landscape_on_grid& rhs ) { @@ -458,7 +467,7 @@ public: bool dbg = true; if ( this->values_of_landscapes.size() != rhs.values_of_landscapes.size() ) { - if (dbg) std::cerr << "values_of_landscapes of incompatable sizes\n"; + if (dbg) std::cerr << "values_of_landscapes of incompatible sizes\n"; return false; } if ( !almost_equal( this->grid_min , rhs.grid_min ) ) @@ -546,28 +555,6 @@ public: std::pair< double , double > get_x_range( size_t level = 0 )const { return std::make_pair( this->grid_min , this->grid_max ); - //std::pair< double , double > result; - //if ( level < this->land.size() ) - //{ - // double dx = (this->grid_max - this->grid_min)/(double)this->values_of_landscapes.size(); - // size_t first_nonzero = 0; - // while ( (first_nonzero != this->values_of_landscapes.size()) && (this->values_of_landscapes[level][first_nonzero] == 0) )++first_nonzero; - // - // if ( first_nonzero == 0 ) - // { - // return std::make_pair( 0,0 );//this landscape is empty. - // } - // - // size_t last_nonzero = 0; - // while ( (last_nonzero != 0) && (this->values_of_landscapes[level][last_nonzero] == 0) )--last_nonzero; - // - // result = std::make_pair( this->grid_min +first_nonzero*dx , this->grid_max - last_nonzero*dx ); - //} - //else - //{ - // result = std::make_pair( 0,0 ); - //} - //return result; } /** @@ -577,16 +564,6 @@ public: std::pair< double , double > get_y_range( size_t level = 0 )const { return this->compute_minimum_maximum(); - //std::pair< double , double > result; - //if ( level < this->land.size() ) - //{ - // result = this->compute_minimum_maximum() - //} - //else - //{ - // result = std::make_pair( 0,0 ); - //} - //return result; } /** @@ -629,13 +606,11 @@ public: * Computations of \f$L^{\infty}\f$ distance between two landscapes. **/ friend double compute_max_norm_distance_of_landscapes( const Persistence_landscape_on_grid& first, const Persistence_landscape_on_grid& second ); - //friend double compute_max_norm_distance_of_landscapes( const Persistence_landscape_on_grid& first, const Persistence_landscape_on_grid& second , unsigned& nrOfLand , double&x , double& y1, double& y2 ); - /** - * Function to compute absolute value of a PL function. The representation of persistence landscapes allow to store general PL-function. When computing distance betwen two landscapes, we compute difference between + * Function to compute absolute value of a PL function. The representation of persistence landscapes allow to store general PL-function. When computing distance between two landscapes, we compute difference between * them. In this case, a general PL-function with negative value can appear as a result. Then in order to compute distance, we need to take its absolute value. This is the purpose of this procedure. **/ void abs() @@ -655,7 +630,7 @@ public: size_t size()const{return this->number_of_nonzero_levels(); } /** - * Computate maximal value of lambda-level landscape. + * Compute maximal value of lambda-level landscape. **/ double find_max( unsigned lambda )const { @@ -742,14 +717,14 @@ public: } //now, to compute the inner product in this interval we need to compute the integral of (ax+b)(cx+d) = acx^2 + (ad+bc)x + bd in the interval from previous_x to current_x: - //The integal is ac/3*x^3 + (ac+bd)/2*x^2 + bd*x + //The integral is ac/3*x^3 + (ac+bd)/2*x^2 + bd*x double added_value = (a*c/3*current_x*current_x*current_x + (a*d+b*c)/2*current_x*current_x + b*d*current_x)- (a*c/3*previous_x*previous_x*previous_x + (a*d+b*c)/2*previous_x*previous_x + b*d*previous_x); if ( dbg ) { - std::cerr << "Value of the integral on the left end ie : " << previous_x << " is : " << a*c/3*previous_x*previous_x*previous_x + (a*d+b*c)/2*previous_x*previous_x + b*d*previous_x << std::endl; + std::cerr << "Value of the integral on the left end i.e. : " << previous_x << " is : " << a*c/3*previous_x*previous_x*previous_x + (a*d+b*c)/2*previous_x*previous_x + b*d*previous_x << std::endl; std::cerr << "Value of the integral on the right end i.e. : " << current_x << " is " << a*c/3*current_x*current_x*current_x + (a*d+b*c)/2*current_x*current_x + b*d*current_x << std::endl; } @@ -775,7 +750,7 @@ public: /** * Computations of \f$L^{p}\f$ distance between two landscapes on a grid. p is the parameter of the procedure. * FIXME: Note that, due to the grid representation, the method below may give non--accurate results in case when the landscape P and Q the difference of which we want to compute - * are interxsecting. This is a consequence of a general way they are computed. In the future, an integral of absolute value of a difference of P and Q will be given as a separated + * are intersecting. This is a consequence of a general way they are computed. In the future, an integral of absolute value of a difference of P and Q will be given as a separated * function to fix that inaccuracy. **/ friend double compute_distance_of_landscapes_on_grid( const Persistence_landscape_on_grid& first, const Persistence_landscape_on_grid& second , double p ) @@ -819,7 +794,7 @@ public: else { result = lan.compute_integral_of_landscape(); - if (dbg){std::cerr << "integral, wihtout power : " << result << std::endl;getchar();} + if (dbg){std::cerr << "integral, without power : " << result << std::endl;getchar();} } //(\int_{- \infty}^{+\infty}| first-second |^p)^(1/p) return pow( result , 1/(double)p ); @@ -830,45 +805,14 @@ public: return lan.compute_maximum(); } } - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - //Functions that are needed for that class to implement the concept. /** * The number of projections to R is defined to the number of nonzero landscape functions. I-th projection is an integral of i-th landscape function over whole R. * This function is required by the Real_valued_topological_data concept. - * At the moment this function is not tested, since it is quite likelly to be changed in the future. Given this, when using it, keep in mind that it - * will be most likelly changed in the next versions. + * At the moment this function is not tested, since it is quite likely to be changed in the future. Given this, when using it, keep in mind that it + * will be most likely changed in the next versions. **/ double project_to_R( int number_of_function )const { @@ -884,8 +828,6 @@ public: } - - /** * This function produce a vector of doubles based on a landscape. It is required in a concept Vectorized_topological_data */ @@ -909,16 +851,13 @@ public: } /** - * This function return the number of functions that allows vectorization of persistence laandscape. It is required in a concept Vectorized_topological_data. + * This function return the number of functions that allows vectorization of persistence landscape. It is required in a concept Vectorized_topological_data. **/ size_t number_of_vectorize_functions()const { return number_of_functions_for_vectorization; } - - - /** * A function to compute averaged persistence landscape on a grid, based on vector of persistence landscapes on grid. @@ -932,7 +871,7 @@ public: this->values_of_landscapes .clear(); this->grid_min = this->grid_max = 0; - //if there is nothing to averate, then the average is a zero landscape. + //if there is nothing to average, then the average is a zero landscape. if ( to_average.size() == 0 )return; //now we need to check if the grids in all objects of to_average are the same: @@ -968,7 +907,7 @@ public: std::cerr << "We are considering the point : " << grid_point << " of the grid. In this point, there are at most : " << maximal_size_of_vector << " nonzero landscape functions \n"; } - //and compute an arythmetic average: + //and compute an arithmetic average: for ( size_t land_no = 0 ; land_no != to_average.size() ; ++land_no ) { //summing: @@ -989,7 +928,7 @@ public: /** * A function to compute distance between persistence landscape on a grid. - * The parameter of this functionis a Persistence_landscape_on_grid. + * The parameter of this function is a Persistence_landscape_on_grid. * This function is required in Topological_data_with_distances concept. * For max norm distance, set power to std::numeric_limits<double>::max() **/ @@ -1007,7 +946,7 @@ public: /** * A function to compute scalar product of persistence landscape on a grid. - * The parameter of this functionis a Persistence_landscape_on_grid. + * The parameter of this function is a Persistence_landscape_on_grid. * This function is required in Topological_data_with_scalar_product concept. **/ double compute_scalar_product( const Persistence_landscape_on_grid& second ) @@ -1016,28 +955,9 @@ public: } //end of implementation of functions needed for concepts. - - - - - - - - - - - - - - - - - - - /** - * A function that returns values of landsapes. It can be used for vizualization + * A function that returns values of landscapes. It can be used for visualization **/ std::vector< std::vector< double > > output_for_visualization()const { @@ -1046,7 +966,7 @@ public: /** * function used to create a gnuplot script for visualization of landscapes. Over here we need to specify which landscapes do we want to plot. - * In addition, the user may specify the range (min and max) where landscape is plot. The fefault values for min and max are std::numeric_limits<double>::max(). If the procedure detect those + * In addition, the user may specify the range (min and max) where landscape is plot. The default values for min and max are std::numeric_limits<double>::max(). If the procedure detect those * values, it will determine the range so that the whole landscape is supported there. If at least one min or max value is different from std::numeric_limits<double>::max(), then the values * provided by the user will be used. **/ @@ -1123,7 +1043,7 @@ void Persistence_landscape_on_grid::set_up_values_of_landscapes( const std::vect if ( grid_max_ <= grid_min_ ) { - throw "Wrong parameters of grid_min and grid_max given to the procedure. THe grid have negative, or zero size. The program will now terminate.\n"; + throw "Wrong parameters of grid_min and grid_max given to the procedure. The grid have negative, or zero size. The program will now terminate.\n"; } double dx = ( grid_max_ - grid_min_ )/(double)(number_of_points_); @@ -1174,7 +1094,7 @@ void Persistence_landscape_on_grid::set_up_values_of_landscapes( const std::vect if ( this->values_of_landscapes[i].size() == number_of_levels-1 ) { //this->values_of_landscapes[i].size() == number_of_levels - //in this case we need to create the heep. + //in this case we need to create the heap. std::make_heap (this->values_of_landscapes[i].begin(),this->values_of_landscapes[i].end()); } } @@ -1212,7 +1132,7 @@ void Persistence_landscape_on_grid::set_up_values_of_landscapes( const std::vect if ( this->values_of_landscapes[i].size() == number_of_levels-1 ) { //this->values_of_landscapes[i].size() == number_of_levels - //in this case we need to create the heep. + //in this case we need to create the heap. std::make_heap (this->values_of_landscapes[i].begin(),this->values_of_landscapes[i].end()); } } @@ -1225,7 +1145,7 @@ void Persistence_landscape_on_grid::set_up_values_of_landscapes( const std::vect if ( dbg ) { - std::cerr << "AAdding landscape value (going down) for a point : " << i << " equal : " << landscape_value << std::endl; + std::cerr << "Adding landscape value (going down) for a point : " << i << " equal : " << landscape_value << std::endl; } } landscape_value -= dx; @@ -1235,11 +1155,10 @@ void Persistence_landscape_on_grid::set_up_values_of_landscapes( const std::vect if ( number_of_levels != std::numeric_limits< unsigned >::max() ) { //in this case, vectors are used as heaps. And, since we want to have the smallest element at the top of - //each heap, we store mminus distances. To get if right at the end, we need to multiply each value + //each heap, we store minus distances. To get if right at the end, we need to multiply each value //in the heap by -1 to get real vector of distances. for ( size_t pt = 0 ; pt != this->values_of_landscapes.size() ; ++pt ) { - //std::cerr << this->values_of_landscapes[pt].size() <<std::endl; for ( size_t j = 0 ; j != this->values_of_landscapes[pt].size() ; ++j ) { this->values_of_landscapes[pt][j] *= -1; @@ -1362,7 +1281,6 @@ void Persistence_landscape_on_grid::load_landscape_from_file( const char* filena //read a line of a file and convert it to a vector. std::vector< double > vv; std::getline(in, line); - //std::cerr << "Reading line : " << line << std::endl;getchar(); std::istringstream stream(line); while (stream >> number) { @@ -1485,7 +1403,7 @@ Persistence_landscape_on_grid operation_on_pair_of_landscapes_on_grid ( const Pe result.grid_min = land1.grid_min; result.grid_max = land1.grid_max; - //now we perorm the operations: + //now we perform the operations: for ( size_t grid_point = 0 ; grid_point != land1.values_of_landscapes.size() ; ++grid_point ) { result.values_of_landscapes[grid_point] = std::vector< double >( std::max( land1.values_of_landscapes[grid_point].size() , land2.values_of_landscapes[grid_point].size() ) ); @@ -1555,9 +1473,7 @@ double compute_max_norm_distance_of_landscapes( const Persistence_landscape_on_g return result; } - - -}//namespace Gudhi_stat +}//namespace Persistence_representations }//namespace Gudhi -#endif +#endif // PERSISTENCE_LANDSCAPE_ON_GRID_H_ diff --git a/src/Persistence_representations/include/gudhi/Persistence_vectors.h b/src/Persistence_representations/include/gudhi/Persistence_vectors.h index 7fde3413..616ec50f 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_vectors.h +++ b/src/Persistence_representations/include/gudhi/Persistence_vectors.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2017 INRIA (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 @@ -21,8 +21,8 @@ */ -#ifndef Vector_distances_in_diagram_H -#define Vector_distances_in_diagram_H +#ifndef PERSISTENCE_VECTORS_H_ +#define PERSISTENCE_VECTORS_H_ #include <fstream> #include <cmath> @@ -42,32 +42,6 @@ namespace Gudhi namespace Persistence_representations { -/* -template <typename T> -struct Euclidean_distance -{ - double operator() ( const std::pair< T,T >& f , const std::pair<T,T>& s ) - { - return sqrt( (f.first-s.first)*(f.first-s.first) + (f.second-s.second)*(f.second-s.second) ); - } - double operator() ( const std::vector< T >& f , const std::vector < T >& s ) - { - if ( f.size() != s.size() ) - { - std::cerr << "Not compatible points dimensions in the procedure to compute Euclidean distance. The program will now terminate. \n"; - std::cout << f.size() << " , " << s.size() << std::endl; - throw "Not compatible points dimensions in the procedure to compute Euclidean distance. The program will now terminate. \n"; - } - double result = 0; - for ( size_t i = 0 ; i != f.size() ; ++i ) - { - result += ( f[i]-s[i] )*( f[i]-s[i] ); - } - return sqrt( result ); - } -}; -* */ - template <typename T> struct Maximum_distance { @@ -79,16 +53,21 @@ struct Maximum_distance - /** -* This is an implementation of idea presented in the paper 'Stable Topological Signatures for Points on 3D Shapes' by -* M. Carriere, S. Y. Oudot and M. Ovsjanikov published in Computer Graphics Forum (proc. SGP 2015). -* The parameter of the class is the class that computes distance used to construct the vectors. The typical function is -* either Eucludean of maximum (Manhattan) distance. -* This class implements the following concepts: Vectorized_topological_data, Topological_data_with_distances, Real_valued_topological_data, Topological_data_with_averages, Topological_data_with_scalar_product -* -**/ - + * \class Vector_distances_in_diagram Vector_distances_in_diagram.h gudhi/Vector_distances_in_diagram.h + * \brief A class implementing persistence vectors. + * + * \ingroup Persistence_representations + * + * \details + * This is an implementation of idea presented in the paper <i>Stable Topological Signatures for Points on 3D + * Shapes</i> \cite Carriere_Oudot_Ovsjanikov_top_signatures_3d .<br> + * The parameter of the class is the class that computes distance used to construct the vectors. The typical function + * is either Euclidean of maximum (Manhattan) distance. + * + * This class implements the following concepts: Vectorized_topological_data, Topological_data_with_distances, + * Real_valued_topological_data, Topological_data_with_averages, Topological_data_with_scalar_product + **/ template <typename F> class Vector_distances_in_diagram { @@ -99,12 +78,12 @@ public: Vector_distances_in_diagram(){}; /** - * The constructor that takes as an input a multiset of persistence intervals (given as vector of birth-death pairs). The second parameter is the desiered length of the output vectors. + * The constructor that takes as an input a multiset of persistence intervals (given as vector of birth-death pairs). The second parameter is the desired length of the output vectors. **/ Vector_distances_in_diagram( const std::vector< std::pair< double , double > >& intervals , size_t where_to_cut ); /** - * The constructor taking as an input a file with birth-death pairs. The second parameter is the desiered length of the output vectors. + * The constructor taking as an input a file with birth-death pairs. The second parameter is the desired length of the output vectors. **/ Vector_distances_in_diagram( const char* filename , size_t where_to_cut , unsigned dimension = std::numeric_limits<unsigned>::max() ); @@ -155,7 +134,7 @@ public: void load_from_file( const char* filename ); /** - * Comparision operators: + * Comparison operators: **/ bool operator == ( const Vector_distances_in_diagram& second )const { @@ -172,14 +151,11 @@ public: return !( *this == second ); } - - - - //Implementations of functions for various concepts. + //Implementations of functions for various concepts. /** * Compute projection to real numbers of persistence vector. This function is required by the Real_valued_topological_data concept - * At the moment this function is not tested, since it is quite likelly to be changed in the future. Given this, when using it, keep in mind that it - * will be most likelly changed in the next versions. + * At the moment this function is not tested, since it is quite likely to be changed in the future. Given this, when using it, keep in mind that it + * will be most likely changed in the next versions. **/ double project_to_R( int number_of_function )const; /** @@ -195,7 +171,7 @@ public: **/ std::vector<double> vectorize( int number_of_function )const; /** - * This function return the number of functions that allows vectorization of a persisence vector. It is required in a concept Vectorized_topological_data. + * This function return the number of functions that allows vectorization of a persistence vector. It is required in a concept Vectorized_topological_data. **/ size_t number_of_vectorize_functions()const { @@ -220,22 +196,6 @@ public: //end of implementation of functions needed for concepts. - - - - - - - - - - - - - - - - /** * For visualization use output from vectorize and build histograms. **/ @@ -246,7 +206,7 @@ public: /** - * Create a gnuplot script to vizualize the data structure. + * Create a gnuplot script to visualize the data structure. **/ void plot( const char* filename )const { @@ -264,7 +224,7 @@ public: } out <<std::endl; out.close(); - std::cout << "To vizualize, open gnuplot and type: load \'" << gnuplot_script.str().c_str() << "\'" << std::endl; + std::cout << "To visualize, open gnuplot and type: load \'" << gnuplot_script.str().c_str() << "\'" << std::endl; } /** @@ -284,7 +244,7 @@ public: return std::make_pair( this->sorted_vector_of_distances[0] , 0); } - //arythmetic operations: + //arithmetic operations: template < typename Operation_type > friend Vector_distances_in_diagram operation_on_pair_of_vectors( const Vector_distances_in_diagram& first , const Vector_distances_in_diagram& second , Operation_type opertion ) { @@ -511,7 +471,6 @@ void Vector_distances_in_diagram<F>::compute_sorted_vector_of_distances_via_heap double value = f( this->intervals[i] , std::make_pair( 0.5*(this->intervals[i].first+this->intervals[i].second) , 0.5*(this->intervals[i].first+this->intervals[i].second) ) ); if ( -value < heap.front() ) { - //std::cerr << "Replacing : " << heap.front() << " with : " << -value <<std::endl;getchar(); //remove the first element from the heap std::pop_heap (heap.begin(),heap.end()); //heap.pop_back(); @@ -669,7 +628,7 @@ double Vector_distances_in_diagram<F>::distance( const Vector_distances_in_diagr } else { - //nax morm + // max norm if ( result < fabs( this->sorted_vector_of_distances[i] - second_.sorted_vector_of_distances[i] ) )result = fabs( this->sorted_vector_of_distances[i] - second_.sorted_vector_of_distances[i] ); } if ( dbg ) @@ -767,12 +726,8 @@ double Vector_distances_in_diagram<F>::compute_scalar_product( const Vector_dist return result; } - - - - -}//namespace Gudhi_stat +}//namespace Persistence_representations }//namespace Gudhi -#endif // Vector_distances_in_diagram_H +#endif // PERSISTENCE_VECTORS_H_ diff --git a/src/Persistence_representations/include/gudhi/common_persistence_representations.h b/src/Persistence_representations/include/gudhi/common_persistence_representations.h index f223079a..f571ca4f 100644 --- a/src/Persistence_representations/include/gudhi/common_persistence_representations.h +++ b/src/Persistence_representations/include/gudhi/common_persistence_representations.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2017 INRIA (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 @@ -20,15 +20,15 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#ifndef common_gudhi_stat_H -#define common_gudhi_stat_H +#ifndef COMMON_PERSISTENCE_REPRESENTATIONS_H_ +#define COMMON_PERSISTENCE_REPRESENTATIONS_H_ namespace Gudhi { namespace Persistence_representations { - //this file contain an implementation of some common procedures used in Gudhi_stat. + //this file contain an implementation of some common procedures used in Persistence_representations. //double epsi = std::numeric_limits<double>::epsilon(); double epsi = 0.000005; @@ -38,8 +38,8 @@ double epsi = 0.000005; /** - * A procedure used to compare doubles. Typically gien two doubles A and B, comparing A == B is not good idea. In this case, we use the procedure almostEqual with the epsi defined at - * the top of the file. Setting up the epsi give the user a tolerance on what should be consider equal. + * A procedure used to compare doubles. Typically given two doubles A and B, comparing A == B is not good idea. In this case, we use the procedure almostEqual with the epsi defined at + * the top of the file. Setting up the epsi gives the user a tolerance on what should be consider equal. **/ inline bool almost_equal( double a , double b ) { @@ -78,7 +78,7 @@ std::pair<double,double> compute_parameters_of_a_line( std::pair<double,double> //landscapes /** - * This procedure given two points which lies on the opposide sides of x axis, compute x for which the line connecting those two points crosses x axis. + * This procedure given two points which lies on the opposite sides of x axis, compute x for which the line connecting those two points crosses x axis. **/ double find_zero_of_a_line_segment_between_those_two_points ( std::pair<double,double> p1, std::pair<double,double> p2 ) { @@ -86,7 +86,7 @@ double find_zero_of_a_line_segment_between_those_two_points ( std::pair<double,d if ( p1.second*p2.second > 0 ) { std::ostringstream errMessage; - errMessage <<"In function find_zero_of_a_line_segment_between_those_two_points the agguments are: (" << p1.first << "," << p1.second << ") and (" << p2.first << "," << p2.second << "). There is no zero in line between those two points. Program terminated."; + errMessage <<"In function find_zero_of_a_line_segment_between_those_two_points the arguments are: (" << p1.first << "," << p1.second << ") and (" << p2.first << "," << p2.second << "). There is no zero in line between those two points. Program terminated."; std::string errMessageStr = errMessage.str(); const char* err = errMessageStr.c_str(); throw(err); @@ -94,8 +94,6 @@ double find_zero_of_a_line_segment_between_those_two_points ( std::pair<double,d //we assume here, that x \in [ p1.first, p2.first ] and p1 and p2 are points between which we will put the line segment double a = (p2.second - p1.second)/(p2.first - p1.first); double b = p1.second - a*p1.first; - //cerr << "Line crossing points : (" << p1.first << "," << p1.second << ") oraz (" << p2.first << "," << p2.second << ") : \n"; - //cerr << "a : " << a << " , b : " << b << " , x : " << x << endl; return -b/a; } @@ -103,7 +101,7 @@ double find_zero_of_a_line_segment_between_those_two_points ( std::pair<double,d //landscapes /** - * This method provides a comparision of points that is used in construction of persistence landscapes. The orderign is lexicographical for the first coordinate, and reverse-lexicographical for the + * This method provides a comparison of points that is used in construction of persistence landscapes. The ordering is lexicographical for the first coordinate, and reverse-lexicographical for the * second coordinate. **/ bool compare_points_sorting( std::pair<double,double> f, std::pair<double,double> s ) @@ -135,7 +133,7 @@ bool compare_points_sorting( std::pair<double,double> f, std::pair<double,double //landscapes /** - * This procedure takes two points in R^2 and a double value x. It conputes the line pasing through those two points and return the value of that linear function at x. + * This procedure takes two points in R^2 and a double value x. It computes the line parsing through those two points and return the value of that linear function at x. **/ double function_value ( std::pair<double,double> p1, std::pair<double,double> p2 , double x ) { @@ -148,7 +146,7 @@ double function_value ( std::pair<double,double> p1, std::pair<double,double> p2 -}//namespace Gudhi_stat -}//namespace Gudhi +} // namespace Persistence_representations +} // namespace Gudhi -#endif +#endif // COMMON_PERSISTENCE_REPRESENTATIONS_H_ diff --git a/src/Persistence_representations/include/gudhi/read_persistence_from_file.h b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h index 058c77a4..a4884314 100644 --- a/src/Persistence_representations/include/gudhi/read_persistence_from_file.h +++ b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2017 INRIA (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 @@ -21,8 +21,8 @@ */ -#ifndef Read_Persitence_From_File_H -#define Read_Persitence_From_File_H +#ifndef READ_PERSISTENCE_FROM_FILE_H_ +#define READ_PERSISTENCE_FROM_FILE_H_ #include <iostream> #include <fstream> @@ -36,86 +36,6 @@ namespace Gudhi { namespace Persistence_representations { - - - -/** - * This procedure reads names of files which are stored in a file. -**/ -std::vector< std::string > readFileNames( const char* filenameWithFilenames ) -{ - bool dbg = false; - - std::ifstream in(filenameWithFilenames); - if ( !in.good() ) - { - std::cerr << "The file : " << filenameWithFilenames << " do not exist. The program will now terminate \n"; - throw "The file from which you are trying to read do not exist. The program will now terminate \n"; - } - - std::vector< std::string > result; - std::string line; - while (!in.eof()) - { - getline(in,line); - line.erase( std::remove_if( line.begin(), line.end(), ::isspace) , line.end() ); - - if (dbg){std::cerr << "line : " << line << std::endl;} - - if ( (line.length() == 0) || (line[0] == '#') ) - { - //in this case we have a file name. First we should remove all the white spaces. - if ( dbg ){std::cerr << "This is a line with comment, it will be ignored n";} - } - else - { - result.push_back( line ); - if (dbg){std::cerr << "Line after removing white spaces : " << line << std::endl;} - } - } - in.close(); - - return result; -}//readFileNames - - - -std::vector< std::vector< double > > read_numbers_from_file_line_by_line( const char* filename ) -{ - bool dbg = false; - std::ifstream in(filename); - if ( !in.good() ) - { - std::cerr << "The file : " << filename << " do not exist. The program will now terminate \n"; - throw "The file from which you are trying to read the persistence landscape do not exist. The program will now terminate \n"; - } - - std::vector< std::vector< double > > result; - double number; - - - std::string line; - while ( in.good() ) - { - std::getline(in,line); - std::stringstream ss(line); - - if ( dbg )std::cerr << "\n Reading line : " << line << std::endl; - - std::vector< double > this_line; - while ( ss.good() ) - { - ss >> number; - this_line.push_back( number ); - if ( dbg )std::cerr << number << " "; - } - if ( this_line.size() && in.good() ) result.push_back( this_line ); - } - in.close(); - - return result; -}//read_numbers_from_file_line_by_line - /** * Universal procedure to read files with persistence. It ignores the lines starting from # (treat them as comments). @@ -123,7 +43,7 @@ std::vector< std::vector< double > > read_numbers_from_file_line_by_line( const * that each other line in the file, which is not a comment, have the same number of numerical entries (2, 3 or 4). * If there are two numerical entries per line, then the function assume that they are birth/death coordinates. * If there are three numerical entries per line, then the function assume that they are: dimension and birth/death coordinates. - * If there are four numerical entries per line, then the function assume that they are: thc characteristic of a filed over which + * If there are four numerical entries per line, then the function assume that they are: the characteristic of a filed over which * persistence was computed, dimension and birth/death coordinates. * The 'inf' string can appear only as a last element of a line. * The procedure returns vector of persistence pairs. @@ -162,7 +82,7 @@ std::vector<std::pair<double,double> > read_persistence_intervals_in_one_dimensi if ( line_copy.find("inf") != std::string::npos ) { size_t np = line_copy.find("inf"); - //replace symbols 'inf' in line_copy with whilespaces: + //replace symbols 'inf' in line_copy with white spaces: line_copy[np] = ' '; line_copy[np+1] = ' '; line_copy[np+2] = ' '; @@ -194,7 +114,7 @@ std::vector<std::pair<double,double> > read_persistence_intervals_in_one_dimensi { std::cerr << "This line: " << line << " contains infinite interval. \n"; } - //first we substitute inf by whitespaces: + //first we substitute inf by white spaces: size_t np = line.find("inf"); line[np] = ' '; line[np+1] = ' '; @@ -288,13 +208,9 @@ std::vector<std::pair<double,double> > read_persistence_intervals_in_one_dimensi if ( dbg )std::cerr << "End of reading \n"; return barcode; -}//read_persistence_intervals_in_one_dimension_from_file +} // read_persistence_intervals_in_one_dimension_from_file -}//namespace Gudhi_stat -}//namespace Gudhi +} // namespace Persistence_representations +} // namespace Gudhi - - - -#endif - +#endif // READ_PERSISTENCE_FROM_FILE_H_ |