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authorpdlotko <pdlotko@636b058d-ea47-450e-bf9e-a15bfbe3eedb>2017-03-24 20:22:47 +0000
committerpdlotko <pdlotko@636b058d-ea47-450e-bf9e-a15bfbe3eedb>2017-03-24 20:22:47 +0000
commitee086a78f61f1ac6dd14ecab6e34d6710c971f64 (patch)
tree91d7bec2f0d8bca9b84f31d523a82240d79cd12a
parent5b6290423812b24cc3f67a4a8e9c9027b9d95cd6 (diff)
Answer to Marc's comments.
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/gudhi_stat@2240 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 20c02d536373553322a3e10eb4aacc2959db654a
-rw-r--r--src/Gudhi_stat/concept/Topological_data_with_averages.h1
-rw-r--r--src/Gudhi_stat/concept/Topological_data_with_distances.h4
-rw-r--r--src/Gudhi_stat/example/persistence_heat_maps.cpp120
-rw-r--r--src/Gudhi_stat/example/persistence_intervals.cpp2
-rw-r--r--src/Gudhi_stat/example/persistence_landscape.cpp128
-rw-r--r--src/Gudhi_stat/example/persistence_landscape_on_grid.cpp109
-rw-r--r--src/Gudhi_stat/example/vector_representation.cpp32
-rw-r--r--src/Gudhi_stat/include/gudhi/multiplicative_bootstrap.h8
-rw-r--r--src/Gudhi_stat/include/gudhi/topological_process.h8
-rw-r--r--src/Gudhi_stat/test/persistence_heat_maps_test.cpp120
-rw-r--r--src/Gudhi_stat/test/persistence_intervals_test.cpp2
-rw-r--r--src/Gudhi_stat/test/persistence_lanscapes_on_grid_test.cpp109
-rw-r--r--src/Gudhi_stat/test/persistence_lanscapes_test.cpp129
-rw-r--r--src/Gudhi_stat/test/vector_representation_test.cpp2
-rw-r--r--src/Gudhi_stat/utilities/Hausdorff_bootstrap.cpp2
-rw-r--r--src/Gudhi_stat/utilities/Landscape_bootstrap.cpp4
-rw-r--r--src/Gudhi_stat/utilities/Multiplicative_bootstrap.cpp2
-rw-r--r--src/Gudhi_stat/utilities/permutation_test.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_heat_maps/create_pssk.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp4
-rw-r--r--src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_Betti_numebrs.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_intervals.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_landscapes/average_landscapes.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_landscapes/create_landscapes.cpp6
-rw-r--r--src/Gudhi_stat/utilities/persistence_landscapes/plot_landscapes.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_vectors/average_persistence_vectors.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_vectors/create_persistence_vectors.cpp2
-rw-r--r--src/Gudhi_stat/utilities/persistence_vectors/plot_persistence_vectors.cpp2
47 files changed, 412 insertions, 436 deletions
diff --git a/src/Gudhi_stat/concept/Topological_data_with_averages.h b/src/Gudhi_stat/concept/Topological_data_with_averages.h
index 67433860..aeeb94f0 100644
--- a/src/Gudhi_stat/concept/Topological_data_with_averages.h
+++ b/src/Gudhi_stat/concept/Topological_data_with_averages.h
@@ -25,6 +25,7 @@
/** \brief The concept Topological_data_with_averages describes the requirements
* for a type to implement a container that allows computations of averages.
+ * Note that the average object after being computed is stored in *this.
*/
class Topological_data_with_averages
{
diff --git a/src/Gudhi_stat/concept/Topological_data_with_distances.h b/src/Gudhi_stat/concept/Topological_data_with_distances.h
index 536ae821..1318b9d1 100644
--- a/src/Gudhi_stat/concept/Topological_data_with_distances.h
+++ b/src/Gudhi_stat/concept/Topological_data_with_distances.h
@@ -22,6 +22,10 @@
/** \brief The concept Topological_data_with_distances describes the requirements
* for a type to implement a container that allows computations of distance to another contained of that type.
+ * The second parameter of the distance function allow to declare power of a distance. The exact meaning of that
+ * number will be different for different distances. A few examples are given below:
+ * In case of p-Wasserstein distance, the power is equal to p. power = std::limit<double>::max() for bottleneck distance.
+ * In case of L^p landscape distance, the power is equal to p. s
*/
class Topological_data_with_distances
{
diff --git a/src/Gudhi_stat/example/persistence_heat_maps.cpp b/src/Gudhi_stat/example/persistence_heat_maps.cpp
index c8dde3cd..0e5f7b79 100644
--- a/src/Gudhi_stat/example/persistence_heat_maps.cpp
+++ b/src/Gudhi_stat/example/persistence_heat_maps.cpp
@@ -23,7 +23,7 @@
#include <gudhi/reader_utils.h>
-#include <gudhi/concretizations/Persistence_heat_maps.h>
+#include <gudhi/persistence_representations/Persistence_heat_maps.h>
#include <iostream>
#include <vector>
@@ -91,121 +91,3 @@ int main( int argc , char** argv )
-
-
-
-//Below I am storing the code used to generate tests for that functionality.
-/*
- std::vector< std::pair< double,double > > intervals;
- intervals.push_back( std::make_pair(0.5,0.5) );
- std::vector< std::vector<double> > filter = create_Gaussian_filter(5,1);
- Persistence_heat_maps p( intervals , filter , constant_function, false , 100 , 0 , 1 );
- p.plot( "heat_map_1" );
-
-
- std::vector< std::pair< double,double > > intervals2;
- intervals2.push_back( std::make_pair(7,12) );
- Persistence_heat_maps q( intervals2 , filter , constant_function, false , 100 , 0 , 10 );
- q.plot( "heat_map_2" );
-*/
-/*
- std::vector< std::pair< double,double > > intervals;
- intervals.push_back( std::make_pair(0.5,0.5) );
- std::vector< std::vector<double> > filter = create_Gaussian_filter(5,1);
- Persistence_heat_maps p( intervals , filter , constant_function, false , 10 , 0 , 1 );
- p.write_to_file( "aaa" );
-
- Persistence_heat_maps q;
- q.load_from_file( "aaa" );
-
- cerr << ( p == q ) << endl;
- */
-
-/*
- std::vector< std::vector<double> > filter = create_Gaussian_filter(30,1);
- Persistence_heat_maps p( "file_with_diagram" , filter , constant_function, false , 100 , 0 , 1 );
- p.plot( "heat_map_1" );
-*/
-
-/*
- //test to construct persistence heat map:
- std::vector< std::vector<double> > filter = create_Gaussian_filter(100,1);
- Persistence_heat_maps p( "file_with_diagram" , filter , constant_function, false , 1000 , 0 , 1 );
- p.print_to_file( "persistence_heat_map_from_file_with_diagram" );
-
- Persistence_heat_maps q;
- q.load_from_file( "persistence_heat_map_from_file_with_diagram" );
-
- cerr << (p == q) << endl;
-*/
-/*
- //test of computations of a mean:
- std::vector< std::pair< double,double > > intervals;
- intervals.push_back( std::make_pair(5,5) );
- std::vector< std::vector<double> > filter = create_Gaussian_filter(5,1);
- Persistence_heat_maps p( intervals , filter , constant_function, false , 100 , 0 , 10 );
- p.plot( "heat_map_1" );
-
-
- std::vector< std::pair< double,double > > intervals2;
- intervals2.push_back( std::make_pair(7,7) );
- Persistence_heat_maps q( intervals2 , filter , constant_function, false , 100 , 0 , 10 );
- q.plot( "heat_map_2" );
-
-
- Persistence_heat_maps av;
- av.compute_average( { &P , &q } );
- av.plot( "average" );
-*/
-
-/*
- std::vector< std::vector<double> > filter = create_Gaussian_filter(30,1);
- Persistence_heat_maps p( "file_with_diagram" , filter , constant_function, false , 1000 , 0 , 10 );
- Persistence_heat_maps q( "file_with_diagram_1" , filter , constant_function, false , 1000 , 0 , 10 );
- Persistence_heat_maps r( "file_with_diagram_2" , filter , constant_function, false , 1000 , 0 , 10 );
- Persistence_heat_maps av;
- av.compute_average( {&p,&q,&r} );
-
- av.print_to_file( "template_average_of_heat_maps" );
-*/
-
-/*
- std::vector< std::pair< double,double > > intervals;
- intervals.push_back( std::make_pair(5,5) );
- std::vector< std::vector<double> > filter = create_Gaussian_filter(5,1);
- Persistence_heat_maps p( intervals , filter , constant_function, false , 10 , 0 , 10 );
- p.plot( "heat_map_1" );
-
- std::vector< std::pair< double,double > > intervals2;
- intervals2.push_back( std::make_pair(7,7) );
- Persistence_heat_maps q( intervals2 , filter , constant_function, false , 10 , 0 , 10 );
- q.plot( "heat_map_2" );
-
- Persistence_heat_maps median;
- median.compute_median( {&p,&q} );
- median.plot( "median" );
-*/
-
-/*
- std::vector< std::vector<double> > filter = create_Gaussian_filter(30,1);
- Persistence_heat_maps p( "file_with_diagram" , filter , constant_function, false , 1000 , 0 , 1 );
- Persistence_heat_maps q( "file_with_diagram_1" , filter , constant_function, false , 1000 , 0 , 1 );
- Persistence_heat_maps r( "file_with_diagram_2" , filter , constant_function, false , 1000 , 0 , 1 );
- Persistence_heat_maps median;
- median.compute_median( {&p,&q,&r} );
- median.print_to_file( "template_median_of_heat_maps" );
-*/
-
-
-/*
- std::vector< std::vector<double> > filter = create_Gaussian_filter(30,1);
- Persistence_heat_maps p( "file_with_diagram" , filter , constant_function, false , 1000 , 0 , 1 );
- Persistence_heat_maps q( "file_with_diagram_1" , filter , constant_function, false , 1000 , 0 , 1 );
- Persistence_heat_maps r( "file_with_diagram_2" , filter , constant_function, false , 1000 , 0 , 1 );
-
- Persistence_heat_maps percentage_of_active;
- percentage_of_active.compute_percentage_of_active( {&p,&q,&r} , 0.1 );
-
- percentage_of_active.print_to_file( "template_percentage_of_active_of_heat_maps" );
- //percentage_of_active.plot( "template_percentage_of_active_of_heat_maps" );
-*/
diff --git a/src/Gudhi_stat/example/persistence_intervals.cpp b/src/Gudhi_stat/example/persistence_intervals.cpp
index 044ba3c3..04c758e6 100644
--- a/src/Gudhi_stat/example/persistence_intervals.cpp
+++ b/src/Gudhi_stat/example/persistence_intervals.cpp
@@ -23,7 +23,7 @@
#include <gudhi/reader_utils.h>
-#include <gudhi/concretizations/Persistence_intervals.h>
+#include <gudhi/persistence_representations/Persistence_intervals.h>
#include <iostream>
diff --git a/src/Gudhi_stat/example/persistence_landscape.cpp b/src/Gudhi_stat/example/persistence_landscape.cpp
index bb1cecea..9385c408 100644
--- a/src/Gudhi_stat/example/persistence_landscape.cpp
+++ b/src/Gudhi_stat/example/persistence_landscape.cpp
@@ -22,7 +22,7 @@
-#include <gudhi/concretizations/Persistence_landscape.h>
+#include <gudhi/persistence_representations/Persistence_landscape.h>
@@ -90,129 +90,3 @@ int main( int argc , char** argv )
return 0;
}
-
-//Below I am storing the code used to generate tests for that functionality.
-/*
-if ( argc != 2 )
- {
- std::cerr << "To run this program, please provide a name of a file with persistence landscape \n";
- //return 1;
- }
- Persistence_landscape p("../test/data/file_with_diagram");
-
- Persistence_landscape q;
- q.load_landscape_from_file( "file_with_landscape_from_file_with_diagram" );
-
- if ( p != q )
- {
- cout << "Not equal \n";
- }
-
- double integral = p.compute_integral_of_landscape();
- cout << "integral : " << integral <<endl;
-
- //compute integral for each level separatelly
- for ( size_t level = 0 ; level != p.size() ; ++level )
- {
- cout << p.compute_integral_of_landscape( level ) << endl;
- }
-
- //compute integral of p-th power of landscspe
- for ( size_t power = 0 ; power != 5 ; ++power )
- {
- cout << p.compute_integral_of_landscape( power ) << endl;
- }
-
- cout << "Value of level 1 at 0 : " << p.compute_value_at_a_given_point(1,0.0) << endl;
- cout << "Value of level 1 at 1 : " << p.compute_value_at_a_given_point(1,0.1) << endl;
- cout << "Value of level 1 at 2 : " << p.compute_value_at_a_given_point(1,0.2) << endl;
- cout << "Value of level 1 at 3 : " << p.compute_value_at_a_given_point(1,0.3) << endl;
-
-
- cout << "Value of level 2 at 0 : " << p.compute_value_at_a_given_point(2,0.0) << endl;
- cout << "Value of level 2 at 1 : " << p.compute_value_at_a_given_point(2,0.1) << endl;
- cout << "Value of level 2 at 2 : " << p.compute_value_at_a_given_point(2,0.2) << endl;
- cout << "Value of level 2 at 3 : " << p.compute_value_at_a_given_point(2,0.3) << endl;
-
-
- cout << "Value of level 3 at 0 : " << p.compute_value_at_a_given_point(3,0.0) << endl;
- cout << "Value of level 3 at 1 : " << p.compute_value_at_a_given_point(3,0.1) << endl;
- cout << "Value of level 3 at 2 : " << p.compute_value_at_a_given_point(3,0.2) << endl;
- cout << "Value of level 3 at 3 : " << p.compute_value_at_a_given_point(3,0.3) << endl;
-
-
-
- Persistence_landscape second;
- second.load_landscape_from_file("file_with_landscape_from_file_with_diagram_1" );
-
- Persistence_landscape sum = p + second;
- Persistence_landscape difference = p - second;
- Persistence_landscape multiply_by_scalar = 10*p;
-
- //sum.print_to_file("sum");
- //difference.print_to_file("difference");
- //multiply_by_scalar.print_to_file("multiply_by_scalar");
-
- Persistence_landscape template_sum;
- template_sum.load_landscape_from_file( "sum" );
- Persistence_landscape template_difference;
- template_difference.load_landscape_from_file( "difference" );
- Persistence_landscape template_multiply_by_scalar;
- template_multiply_by_scalar.load_landscape_from_file( "multiply_by_scalar" );
-
- if ( sum != template_sum )
- {
- cerr << "Problem with sums \n";
- }
- if ( difference != template_difference )
- {
- cerr << "Problem with differences \n";
- }
- if ( multiply_by_scalar != template_multiply_by_scalar )
- {
- cerr << "Problem with multiplication by scalar \n";
- }
-
-
-
- cout << "Maximum : " << p.compute_maximum() << endl;
-
- cout << "L^1 norm : " << p.compute_norm_of_landscape(1) << endl;
- cout << "L^2 norm : " << p.compute_norm_of_landscape(2) << endl;
- cout << "L^3 norm : " << p.compute_norm_of_landscape(3) << endl;
-
-
- cout << "L^1 distance : " << compute_distance_of_landscapes(p,sum,1) << endl;
- cout << "L^2 distance : " << compute_distance_of_landscapes(p,sum,2) << endl;
- cout << "L^infty distance : " << compute_distance_of_landscapes(p,sum,std::numeric_limits<double>::max() ) << endl;
-
- {
- Persistence_landscape p( "../test/data/file_with_diagram" );
- Persistence_landscape q( "../test/data/file_with_diagram_1" );
- Persistence_landscape av;
- av.compute_average( {&p,&q} );
-
- Persistence_landscape template_average;
- template_average.load_landscape_from_file( "average" );
- if ( template_average != av )
- {
- cerr << "We have a problem with average \n";
- }
- }
-
-
- {
- Persistence_landscape p( "../test/data/file_with_diagram" );
- Persistence_landscape q( "../test/data/file_with_diagram_1" );
- cout << "L^1 distance : " << p.distance( &q ) << endl;
- cout << "L^2 distance : " << p.distance( &q , 2) << endl;
- cout << "L^infty distance : " << p.distance( &q , std::numeric_limits<double>::max() ) << endl;
- }
-
-
- {
- Persistence_landscape p( "../test/data/file_with_diagram" );
- Persistence_landscape q( "../test/data/file_with_diagram_1" );
- cout << "Scalar product : " << p.compute_scalar_product( &q ) << endl;
- }
-*/
diff --git a/src/Gudhi_stat/example/persistence_landscape_on_grid.cpp b/src/Gudhi_stat/example/persistence_landscape_on_grid.cpp
index 9133944d..d432d757 100644
--- a/src/Gudhi_stat/example/persistence_landscape_on_grid.cpp
+++ b/src/Gudhi_stat/example/persistence_landscape_on_grid.cpp
@@ -22,7 +22,7 @@
-#include <gudhi/concretizations/Persistence_landscape_on_grid.h>
+#include <gudhi/persistence_representations/Persistence_landscape_on_grid.h>
@@ -86,110 +86,3 @@ int main( int argc , char** argv )
return 0;
}
-
-
-//Below I am storing the code used to generate tests for that functionality.
-/*
- Persistence_landscape_on_grid l( "file_with_diagram_1" , 100 );
- l.print_to_file( "landscape_from_file_with_diagram_1" );
-
- Persistence_landscape_on_grid g;
- g.load_landscape_from_file( "landscape_from_file_with_diagram_1" );
-
- cerr << ( l == g );
- */
-
- /*
- Persistence_landscape_on_grid l( "file_with_diagram_1" , 100 );
- cerr << l << endl;
- cerr << l.compute_integral_of_landscape() << endl;
- */
-
- /*
- Persistence_landscape_on_grid p( "file_with_diagram_1" , 100 );
- for ( size_t level = 0 ; level != 30 ; ++level )
- {
- double integral = p.compute_integral_of_landscape( level );
- cerr << integral << endl;
- }
- */
-
- /*
- Persistence_landscape_on_grid p( "file_with_diagram_1" , 100 );
- for ( size_t power = 0 ; power != 5 ; ++power )
- {
- double integral = p.compute_integral_of_landscape( (double)power );
- cerr << integral << endl;
- }
- */
-
- /*
- Persistence_landscape_on_grid p( "file_with_diagram_1" , 100 );
- double x = 0.0012321;
- double dx = 0.05212;
- for ( size_t i = 0 ; i != 10 ; ++i )
- {
- cerr << p.compute_value_at_a_given_point(10,x) << endl;
- x += dx;
- }
- */
-
- /*
- Persistence_landscape_on_grid p( "file_with_diagram_1",100 );
- Persistence_landscape_on_grid second("file_with_diagram_1",100 );
- Persistence_landscape_on_grid sum = p + second;
- Persistence_landscape_on_grid difference = p - second;
- Persistence_landscape_on_grid multiply_by_scalar = 10*p;
- sum.print_to_file( "sum_on_grid_test" );
- difference.print_to_file( "difference_on_grid_test" );
- multiply_by_scalar.print_to_file( "multiply_by_scalar_on_grid_test" );
- */
-
-
- /*
- Persistence_landscape_on_grid p( "file_with_diagram_1" , 0 , 1 , 100 );
- Persistence_landscape_on_grid second("file_with_diagram_1", 0 , 1 , 100 );
- Persistence_landscape_on_grid sum = p + second;
-
- cerr << "max : " << p.compute_maximum() << endl;
- cerr << "1-norm : " << p.compute_norm_of_landscape(1) << endl;
- cerr << "2-norm : " << p.compute_norm_of_landscape(2) << endl;
- cerr << "3-norm : " << p.compute_norm_of_landscape(3) << endl;
-
- cerr << compute_distance_of_landscapes_on_grid(p,sum,1) << endl;
- cerr << compute_distance_of_landscapes_on_grid(p,sum,2) << endl;
- cerr << compute_distance_of_landscapes_on_grid(p,sum,-1) << endl;
- */
-
- /*
- Persistence_landscape_on_grid p( "file_with_diagram", 0,1,100 );
- Persistence_landscape_on_grid q( "file_with_diagram_1", 0,1,100 );
- Persistence_landscape_on_grid av;
- av.compute_average( {&p,&q} );
- av.print_to_file("average_on_a_grid");
-
- Persistence_landscape_on_grid template_average;
- template_average.load_landscape_from_file( "average_on_a_grid" );
- if ( template_average == av )
- {
- cerr << "OK OK \n";
- }*/
-
- /*
- Persistence_landscape_on_grid p( "file_with_diagram" , 0,1,10000);
- Persistence_landscape_on_grid q( "file_with_diagram_1" , 0,1,10000);
- cerr << p.distance( &q )<< endl;
- cerr << p.distance( &q , 2 ) << endl;
- cerr << p.distance( &q , std::numeric_limits<double>::max() ) << endl;
- */
-
-/*
- Persistence_landscape_on_grid p( "file_with_diagram", 0,1,10000 );
- Persistence_landscape_on_grid q( "file_with_diagram_1", 0,1,10000 );
-
- //std::vector< std::pair< double,double > > aa;
- //aa.push_back( std::make_pair( 0,1 ) );
- //Persistence_landscape_on_grid p( aa, 0,1,10 );
- //Persistence_landscape_on_grid q( aa, 0,1,10 );
- cerr << p.compute_scalar_product( &q ) << endl;
-*/
diff --git a/src/Gudhi_stat/example/vector_representation.cpp b/src/Gudhi_stat/example/vector_representation.cpp
index 981e63de..476deeba 100644
--- a/src/Gudhi_stat/example/vector_representation.cpp
+++ b/src/Gudhi_stat/example/vector_representation.cpp
@@ -22,7 +22,7 @@
-#include <gudhi/concretizations/Vector_distances_in_diagram.h>
+#include <gudhi/persistence_representations/Vector_distances_in_diagram.h>
#include <iostream>
@@ -78,33 +78,3 @@ int main( int argc , char** argv )
return 0;
}
-
-
-
-
-/*
- if ( argc < 2 )
- {
- cout << "To run this program, please provide the name of a file with persistence diagram. If you provide two files, we will do distance, scalar produc and average computations \n";
- return 1;
- }
-
- Vector_distances_in_diagram< Euclidean_distance<double> > p( argv[1] , 100 );
- cout << "This is a vector corresponding to the input persistence diagram : \n";
- cout << p << endl;
-
-
-
- if ( argc == 3 )
- {
- Vector_distances_in_diagram< Euclidean_distance<double> > p_prime( argv[2] , 100);
-
- cout << "p_prime : " <<p_prime << endl;
-
- cout << "Distance between input persistence diagrams : " << p.distance( &p_prime ) << endl;
- Vector_distances_in_diagram< Euclidean_distance<double> > average;
- average.compute_average( {&p,&p_prime} );
-
- cout << "Here is an average : " << average << endl;
- }
-*/
diff --git a/src/Gudhi_stat/include/gudhi/multiplicative_bootstrap.h b/src/Gudhi_stat/include/gudhi/multiplicative_bootstrap.h
index b38536d9..c350349c 100644
--- a/src/Gudhi_stat/include/gudhi/multiplicative_bootstrap.h
+++ b/src/Gudhi_stat/include/gudhi/multiplicative_bootstrap.h
@@ -24,10 +24,10 @@
#define BOOTSTRAP_H
//concretizations
-#include <gudhi/concretizations/Vector_distances_in_diagram.h>
-#include <gudhi/concretizations/Persistence_landscape.h>
-#include <gudhi/concretizations/Persistence_landscape_on_grid.h>
-#include <gudhi/concretizations/Persistence_heat_maps.h>
+#include <gudhi/persistence_representations/Vector_distances_in_diagram.h>
+#include <gudhi/persistence_representations/Persistence_landscape.h>
+#include <gudhi/persistence_representations/Persistence_landscape_on_grid.h>
+#include <gudhi/persistence_representations/Persistence_heat_maps.h>
#ifdef GUDHI_USE_TBB
#include <tbb/parallel_sort.h>
diff --git a/src/Gudhi_stat/include/gudhi/topological_process.h b/src/Gudhi_stat/include/gudhi/topological_process.h
index ac658aee..4a41c0a7 100644
--- a/src/Gudhi_stat/include/gudhi/topological_process.h
+++ b/src/Gudhi_stat/include/gudhi/topological_process.h
@@ -25,10 +25,10 @@
//concretizations
-#include <gudhi/concretizations/Vector_distances_in_diagram.h>
-#include <gudhi/concretizations/Persistence_landscape.h>
-#include <gudhi/concretizations/Persistence_landscape_on_grid.h>
-#include <gudhi/concretizations/Persistence_heat_maps.h>
+#include <gudhi/persistence_representations/Vector_distances_in_diagram.h>
+#include <gudhi/persistence_representations/Persistence_landscape.h>
+#include <gudhi/persistence_representations/Persistence_landscape_on_grid.h>
+#include <gudhi/persistence_representations/Persistence_heat_maps.h>
#include <vector>
#include <limits>
diff --git a/src/Gudhi_stat/test/persistence_heat_maps_test.cpp b/src/Gudhi_stat/test/persistence_heat_maps_test.cpp
index 4447ba37..fb094912 100644
--- a/src/Gudhi_stat/test/persistence_heat_maps_test.cpp
+++ b/src/Gudhi_stat/test/persistence_heat_maps_test.cpp
@@ -26,7 +26,7 @@
#define BOOST_TEST_MODULE "gudhi_stat"
#include <boost/test/unit_test.hpp>
#include <gudhi/reader_utils.h>
-#include <gudhi/concretizations/Persistence_heat_maps.h>
+#include <gudhi/persistence_representations/Persistence_heat_maps.h>
#include <iostream>
@@ -258,3 +258,121 @@ BOOST_AUTO_TEST_CASE(check_arythmetic_operations_for_heat_maps)
}
+
+
+
+//Below I am storing the code used to generate tests for that functionality.
+/*
+ std::vector< std::pair< double,double > > intervals;
+ intervals.push_back( std::make_pair(0.5,0.5) );
+ std::vector< std::vector<double> > filter = create_Gaussian_filter(5,1);
+ Persistence_heat_maps p( intervals , filter , constant_function, false , 100 , 0 , 1 );
+ p.plot( "heat_map_1" );
+
+
+ std::vector< std::pair< double,double > > intervals2;
+ intervals2.push_back( std::make_pair(7,12) );
+ Persistence_heat_maps q( intervals2 , filter , constant_function, false , 100 , 0 , 10 );
+ q.plot( "heat_map_2" );
+*/
+/*
+ std::vector< std::pair< double,double > > intervals;
+ intervals.push_back( std::make_pair(0.5,0.5) );
+ std::vector< std::vector<double> > filter = create_Gaussian_filter(5,1);
+ Persistence_heat_maps p( intervals , filter , constant_function, false , 10 , 0 , 1 );
+ p.write_to_file( "aaa" );
+
+ Persistence_heat_maps q;
+ q.load_from_file( "aaa" );
+
+ cerr << ( p == q ) << endl;
+ */
+
+/*
+ std::vector< std::vector<double> > filter = create_Gaussian_filter(30,1);
+ Persistence_heat_maps p( "file_with_diagram" , filter , constant_function, false , 100 , 0 , 1 );
+ p.plot( "heat_map_1" );
+*/
+
+/*
+ //test to construct persistence heat map:
+ std::vector< std::vector<double> > filter = create_Gaussian_filter(100,1);
+ Persistence_heat_maps p( "file_with_diagram" , filter , constant_function, false , 1000 , 0 , 1 );
+ p.print_to_file( "persistence_heat_map_from_file_with_diagram" );
+
+ Persistence_heat_maps q;
+ q.load_from_file( "persistence_heat_map_from_file_with_diagram" );
+
+ cerr << (p == q) << endl;
+*/
+/*
+ //test of computations of a mean:
+ std::vector< std::pair< double,double > > intervals;
+ intervals.push_back( std::make_pair(5,5) );
+ std::vector< std::vector<double> > filter = create_Gaussian_filter(5,1);
+ Persistence_heat_maps p( intervals , filter , constant_function, false , 100 , 0 , 10 );
+ p.plot( "heat_map_1" );
+
+
+ std::vector< std::pair< double,double > > intervals2;
+ intervals2.push_back( std::make_pair(7,7) );
+ Persistence_heat_maps q( intervals2 , filter , constant_function, false , 100 , 0 , 10 );
+ q.plot( "heat_map_2" );
+
+
+ Persistence_heat_maps av;
+ av.compute_average( { &P , &q } );
+ av.plot( "average" );
+*/
+
+/*
+ std::vector< std::vector<double> > filter = create_Gaussian_filter(30,1);
+ Persistence_heat_maps p( "file_with_diagram" , filter , constant_function, false , 1000 , 0 , 10 );
+ Persistence_heat_maps q( "file_with_diagram_1" , filter , constant_function, false , 1000 , 0 , 10 );
+ Persistence_heat_maps r( "file_with_diagram_2" , filter , constant_function, false , 1000 , 0 , 10 );
+ Persistence_heat_maps av;
+ av.compute_average( {&p,&q,&r} );
+
+ av.print_to_file( "template_average_of_heat_maps" );
+*/
+
+/*
+ std::vector< std::pair< double,double > > intervals;
+ intervals.push_back( std::make_pair(5,5) );
+ std::vector< std::vector<double> > filter = create_Gaussian_filter(5,1);
+ Persistence_heat_maps p( intervals , filter , constant_function, false , 10 , 0 , 10 );
+ p.plot( "heat_map_1" );
+
+ std::vector< std::pair< double,double > > intervals2;
+ intervals2.push_back( std::make_pair(7,7) );
+ Persistence_heat_maps q( intervals2 , filter , constant_function, false , 10 , 0 , 10 );
+ q.plot( "heat_map_2" );
+
+ Persistence_heat_maps median;
+ median.compute_median( {&p,&q} );
+ median.plot( "median" );
+*/
+
+/*
+ std::vector< std::vector<double> > filter = create_Gaussian_filter(30,1);
+ Persistence_heat_maps p( "file_with_diagram" , filter , constant_function, false , 1000 , 0 , 1 );
+ Persistence_heat_maps q( "file_with_diagram_1" , filter , constant_function, false , 1000 , 0 , 1 );
+ Persistence_heat_maps r( "file_with_diagram_2" , filter , constant_function, false , 1000 , 0 , 1 );
+ Persistence_heat_maps median;
+ median.compute_median( {&p,&q,&r} );
+ median.print_to_file( "template_median_of_heat_maps" );
+*/
+
+
+/*
+ std::vector< std::vector<double> > filter = create_Gaussian_filter(30,1);
+ Persistence_heat_maps p( "file_with_diagram" , filter , constant_function, false , 1000 , 0 , 1 );
+ Persistence_heat_maps q( "file_with_diagram_1" , filter , constant_function, false , 1000 , 0 , 1 );
+ Persistence_heat_maps r( "file_with_diagram_2" , filter , constant_function, false , 1000 , 0 , 1 );
+
+ Persistence_heat_maps percentage_of_active;
+ percentage_of_active.compute_percentage_of_active( {&p,&q,&r} , 0.1 );
+
+ percentage_of_active.print_to_file( "template_percentage_of_active_of_heat_maps" );
+ //percentage_of_active.plot( "template_percentage_of_active_of_heat_maps" );
+*/
diff --git a/src/Gudhi_stat/test/persistence_intervals_test.cpp b/src/Gudhi_stat/test/persistence_intervals_test.cpp
index 96d913e0..d46d009b 100644
--- a/src/Gudhi_stat/test/persistence_intervals_test.cpp
+++ b/src/Gudhi_stat/test/persistence_intervals_test.cpp
@@ -26,7 +26,7 @@
#define BOOST_TEST_MODULE "gudhi_stat"
#include <boost/test/unit_test.hpp>
#include <gudhi/reader_utils.h>
-#include "gudhi/concretizations/Persistence_intervals.h"
+#include "gudhi/persistence_representations/Persistence_intervals.h"
#include <iostream>
diff --git a/src/Gudhi_stat/test/persistence_lanscapes_on_grid_test.cpp b/src/Gudhi_stat/test/persistence_lanscapes_on_grid_test.cpp
index 84b01f3e..2e4ba8d9 100644
--- a/src/Gudhi_stat/test/persistence_lanscapes_on_grid_test.cpp
+++ b/src/Gudhi_stat/test/persistence_lanscapes_on_grid_test.cpp
@@ -26,7 +26,7 @@
#define BOOST_TEST_MODULE "gudhi_stat"
#include <boost/test/unit_test.hpp>
#include <gudhi/reader_utils.h>
-#include <gudhi/concretizations/Persistence_landscape_on_grid.h>
+#include <gudhi/persistence_representations/Persistence_landscape_on_grid.h>
#include <iostream>
@@ -247,3 +247,110 @@ BOOST_AUTO_TEST_CASE(check_computations_of_scalar_product)
}
+
+
+//Below I am storing the code used to generate tests for that functionality.
+/*
+ Persistence_landscape_on_grid l( "file_with_diagram_1" , 100 );
+ l.print_to_file( "landscape_from_file_with_diagram_1" );
+
+ Persistence_landscape_on_grid g;
+ g.load_landscape_from_file( "landscape_from_file_with_diagram_1" );
+
+ cerr << ( l == g );
+ */
+
+ /*
+ Persistence_landscape_on_grid l( "file_with_diagram_1" , 100 );
+ cerr << l << endl;
+ cerr << l.compute_integral_of_landscape() << endl;
+ */
+
+ /*
+ Persistence_landscape_on_grid p( "file_with_diagram_1" , 100 );
+ for ( size_t level = 0 ; level != 30 ; ++level )
+ {
+ double integral = p.compute_integral_of_landscape( level );
+ cerr << integral << endl;
+ }
+ */
+
+ /*
+ Persistence_landscape_on_grid p( "file_with_diagram_1" , 100 );
+ for ( size_t power = 0 ; power != 5 ; ++power )
+ {
+ double integral = p.compute_integral_of_landscape( (double)power );
+ cerr << integral << endl;
+ }
+ */
+
+ /*
+ Persistence_landscape_on_grid p( "file_with_diagram_1" , 100 );
+ double x = 0.0012321;
+ double dx = 0.05212;
+ for ( size_t i = 0 ; i != 10 ; ++i )
+ {
+ cerr << p.compute_value_at_a_given_point(10,x) << endl;
+ x += dx;
+ }
+ */
+
+ /*
+ Persistence_landscape_on_grid p( "file_with_diagram_1",100 );
+ Persistence_landscape_on_grid second("file_with_diagram_1",100 );
+ Persistence_landscape_on_grid sum = p + second;
+ Persistence_landscape_on_grid difference = p - second;
+ Persistence_landscape_on_grid multiply_by_scalar = 10*p;
+ sum.print_to_file( "sum_on_grid_test" );
+ difference.print_to_file( "difference_on_grid_test" );
+ multiply_by_scalar.print_to_file( "multiply_by_scalar_on_grid_test" );
+ */
+
+
+ /*
+ Persistence_landscape_on_grid p( "file_with_diagram_1" , 0 , 1 , 100 );
+ Persistence_landscape_on_grid second("file_with_diagram_1", 0 , 1 , 100 );
+ Persistence_landscape_on_grid sum = p + second;
+
+ cerr << "max : " << p.compute_maximum() << endl;
+ cerr << "1-norm : " << p.compute_norm_of_landscape(1) << endl;
+ cerr << "2-norm : " << p.compute_norm_of_landscape(2) << endl;
+ cerr << "3-norm : " << p.compute_norm_of_landscape(3) << endl;
+
+ cerr << compute_distance_of_landscapes_on_grid(p,sum,1) << endl;
+ cerr << compute_distance_of_landscapes_on_grid(p,sum,2) << endl;
+ cerr << compute_distance_of_landscapes_on_grid(p,sum,-1) << endl;
+ */
+
+ /*
+ Persistence_landscape_on_grid p( "file_with_diagram", 0,1,100 );
+ Persistence_landscape_on_grid q( "file_with_diagram_1", 0,1,100 );
+ Persistence_landscape_on_grid av;
+ av.compute_average( {&p,&q} );
+ av.print_to_file("average_on_a_grid");
+
+ Persistence_landscape_on_grid template_average;
+ template_average.load_landscape_from_file( "average_on_a_grid" );
+ if ( template_average == av )
+ {
+ cerr << "OK OK \n";
+ }*/
+
+ /*
+ Persistence_landscape_on_grid p( "file_with_diagram" , 0,1,10000);
+ Persistence_landscape_on_grid q( "file_with_diagram_1" , 0,1,10000);
+ cerr << p.distance( &q )<< endl;
+ cerr << p.distance( &q , 2 ) << endl;
+ cerr << p.distance( &q , std::numeric_limits<double>::max() ) << endl;
+ */
+
+/*
+ Persistence_landscape_on_grid p( "file_with_diagram", 0,1,10000 );
+ Persistence_landscape_on_grid q( "file_with_diagram_1", 0,1,10000 );
+
+ //std::vector< std::pair< double,double > > aa;
+ //aa.push_back( std::make_pair( 0,1 ) );
+ //Persistence_landscape_on_grid p( aa, 0,1,10 );
+ //Persistence_landscape_on_grid q( aa, 0,1,10 );
+ cerr << p.compute_scalar_product( &q ) << endl;
+*/
diff --git a/src/Gudhi_stat/test/persistence_lanscapes_test.cpp b/src/Gudhi_stat/test/persistence_lanscapes_test.cpp
index dd010174..9b9f9d7b 100644
--- a/src/Gudhi_stat/test/persistence_lanscapes_test.cpp
+++ b/src/Gudhi_stat/test/persistence_lanscapes_test.cpp
@@ -26,7 +26,7 @@
#define BOOST_TEST_MODULE "gudhi_stat"
#include <boost/test/unit_test.hpp>
#include <gudhi/reader_utils.h>
-#include <gudhi/concretizations/Persistence_landscape.h>
+#include <gudhi/persistence_representations/Persistence_landscape.h>
#include <iostream>
@@ -217,3 +217,130 @@ BOOST_AUTO_TEST_CASE(check_computations_of_scalar_product)
BOOST_CHECK( fabs( p.compute_scalar_product( q ) - 0.754498 ) <= 0.00001 );
}
+
+
+//Below I am storing the code used to generate tests for that functionality.
+/*
+if ( argc != 2 )
+ {
+ std::cerr << "To run this program, please provide a name of a file with persistence landscape \n";
+ //return 1;
+ }
+ Persistence_landscape p("../test/data/file_with_diagram");
+
+ Persistence_landscape q;
+ q.load_landscape_from_file( "file_with_landscape_from_file_with_diagram" );
+
+ if ( p != q )
+ {
+ cout << "Not equal \n";
+ }
+
+ double integral = p.compute_integral_of_landscape();
+ cout << "integral : " << integral <<endl;
+
+ //compute integral for each level separatelly
+ for ( size_t level = 0 ; level != p.size() ; ++level )
+ {
+ cout << p.compute_integral_of_landscape( level ) << endl;
+ }
+
+ //compute integral of p-th power of landscspe
+ for ( size_t power = 0 ; power != 5 ; ++power )
+ {
+ cout << p.compute_integral_of_landscape( power ) << endl;
+ }
+
+ cout << "Value of level 1 at 0 : " << p.compute_value_at_a_given_point(1,0.0) << endl;
+ cout << "Value of level 1 at 1 : " << p.compute_value_at_a_given_point(1,0.1) << endl;
+ cout << "Value of level 1 at 2 : " << p.compute_value_at_a_given_point(1,0.2) << endl;
+ cout << "Value of level 1 at 3 : " << p.compute_value_at_a_given_point(1,0.3) << endl;
+
+
+ cout << "Value of level 2 at 0 : " << p.compute_value_at_a_given_point(2,0.0) << endl;
+ cout << "Value of level 2 at 1 : " << p.compute_value_at_a_given_point(2,0.1) << endl;
+ cout << "Value of level 2 at 2 : " << p.compute_value_at_a_given_point(2,0.2) << endl;
+ cout << "Value of level 2 at 3 : " << p.compute_value_at_a_given_point(2,0.3) << endl;
+
+
+ cout << "Value of level 3 at 0 : " << p.compute_value_at_a_given_point(3,0.0) << endl;
+ cout << "Value of level 3 at 1 : " << p.compute_value_at_a_given_point(3,0.1) << endl;
+ cout << "Value of level 3 at 2 : " << p.compute_value_at_a_given_point(3,0.2) << endl;
+ cout << "Value of level 3 at 3 : " << p.compute_value_at_a_given_point(3,0.3) << endl;
+
+
+
+ Persistence_landscape second;
+ second.load_landscape_from_file("file_with_landscape_from_file_with_diagram_1" );
+
+ Persistence_landscape sum = p + second;
+ Persistence_landscape difference = p - second;
+ Persistence_landscape multiply_by_scalar = 10*p;
+
+ //sum.print_to_file("sum");
+ //difference.print_to_file("difference");
+ //multiply_by_scalar.print_to_file("multiply_by_scalar");
+
+ Persistence_landscape template_sum;
+ template_sum.load_landscape_from_file( "sum" );
+ Persistence_landscape template_difference;
+ template_difference.load_landscape_from_file( "difference" );
+ Persistence_landscape template_multiply_by_scalar;
+ template_multiply_by_scalar.load_landscape_from_file( "multiply_by_scalar" );
+
+ if ( sum != template_sum )
+ {
+ cerr << "Problem with sums \n";
+ }
+ if ( difference != template_difference )
+ {
+ cerr << "Problem with differences \n";
+ }
+ if ( multiply_by_scalar != template_multiply_by_scalar )
+ {
+ cerr << "Problem with multiplication by scalar \n";
+ }
+
+
+
+ cout << "Maximum : " << p.compute_maximum() << endl;
+
+ cout << "L^1 norm : " << p.compute_norm_of_landscape(1) << endl;
+ cout << "L^2 norm : " << p.compute_norm_of_landscape(2) << endl;
+ cout << "L^3 norm : " << p.compute_norm_of_landscape(3) << endl;
+
+
+ cout << "L^1 distance : " << compute_distance_of_landscapes(p,sum,1) << endl;
+ cout << "L^2 distance : " << compute_distance_of_landscapes(p,sum,2) << endl;
+ cout << "L^infty distance : " << compute_distance_of_landscapes(p,sum,std::numeric_limits<double>::max() ) << endl;
+
+ {
+ Persistence_landscape p( "../test/data/file_with_diagram" );
+ Persistence_landscape q( "../test/data/file_with_diagram_1" );
+ Persistence_landscape av;
+ av.compute_average( {&p,&q} );
+
+ Persistence_landscape template_average;
+ template_average.load_landscape_from_file( "average" );
+ if ( template_average != av )
+ {
+ cerr << "We have a problem with average \n";
+ }
+ }
+
+
+ {
+ Persistence_landscape p( "../test/data/file_with_diagram" );
+ Persistence_landscape q( "../test/data/file_with_diagram_1" );
+ cout << "L^1 distance : " << p.distance( &q ) << endl;
+ cout << "L^2 distance : " << p.distance( &q , 2) << endl;
+ cout << "L^infty distance : " << p.distance( &q , std::numeric_limits<double>::max() ) << endl;
+ }
+
+
+ {
+ Persistence_landscape p( "../test/data/file_with_diagram" );
+ Persistence_landscape q( "../test/data/file_with_diagram_1" );
+ cout << "Scalar product : " << p.compute_scalar_product( &q ) << endl;
+ }
+*/
diff --git a/src/Gudhi_stat/test/vector_representation_test.cpp b/src/Gudhi_stat/test/vector_representation_test.cpp
index dd84fc33..f69673dd 100644
--- a/src/Gudhi_stat/test/vector_representation_test.cpp
+++ b/src/Gudhi_stat/test/vector_representation_test.cpp
@@ -21,7 +21,7 @@
*/
-#include <gudhi/concretizations/Vector_distances_in_diagram.h>
+#include <gudhi/persistence_representations/Vector_distances_in_diagram.h>
#include <gudhi/common_gudhi_stat.h>
#include <iostream>
diff --git a/src/Gudhi_stat/utilities/Hausdorff_bootstrap.cpp b/src/Gudhi_stat/utilities/Hausdorff_bootstrap.cpp
index 78c75bd4..7fd665c3 100644
--- a/src/Gudhi_stat/utilities/Hausdorff_bootstrap.cpp
+++ b/src/Gudhi_stat/utilities/Hausdorff_bootstrap.cpp
@@ -24,7 +24,7 @@
#include <gudhi/Hausdorff_distances.h>
#include <gudhi/bootstrap.h>
#include <gudhi/read_persitence_from_file.h>
-#include <gudhi/concretizations/Vector_distances_in_diagram.h>
+#include <gudhi/persistence_representations/Vector_distances_in_diagram.h>
using namespace Gudhi;
diff --git a/src/Gudhi_stat/utilities/Landscape_bootstrap.cpp b/src/Gudhi_stat/utilities/Landscape_bootstrap.cpp
index 1b24771a..0827bfdf 100644
--- a/src/Gudhi_stat/utilities/Landscape_bootstrap.cpp
+++ b/src/Gudhi_stat/utilities/Landscape_bootstrap.cpp
@@ -23,9 +23,9 @@
//stat part:
#include <gudhi/Hausdorff_distances.h>
#include <gudhi/bootstrap.h>
-#include <gudhi/concretizations/Persistence_landscape.h>
+#include <gudhi/persistence_representations/Persistence_landscape.h>
#include <gudhi/read_persitence_from_file.h>
-#include <gudhi/concretizations/Vector_distances_in_diagram.h>
+#include <gudhi/persistence_representations/Vector_distances_in_diagram.h>
//persistence part:
#include <gudhi/reader_utils.h>
#include <gudhi/graph_simplicial_complex.h>
diff --git a/src/Gudhi_stat/utilities/Multiplicative_bootstrap.cpp b/src/Gudhi_stat/utilities/Multiplicative_bootstrap.cpp
index 92020c21..9a607251 100644
--- a/src/Gudhi_stat/utilities/Multiplicative_bootstrap.cpp
+++ b/src/Gudhi_stat/utilities/Multiplicative_bootstrap.cpp
@@ -24,7 +24,7 @@
#include <gudhi/Hausdorff_distances.h>
#include <gudhi/multiplicative_bootstrap.h>
#include <gudhi/read_persitence_from_file.h>
-#include <gudhi/concretizations/Vector_distances_in_diagram.h>
+#include <gudhi/persistence_representations/Vector_distances_in_diagram.h>
using namespace Gudhi;
using namespace Gudhi::Gudhi_stat;
diff --git a/src/Gudhi_stat/utilities/permutation_test.cpp b/src/Gudhi_stat/utilities/permutation_test.cpp
index dfbe3129..94f92d29 100644
--- a/src/Gudhi_stat/utilities/permutation_test.cpp
+++ b/src/Gudhi_stat/utilities/permutation_test.cpp
@@ -22,7 +22,7 @@
#include <gudhi/permutation_test.h>
-#include <gudhi/concretizations/Persistence_landscape.h>
+#include <gudhi/persistence_representations/Persistence_landscape.h>
#include <iostream>
#include <cstring>
diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp
index 3ef863c6..901f1a03 100644
--- a/src/Gudhi_stat/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp
+++ b/src/Gudhi_stat/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp
@@ -22,7 +22,7 @@
-#include <gudhi/concretizations/Persistence_heat_maps.h>
+#include <gudhi/persistence_representations/Persistence_heat_maps.h>
diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp
index cb094dff..e4f5fca6 100644
--- a/src/Gudhi_stat/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp
+++ b/src/Gudhi_stat/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp
@@ -21,7 +21,7 @@
*/
-#include <gudhi/concretizations/Persistence_heat_maps.h>
+#include <gudhi/persistence_representations/Persistence_heat_maps.h>
diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp
index 46edbc28..cdeba692 100644
--- a/src/Gudhi_stat/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp
+++ b/src/Gudhi_stat/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp
@@ -21,7 +21,7 @@
*/
-#include <gudhi/concretizations/Persistence_heat_maps.h>
+#include <gudhi/persistence_representations/Persistence_heat_maps.h>
diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp
index d5f5d75f..5d2100aa 100644
--- a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp
+++ b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp
@@ -22,7 +22,7 @@
-#include <gudhi/concretizations/Persistence_heat_maps.h>
+#include <gudhi/persistence_representations/Persistence_heat_maps.h>
diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp
index 6c306566..8496e33e 100644
--- a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp
+++ b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp
@@ -22,7 +22,7 @@
-#include <gudhi/concretizations/Persistence_heat_maps.h>
+#include <gudhi/persistence_representations/Persistence_heat_maps.h>
diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp
index 6ac9e40c..83d4f3bc 100644
--- a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp
+++ b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp
@@ -21,7 +21,7 @@
*/
-#include <gudhi/concretizations/Persistence_heat_maps.h>
+#include <gudhi/persistence_representations/Persistence_heat_maps.h>
diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp
index 91b3fb22..f62615f5 100644
--- a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp
+++ b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp
@@ -21,7 +21,7 @@
*/
-#include <gudhi/concretizations/Persistence_heat_maps.h>
+#include <gudhi/persistence_representations/Persistence_heat_maps.h>
diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/create_pssk.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/create_pssk.cpp
index ec35f81c..d38bb8b9 100644
--- a/src/Gudhi_stat/utilities/persistence_heat_maps/create_pssk.cpp
+++ b/src/Gudhi_stat/utilities/persistence_heat_maps/create_pssk.cpp
@@ -20,7 +20,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
-#include <gudhi/concretizations/PSSK.h>
+#include <gudhi/persistence_representations/PSSK.h>
diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp
index 39a46adb..59b14fe8 100644
--- a/src/Gudhi_stat/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp
+++ b/src/Gudhi_stat/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp
@@ -21,7 +21,7 @@
*/
-#include <gudhi/concretizations/Persistence_heat_maps.h>
+#include <gudhi/persistence_representations/Persistence_heat_maps.h>
diff --git a/src/Gudhi_stat/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp b/src/Gudhi_stat/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp
index 46711d27..145040fe 100644
--- a/src/Gudhi_stat/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp
+++ b/src/Gudhi_stat/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp
@@ -23,7 +23,7 @@
#include <gudhi/reader_utils.h>
-#include <gudhi/concretizations/Persistence_intervals.h>
+#include <gudhi/persistence_representations/Persistence_intervals.h>
#include <iostream>
#include <vector>
diff --git a/src/Gudhi_stat/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp b/src/Gudhi_stat/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp
index 8c263705..eeda703a 100644
--- a/src/Gudhi_stat/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp
+++ b/src/Gudhi_stat/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp
@@ -23,7 +23,7 @@
#include <gudhi/reader_utils.h>
-#include <gudhi/concretizations/Persistence_intervals.h>
+#include <gudhi/persistence_representations/Persistence_intervals.h>
#include <iostream>
diff --git a/src/Gudhi_stat/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp b/src/Gudhi_stat/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp
index f21afdd2..db9c3f98 100644
--- a/src/Gudhi_stat/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp
+++ b/src/Gudhi_stat/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp
@@ -23,7 +23,7 @@
#include <gudhi/reader_utils.h>
-#include <gudhi/concretizations/Persistence_intervals.h>
+#include <gudhi/persistence_representations/Persistence_intervals.h>
#include <iostream>
@@ -44,7 +44,7 @@ int main( int argc , char** argv )
Persistence_intervals p( argv[1] );
std::vector< std::pair<double,double> > dominant_intervals = p.dominant_intervals( atoi( argv[2] ) );
- std::vector< size_t > histogram = p.histograms_of_lengths( 10 );
+ std::vector< size_t > histogram = p.histogram_of_lengths( 10 );
std::stringstream gnuplot_script;
gnuplot_script << argv[1] << "_Gnuplot_script";
diff --git a/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_Betti_numebrs.cpp b/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_Betti_numebrs.cpp
index d12c4605..cb89f6b9 100644
--- a/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_Betti_numebrs.cpp
+++ b/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_Betti_numebrs.cpp
@@ -23,7 +23,7 @@
#include <gudhi/reader_utils.h>
-#include <gudhi/concretizations/Persistence_intervals.h>
+#include <gudhi/persistence_representations/Persistence_intervals.h>
#include <iostream>
diff --git a/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_intervals.cpp b/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_intervals.cpp
index d2e49ef3..40f6fbaf 100644
--- a/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_intervals.cpp
+++ b/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_intervals.cpp
@@ -23,7 +23,7 @@
#include <gudhi/reader_utils.h>
-#include <gudhi/concretizations/Persistence_intervals.h>
+#include <gudhi/persistence_representations/Persistence_intervals.h>
#include <gudhi/read_persitence_from_file.h>
#include <iostream>
diff --git a/src/Gudhi_stat/utilities/persistence_landscapes/average_landscapes.cpp b/src/Gudhi_stat/utilities/persistence_landscapes/average_landscapes.cpp
index 35aec203..2a50acd8 100644
--- a/src/Gudhi_stat/utilities/persistence_landscapes/average_landscapes.cpp
+++ b/src/Gudhi_stat/utilities/persistence_landscapes/average_landscapes.cpp
@@ -22,7 +22,7 @@
-#include <gudhi/concretizations/Persistence_landscape.h>
+#include <gudhi/persistence_representations/Persistence_landscape.h>
diff --git a/src/Gudhi_stat/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp b/src/Gudhi_stat/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp
index 937a902e..0b16ac26 100644
--- a/src/Gudhi_stat/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp
+++ b/src/Gudhi_stat/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp
@@ -20,7 +20,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
-#include <gudhi/concretizations/Persistence_landscape.h>
+#include <gudhi/persistence_representations/Persistence_landscape.h>
diff --git a/src/Gudhi_stat/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp b/src/Gudhi_stat/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp
index 39772b9b..16a15174 100644
--- a/src/Gudhi_stat/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp
+++ b/src/Gudhi_stat/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp
@@ -20,7 +20,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
-#include <gudhi/concretizations/Persistence_landscape.h>
+#include <gudhi/persistence_representations/Persistence_landscape.h>
diff --git a/src/Gudhi_stat/utilities/persistence_landscapes/create_landscapes.cpp b/src/Gudhi_stat/utilities/persistence_landscapes/create_landscapes.cpp
index b67ec566..5485bf2a 100644
--- a/src/Gudhi_stat/utilities/persistence_landscapes/create_landscapes.cpp
+++ b/src/Gudhi_stat/utilities/persistence_landscapes/create_landscapes.cpp
@@ -20,8 +20,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
-#include <gudhi/concretizations/Persistence_landscape.h>
-
+#include <gudhi/persistence_representations/Persistence_landscape.h>
using namespace Gudhi;
@@ -43,7 +42,8 @@ int main( int argc , char** argv )
std::cout << "Creating persistence landscapes...\n";
for ( size_t i = 0 ; i != filenames.size() ; ++i )
{
- Persistence_landscape l( filenames[i] , 0 );
+ //std::vector< std::pair< double , double > > pers = read_standard_file( filename );
+ Persistence_landscape l( filenames[i] , 1 );
std::stringstream ss;
ss << filenames[i] << ".land";
l.print_to_file( ss.str().c_str() );
diff --git a/src/Gudhi_stat/utilities/persistence_landscapes/plot_landscapes.cpp b/src/Gudhi_stat/utilities/persistence_landscapes/plot_landscapes.cpp
index 0d72a17c..aad8e147 100644
--- a/src/Gudhi_stat/utilities/persistence_landscapes/plot_landscapes.cpp
+++ b/src/Gudhi_stat/utilities/persistence_landscapes/plot_landscapes.cpp
@@ -20,7 +20,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
-#include <gudhi/concretizations/Persistence_landscape.h>
+#include <gudhi/persistence_representations/Persistence_landscape.h>
diff --git a/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp
index 2f6875b2..d3851734 100644
--- a/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp
+++ b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp
@@ -20,7 +20,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
-#include <gudhi/concretizations/Persistence_landscape_on_grid.h>
+#include <gudhi/persistence_representations/Persistence_landscape_on_grid.h>
diff --git a/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp
index 58c5ec47..29c37159 100644
--- a/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp
+++ b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp
@@ -20,7 +20,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
-#include <gudhi/concretizations/Persistence_landscape_on_grid.h>
+#include <gudhi/persistence_representations/Persistence_landscape_on_grid.h>
diff --git a/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp
index e1a4788f..326e5587 100644
--- a/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp
+++ b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp
@@ -21,7 +21,7 @@
*/
-#include <gudhi/concretizations/Persistence_landscape_on_grid.h>
+#include <gudhi/persistence_representations/Persistence_landscape_on_grid.h>
diff --git a/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp
index 2b205513..4f36f02d 100644
--- a/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp
+++ b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp
@@ -20,7 +20,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
-#include <gudhi/concretizations/Persistence_landscape_on_grid.h>
+#include <gudhi/persistence_representations/Persistence_landscape_on_grid.h>
diff --git a/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp
index 27946075..b5687ea2 100644
--- a/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp
+++ b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp
@@ -20,7 +20,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
-#include <gudhi/concretizations/Persistence_landscape_on_grid.h>
+#include <gudhi/persistence_representations/Persistence_landscape_on_grid.h>
diff --git a/src/Gudhi_stat/utilities/persistence_vectors/average_persistence_vectors.cpp b/src/Gudhi_stat/utilities/persistence_vectors/average_persistence_vectors.cpp
index 3f6409c6..822d0e2a 100644
--- a/src/Gudhi_stat/utilities/persistence_vectors/average_persistence_vectors.cpp
+++ b/src/Gudhi_stat/utilities/persistence_vectors/average_persistence_vectors.cpp
@@ -21,7 +21,7 @@
*/
-#include <gudhi/concretizations/Vector_distances_in_diagram.h>
+#include <gudhi/persistence_representations/Vector_distances_in_diagram.h>
diff --git a/src/Gudhi_stat/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp b/src/Gudhi_stat/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp
index 2ca5989e..6d242cd1 100644
--- a/src/Gudhi_stat/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp
+++ b/src/Gudhi_stat/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp
@@ -20,7 +20,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
-#include <gudhi/concretizations/Vector_distances_in_diagram.h>
+#include <gudhi/persistence_representations/Vector_distances_in_diagram.h>
diff --git a/src/Gudhi_stat/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp b/src/Gudhi_stat/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp
index 78c6ab91..e4c62194 100644
--- a/src/Gudhi_stat/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp
+++ b/src/Gudhi_stat/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp
@@ -20,7 +20,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
-#include <gudhi/concretizations/Vector_distances_in_diagram.h>
+#include <gudhi/persistence_representations/Vector_distances_in_diagram.h>
diff --git a/src/Gudhi_stat/utilities/persistence_vectors/create_persistence_vectors.cpp b/src/Gudhi_stat/utilities/persistence_vectors/create_persistence_vectors.cpp
index f3cf7289..926e46fd 100644
--- a/src/Gudhi_stat/utilities/persistence_vectors/create_persistence_vectors.cpp
+++ b/src/Gudhi_stat/utilities/persistence_vectors/create_persistence_vectors.cpp
@@ -20,7 +20,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
-#include <gudhi/concretizations/Vector_distances_in_diagram.h>
+#include <gudhi/persistence_representations/Vector_distances_in_diagram.h>
diff --git a/src/Gudhi_stat/utilities/persistence_vectors/plot_persistence_vectors.cpp b/src/Gudhi_stat/utilities/persistence_vectors/plot_persistence_vectors.cpp
index 06411283..0ef30be8 100644
--- a/src/Gudhi_stat/utilities/persistence_vectors/plot_persistence_vectors.cpp
+++ b/src/Gudhi_stat/utilities/persistence_vectors/plot_persistence_vectors.cpp
@@ -20,7 +20,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
-#include <gudhi/concretizations/Vector_distances_in_diagram.h>
+#include <gudhi/persistence_representations/Vector_distances_in_diagram.h>