adding better examples in /example folder.

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/gudhi_stat@1691 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 78b3c03fdc58cebe5bfae75bf624ab982702d7dc

4 files changed, 233 insertions, 40 deletions

diff --git a/src/Gudhi_stat/example/persistence_heat_maps.cpp b/src/Gudhi_stat/example/persistence_heat_maps.cpp
index e336ab44..7f5580da 100644
--- a/src/Gudhi_stat/example/persistence_heat_maps.cpp
+++ b/src/Gudhi_stat/example/persistence_heat_maps.cpp
@@ -27,6 +27,7 @@
 #include <gudhi/concretizations/Persistence_heat_maps.h>
 
 #include <iostream>
+#include <vector>
 
 
 
@@ -40,13 +41,62 @@ using namespace std;
 
 	
 int main( int argc , char** argv )
-{
-	//if ( argc != 2 )
-	//{
-	//	cout << "To run this program, please provide the name of a file with persistence diagram \n";
-	//	return 1;
-	//}
+{	
+	//create two simple vectors with birth--death pairs:
+	
+	std::vector< std::pair< double , double > > persistence1;
+	std::vector< std::pair< double , double > > persistence2;
+	
+	persistence1.push_back( std::make_pair(1,2) );
+	persistence1.push_back( std::make_pair(6,8) );
+	persistence1.push_back( std::make_pair(0,4) );
+	persistence1.push_back( std::make_pair(3,8) );
+	
+	persistence2.push_back( std::make_pair(2,9) );
+	persistence2.push_back( std::make_pair(1,6) );
+	persistence2.push_back( std::make_pair(3,5) );
+	persistence2.push_back( std::make_pair(6,10) );
+	
+	//over here we define a function we sill put on a top on every birth--death pair in the persistence interval. It can be anything. Over here we will use standarg Gaussian
+	std::vector< std::vector<double> > filter = create_Gaussian_filter(5,1);
+			
+	//creating two heat maps. 
+	Persistence_heat_maps hm1( persistence1 , filter , constant_function, false , 20 , 0 , 11 );		
+	Persistence_heat_maps hm2( persistence2 , filter , constant_function, false , 20 , 0 , 11 );
+	
+	std::vector<Persistence_heat_maps*> vector_of_maps;
+	vector_of_maps.push_back( &hm1 );
+	vector_of_maps.push_back( &hm2 );
+	
+	//compute median/mean of a vector of heat maps:	
+	Persistence_heat_maps mean;
+	mean.compute_mean( vector_of_maps );	
+	Persistence_heat_maps median;
+	median.compute_median( vector_of_maps );
+	
+	//to compute L^1 disance between hm1 and hm2:
+	std::cout << "The L^1 distance is : " << hm1.distance( (Abs_Topological_data_with_distances*)(&hm2) , 1 ) << std::endl;
+	
+	//to average of hm1 and hm2:
+	std::vector< Abs_Topological_data_with_averages* > to_average;
+	to_average.push_back( (Abs_Topological_data_with_averages*)(&hm1) );
+	to_average.push_back( (Abs_Topological_data_with_averages*)(&hm2) );
+	Persistence_heat_maps av;	
+	av.compute_average( to_average );	
 	
+	//to compute scalar product of hm1 and hm2:
+	std::cout << "Scalar product is : " << hm1.compute_scalar_product( (Abs_Topological_data_with_scalar_product*)(&hm2) ) << std::endl;
+	
+	return 0;
+}
+
+
+
+
+
+
+
+//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) );	
@@ -166,7 +216,7 @@ int main( int argc , char** argv )
 */
 
 
-
+/*
 	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 );
@@ -181,16 +231,4 @@ int main( int argc , char** argv )
 	
 	percentage_of_active.print_to_file( "template_percentage_of_active_of_heat_maps" );
 	//percentage_of_active.plot( "template_percentage_of_active_of_heat_maps" );
-	
-	
-
-	
-	return 0;
-}
-
-
-
-
-
-
-
+*/
diff --git a/src/Gudhi_stat/example/persistence_landscape.cpp b/src/Gudhi_stat/example/persistence_landscape.cpp
index 3204148b..f5110153 100644
--- a/src/Gudhi_stat/example/persistence_landscape.cpp
+++ b/src/Gudhi_stat/example/persistence_landscape.cpp
@@ -34,9 +34,70 @@ using namespace Gudhi::Gudhi_stat;
 
 
 int main( int argc , char** argv )
-{
-	
-	if ( argc != 2 )
+{	
+	//create two simple vectors with birth--death pairs:
+	
+	std::vector< std::pair< double , double > > persistence1;
+	std::vector< std::pair< double , double > > persistence2;
+	
+	persistence1.push_back( std::make_pair(1,2) );
+	persistence1.push_back( std::make_pair(6,8) );
+	persistence1.push_back( std::make_pair(0,4) );
+	persistence1.push_back( std::make_pair(3,8) );
+	
+	persistence2.push_back( std::make_pair(2,9) );
+	persistence2.push_back( std::make_pair(1,6) );
+	persistence2.push_back( std::make_pair(3,5) );
+	persistence2.push_back( std::make_pair(6,10) );
+	
+	//create two persistence landscapes based on persistence1 and persistence2:
+	Persistence_landscape l1( persistence1 );
+	Persistence_landscape l2( persistence2 );
+	
+	//This is how to compute integral of landscapes:
+	std::cout << "Integral of the first landscape : " << l1.compute_integral_of_landscape() << endl;
+	std::cout << "Integral of the second landscape : " << l2.compute_integral_of_landscape() << endl;
+	
+	//And here how to write landscapes to stream:
+	std::cout << "l1 : " << l1 << std::endl;
+	std::cout << "l2 : " << l2 << std::endl;
+	
+	//Arythmetic operations on landscapes:
+	Persistence_landscape sum = l1+l2;
+	std::cout << "sum : " << sum << std::endl;
+	
+	//here are the maxima of the functions:
+	std::cout << "Maximum of l1 : " << l1.compute_maximum() << std::endl;
+	std::cout << "Maximum of l2 : " << l2.compute_maximum() << std::endl;
+	
+	//here are the norms of landscapes:
+	std::cout << "L^1 Norm of l1 : " << l1.compute_norm_of_landscape( 1. ) << std::endl;
+	std::cout << "L^1 Norm of l2 : " << l2.compute_norm_of_landscape( 1. ) << std::endl;
+	
+	//here is the average of landscapes:
+	Persistence_landscape average;
+	std::vector< Abs_Topological_data_with_averages* > to_average;
+	to_average.push_back( (Abs_Topological_data_with_averages*)(&l1) );
+	to_average.push_back( (Abs_Topological_data_with_averages*)(&l2) );
+	average.compute_average( to_average );
+	std::cout << "average : " << average << std::endl;
+	
+	//here is the distance of landscapes:
+	std::cout << "Distance : " << l1.distance( (Abs_Topological_data_with_distances*)(&l2) ) << std::endl;
+	
+	//here is the scalar product of landscapes:
+	std::cout << "Scalar product : " << l1.compute_scalar_product( (Abs_Topological_data_with_scalar_product*)(&l2) ) << std::endl;
+	
+	//here is how to create a file which is suitable for vizualization via gnuplot:
+	average.plot( "average_landscape" );
+		
+	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;
@@ -161,7 +222,4 @@ int main( int argc , char** argv )
 		Persistence_landscape q( "../test/data/file_with_diagram_1" );
 		cout << "Scalar product : " <<  p.compute_scalar_product( &q ) << endl;		
 	}
-
-	
-	return 0;
-}
+*/ 
diff --git a/src/Gudhi_stat/example/persistence_landscape_on_grid.cpp b/src/Gudhi_stat/example/persistence_landscape_on_grid.cpp
index e1a0ba5d..ddda78d2 100644
--- a/src/Gudhi_stat/example/persistence_landscape_on_grid.cpp
+++ b/src/Gudhi_stat/example/persistence_landscape_on_grid.cpp
@@ -35,7 +35,65 @@ using namespace Gudhi::Gudhi_stat;
 
 int main( int argc , char** argv )
 {
-	/*
+	//create two simple vectors with birth--death pairs:
+	
+	std::vector< std::pair< double , double > > persistence1;
+	std::vector< std::pair< double , double > > persistence2;
+	
+	persistence1.push_back( std::make_pair(1,2) );
+	persistence1.push_back( std::make_pair(6,8) );
+	persistence1.push_back( std::make_pair(0,4) );
+	persistence1.push_back( std::make_pair(3,8) );
+	
+	persistence2.push_back( std::make_pair(2,9) );
+	persistence2.push_back( std::make_pair(1,6) );
+	persistence2.push_back( std::make_pair(3,5) );
+	persistence2.push_back( std::make_pair(6,10) );
+	
+	//create two persistence landscapes based on persistence1 and persistence2:
+	Persistence_landscape_on_grid l1( persistence1 , 0 , 11 , 20 );
+	Persistence_landscape_on_grid l2( persistence2 , 0 , 11 , 20 );
+	
+	//This is how to compute integral of landscapes:
+	std::cout << "Integral of the first landscape : " << l1.compute_integral_of_landscape() << endl;
+	std::cout << "Integral of the second landscape : " << l2.compute_integral_of_landscape() << endl;
+	
+	//And here how to write landscapes to stream:
+	std::cout << "l1 : " << l1 << std::endl;
+	std::cout << "l2 : " << l2 << std::endl;
+	
+	//here are the maxima of the functions:
+	std::cout << "Maximum of l1 : " << l1.compute_maximum() << std::endl;
+	std::cout << "Maximum of l2 : " << l2.compute_maximum() << std::endl;
+	
+	//here are the norms of landscapes:
+	std::cout << "L^1 Norm of l1 : " << l1.compute_norm_of_landscape( 1. ) << std::endl;
+	std::cout << "L^1 Norm of l2 : " << l2.compute_norm_of_landscape( 1. ) << std::endl;
+	
+	//here is the average of landscapes:
+	Persistence_landscape_on_grid average;
+	std::vector< Abs_Topological_data_with_averages* > to_average;
+	to_average.push_back( (Abs_Topological_data_with_averages*)(&l1) );
+	to_average.push_back( (Abs_Topological_data_with_averages*)(&l2) );
+	average.compute_average( to_average );
+	std::cout << "average : " << average << std::endl;
+	
+	//here is the distance of landscapes:
+	std::cout << "Distance : " << l1.distance( (Abs_Topological_data_with_distances*)(&l2) ) << std::endl;
+	
+	//here is the scalar product of landscapes:
+	std::cout << "Scalar product : " << l1.compute_scalar_product( (Abs_Topological_data_with_scalar_product*)(&l2) ) << std::endl;
+	
+	//here is how to create a file which is suitable for vizualization via gnuplot:
+	average.plot( "average_landscape" );
+		
+		
+	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" );
 	
@@ -132,7 +190,7 @@ int main( int argc , char** argv )
 	cerr <<  p.distance( &q , -1 ) << endl;
 	*/
 	
-
+/*
 	Persistence_landscape_on_grid p( "file_with_diagram", 0,1,10000 );
 	Persistence_landscape_on_grid q( "file_with_diagram_1", 0,1,10000 );
 	
@@ -141,7 +199,4 @@ int main( int argc , char** argv )
 	//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;
-
-		
-	return 0;
-}
+*/
diff --git a/src/Gudhi_stat/example/vector_representation.cpp b/src/Gudhi_stat/example/vector_representation.cpp
index 0581baf4..773c60fa 100644
--- a/src/Gudhi_stat/example/vector_representation.cpp
+++ b/src/Gudhi_stat/example/vector_representation.cpp
@@ -37,13 +37,58 @@ using namespace Gudhi::Gudhi_stat;
 using namespace std;
 
 
-double epsilon = 0.000005;
-
 
 
 int main( int argc , char** argv )
 {
-	if ( argc < 2 )
+	//create two simple vectors with birth--death pairs:
+	
+	std::vector< std::pair< double , double > > persistence1;
+	std::vector< std::pair< double , double > > persistence2;
+	
+	persistence1.push_back( std::make_pair(1,2) );
+	persistence1.push_back( std::make_pair(6,8) );
+	persistence1.push_back( std::make_pair(0,4) );
+	persistence1.push_back( std::make_pair(3,8) );
+	
+	persistence2.push_back( std::make_pair(2,9) );
+	persistence2.push_back( std::make_pair(1,6) );
+	persistence2.push_back( std::make_pair(3,5) );
+	persistence2.push_back( std::make_pair(6,10) );
+	
+	//create two persistence vectors based on persistence1 and persistence2:
+	Vector_distances_in_diagram<euclidean_distance<double> > v1 = Vector_distances_in_diagram<euclidean_distance<double> >( persistence1 , std::numeric_limits<size_t>::max() );
+	Vector_distances_in_diagram<euclidean_distance<double> > v2 = Vector_distances_in_diagram<euclidean_distance<double> >( persistence2 , std::numeric_limits<size_t>::max() );
+	
+	//writing to a stream:
+	std::cout << "v1 : " << v1 << std::endl;
+	std::cout << "v2 : " << v2 << std::endl;
+	
+	//averages:
+	Vector_distances_in_diagram<euclidean_distance<double> > average;
+	std::vector< Abs_Topological_data_with_averages* > to_average;
+	to_average.push_back( (Abs_Topological_data_with_averages*)(&v1) );
+	to_average.push_back( (Abs_Topological_data_with_averages*)(&v2) );
+	average.compute_average( to_average );
+	std::cout << "Average : " << average << std::endl;
+	
+	//computations of distances:
+	std::cout << "l^1 distance : " << v1.distance( (Abs_Topological_data_with_distances*)(&v2) ) << std::endl;
+    
+   //computations of scalar product:
+    std::cout << "Scalar product of l1 and l2 : " << v1.compute_scalar_product( (Abs_Topological_data_with_scalar_product*)(&v2) ) << std::endl;
+    
+    //create a file with a gnuplot script:
+    v1.plot( "plot_of_vector_representation" );
+
+	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;
@@ -71,7 +116,4 @@ int main( int argc , char** argv )
 	
 		cout << "Here is an average : " << average << endl;
 	}
-	return 0;
-}
-
-
+*/