Answer to Marc's comment from Sunday.

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/gudhi_stat@1845 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: cb4c277633d435bfe9111150f40de46d2fa598c2

20 files changed, 126 insertions, 147 deletions

diff --git a/src/Gudhi_stat/example/persistence_heat_maps.cpp b/src/Gudhi_stat/example/persistence_heat_maps.cpp
index 052b435f..c8dde3cd 100644
--- a/src/Gudhi_stat/example/persistence_heat_maps.cpp
+++ b/src/Gudhi_stat/example/persistence_heat_maps.cpp
@@ -36,7 +36,6 @@ using namespace Gudhi::Gudhi_stat;
 
 double epsilon = 0.0000005;
 
-using namespace std;
 
 	
 int main( int argc , char** argv )
diff --git a/src/Gudhi_stat/example/persistence_intervals.cpp b/src/Gudhi_stat/example/persistence_intervals.cpp
index 04a3d948..044ba3c3 100644
--- a/src/Gudhi_stat/example/persistence_intervals.cpp
+++ b/src/Gudhi_stat/example/persistence_intervals.cpp
@@ -32,8 +32,6 @@
 using namespace Gudhi;
 using namespace Gudhi::Gudhi_stat;
 
-using namespace std;
-
 	
 int main( int argc , char** argv )
 {
diff --git a/src/Gudhi_stat/example/vector_representation.cpp b/src/Gudhi_stat/example/vector_representation.cpp
index 20d46d26..981e63de 100644
--- a/src/Gudhi_stat/example/vector_representation.cpp
+++ b/src/Gudhi_stat/example/vector_representation.cpp
@@ -34,8 +34,6 @@
 using namespace Gudhi;
 using namespace Gudhi::Gudhi_stat;
 
-using namespace std;
-
 
 
 
diff --git a/src/Gudhi_stat/include/gudhi/concretizations/Persistence_landscape_on_grid.h b/src/Gudhi_stat/include/gudhi/concretizations/Persistence_landscape_on_grid.h
index 08b93a0a..d91b7431 100644
--- a/src/Gudhi_stat/include/gudhi/concretizations/Persistence_landscape_on_grid.h
+++ b/src/Gudhi_stat/include/gudhi/concretizations/Persistence_landscape_on_grid.h
@@ -992,6 +992,9 @@ 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
+	* 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. 
 	**/ 
 	void plot( const char* filename , size_t from_ , size_t to_ )const
 	{
diff --git a/src/Gudhi_stat/include/gudhi/fill_in_missing_data.h b/src/Gudhi_stat/include/gudhi/fill_in_missing_data.h
index d6ae6fe1..a9997aa2 100644
--- a/src/Gudhi_stat/include/gudhi/fill_in_missing_data.h
+++ b/src/Gudhi_stat/include/gudhi/fill_in_missing_data.h
@@ -70,7 +70,7 @@ void fill_in_missing_data( std::vector< Representation_of_topology* >& data , st
 			while ( (is_the_position_filled_in[i+j] == false) && ( i+j != data.size() ) )++j;
 			if ( dbg )
 			{
-				std::cout << "The position number : " << i << " is not filled in. The next filled-in position is : " << i+j << endl;
+				std::cout << "The position number : " << i << " is not filled in. The next filled-in position is : " << i+j << std::endl;
 			}
 			if ( i != 0 )
 			{
@@ -86,7 +86,7 @@ void fill_in_missing_data( std::vector< Representation_of_topology* >& data , st
 						is_the_position_filled_in[i+k] = true;
 						if ( dbg )
 						{
-							cerr << "We fill in a position : " << i+k << " with: position " << i-1 << " with weight " << weight1 << " and position " << i+j << " with weight " << weight2 << endl;
+							std::cerr << "We fill in a position : " << i+k << " with: position " << i-1 << " with weight " << weight1 << " and position " << i+j << " with weight " << weight2 << std::endl;
 						}
 					}
 				}					
@@ -115,7 +115,7 @@ void fill_in_missing_data( std::vector< Representation_of_topology* >& data , st
 			is_the_position_filled_in[j-1] = true;
 			if ( dbg )
 			{
-				cerr << "Filling in a position : " << j-1 << " by using: " << j << " and " << j+1 <<endl;
+				std::cerr << "Filling in a position : " << j-1 << " by using: " << j << " and " << j+1 <<std::endl;
 			}
 		}
 	}
@@ -132,7 +132,7 @@ void fill_in_missing_data( std::vector< Representation_of_topology* >& data , st
 			is_the_position_filled_in[j] = true;
 			if ( dbg )
 			{
-				cerr << "Filling in a position : " << j << " by using: " << j-1 << " and " << j-2 <<endl;
+				std::cerr << "Filling in a position : " << j << " by using: " << j-1 << " and " << j-2 <<std::endl;
 			}
 		}
 	}
diff --git a/src/Gudhi_stat/include/gudhi/permutation_test.h b/src/Gudhi_stat/include/gudhi/permutation_test.h
index fa31c3c0..1618d7ef 100644
--- a/src/Gudhi_stat/include/gudhi/permutation_test.h
+++ b/src/Gudhi_stat/include/gudhi/permutation_test.h
@@ -31,7 +31,6 @@
 #include <algorithm>
 #include <gudhi/read_persitence_from_file.h>
 
-using namespace std;
 
 namespace Gudhi 
 {
diff --git a/src/Gudhi_stat/test/persistence_heat_maps_test.cpp b/src/Gudhi_stat/test/persistence_heat_maps_test.cpp
index ccfc208b..4447ba37 100644
--- a/src/Gudhi_stat/test/persistence_heat_maps_test.cpp
+++ b/src/Gudhi_stat/test/persistence_heat_maps_test.cpp
@@ -35,7 +35,6 @@
 using namespace Gudhi;
 using namespace Gudhi::Gudhi_stat;
 
-using namespace std;
 
 
 	
diff --git a/src/Gudhi_stat/test/persistence_intervals_test.cpp b/src/Gudhi_stat/test/persistence_intervals_test.cpp
index 02af8347..7f18750a 100644
--- a/src/Gudhi_stat/test/persistence_intervals_test.cpp
+++ b/src/Gudhi_stat/test/persistence_intervals_test.cpp
@@ -38,19 +38,18 @@ using namespace Gudhi::Gudhi_stat;
 
 double epsilon = 0.0000005;
 
-using namespace std;
 
 	
 
 
-//cout << "Left most end of the interval : " << min_max_.first << endl;
-//cout << "Right most end of the interval : " << min_max_.second << endl;
+//cout << "Left most end of the interval : " << min_max_.first << std::endl;
+//cout << "Right most end of the interval : " << min_max_.second << std::endl;
 BOOST_AUTO_TEST_CASE(check_min_max_function) 
 {
 	Persistence_intervals p( "data/file_with_diagram" );
 	std::pair<double,double> min_max_ = p.min_max();
 	
-	//cout << min_max_.first << " " << min_max_.second << endl;getchar();
+	//cout << min_max_.first << " " << min_max_.second << std::endl;getchar();
 	
 	BOOST_CHECK( fabs ( min_max_.first - 0.0290362 ) <= epsilon );
 	BOOST_CHECK( fabs ( min_max_.second - 0.994537 ) <= epsilon );
@@ -167,13 +166,13 @@ BOOST_AUTO_TEST_CASE(check_characteristic_function_of_diagram)
 
 	for ( size_t i = 0 ; i != char_funct_diag.size() ; ++i )
 	{
-		//cout << char_funct_diag[i] << endl;
+		//cout << char_funct_diag[i] << std::endl;
 		if ( fabs ( char_funct_diag[i] - template_char_funct_diag[i] ) >= 0.0001  )
 		{
-			cout << "Boost test fail  check_characteristic_function_of_diagram : " << endl;
-			cerr << char_funct_diag[i] << " " << template_char_funct_diag[i] << endl;
-			cerr << fabs ( char_funct_diag[i] - template_char_funct_diag[i] ) << endl;
-			cerr << 0.0001 << endl;
+			std::cout << "Boost test fail  check_characteristic_function_of_diagram : " << std::endl;
+			std::cerr << char_funct_diag[i] << " " << template_char_funct_diag[i] << std::endl;
+			std::cerr << fabs ( char_funct_diag[i] - template_char_funct_diag[i] ) << std::endl;
+			std::cerr << 0.0001 << std::endl;
 			getchar();
 		}
 		BOOST_CHECK( fabs ( char_funct_diag[i] - template_char_funct_diag[i] ) <= 0.0001 );
@@ -201,7 +200,7 @@ BOOST_AUTO_TEST_CASE(check_cumulative_characteristic_function_of_diagram)
 
 	for ( size_t i = 0 ; i != cumul_char_funct_diag.size() ; ++i )
 	{		
-		//cout << cumul_char_funct_diag[i] << endl;
+		//cout << cumul_char_funct_diag[i] << std::endl;
 		BOOST_CHECK( fabs (cumul_char_funct_diag[i] - template_char_funct_diag_cumul[i] ) <= 0.0001 );
 	}	
 }
@@ -211,96 +210,96 @@ BOOST_AUTO_TEST_CASE(check_compute_persistent_betti_numbers)
 {
 	Persistence_intervals p( "data/file_with_diagram" );
 	std::vector< std::pair< double , double > > pbns;
-	pbns.push_back(make_pair<double,double>(	0.0290362,1	));
-	pbns.push_back(make_pair<double,double>(	0.0307676,2	));
-	pbns.push_back(make_pair<double,double>(	0.0366312,3	));
-	pbns.push_back(make_pair<double,double>(	0.0544614,4	));
-	pbns.push_back(make_pair<double,double>(	0.0920033,5	));
-	pbns.push_back(make_pair<double,double>(	0.104599,6	));
-	pbns.push_back(make_pair<double,double>(	0.114718,7	));
-	pbns.push_back(make_pair<double,double>(	0.117379,8	));
-	pbns.push_back(make_pair<double,double>(	0.123493,9	));
-	pbns.push_back(make_pair<double,double>(	0.133638,10	));
-	pbns.push_back(make_pair<double,double>(	0.137798,9	));
-	pbns.push_back(make_pair<double,double>(	0.149798,10	));
-	pbns.push_back(make_pair<double,double>(	0.155421,11	));
-	pbns.push_back(make_pair<double,double>(	0.158443,12	));
-	pbns.push_back(make_pair<double,double>(	0.176956,13	));
-	pbns.push_back(make_pair<double,double>(	0.183234,12	));
-	pbns.push_back(make_pair<double,double>(	0.191069,13	));
-	pbns.push_back(make_pair<double,double>(	0.191333,14	));
-	pbns.push_back(make_pair<double,double>(	0.191836,15	));
-	pbns.push_back(make_pair<double,double>(	0.192675,16	));
-	pbns.push_back(make_pair<double,double>(	0.208564,17	));
-	pbns.push_back(make_pair<double,double>(	0.218425,18	));
-	pbns.push_back(make_pair<double,double>(	0.219902,17	));
-	pbns.push_back(make_pair<double,double>(	0.23233,16	));
-	pbns.push_back(make_pair<double,double>(	0.234558,17	));
-	pbns.push_back(make_pair<double,double>(	0.237166,16	));
-	pbns.push_back(make_pair<double,double>(	0.247352,17	));
-	pbns.push_back(make_pair<double,double>(	0.267421,18	));
-	pbns.push_back(make_pair<double,double>(	0.268093,19	));
-	pbns.push_back(make_pair<double,double>(	0.278734,18	));
-	pbns.push_back(make_pair<double,double>(	0.284722,19	));
-	pbns.push_back(make_pair<double,double>(	0.284998,20	));
-	pbns.push_back(make_pair<double,double>(	0.294069,21	));
-	pbns.push_back(make_pair<double,double>(	0.306293,22	));
-	pbns.push_back(make_pair<double,double>(	0.322361,21	));
-	pbns.push_back(make_pair<double,double>(	0.323152,22	));
-	pbns.push_back(make_pair<double,double>(	0.371021,23	));
-	pbns.push_back(make_pair<double,double>(	0.372395,24	));
-	pbns.push_back(make_pair<double,double>(	0.387744,25	));
-	pbns.push_back(make_pair<double,double>(	0.435537,26	));
-	pbns.push_back(make_pair<double,double>(	0.462911,25	));
-	pbns.push_back(make_pair<double,double>(	0.483569,26	));
-	pbns.push_back(make_pair<double,double>(	0.489209,25	));
-	pbns.push_back(make_pair<double,double>(	0.517115,24	));
-	pbns.push_back(make_pair<double,double>(	0.522197,23	));
-	pbns.push_back(make_pair<double,double>(	0.532665,22	));
-	pbns.push_back(make_pair<double,double>(	0.545262,23	));
-	pbns.push_back(make_pair<double,double>(	0.587227,22	));
-	pbns.push_back(make_pair<double,double>(	0.593036,23	));
-	pbns.push_back(make_pair<double,double>(	0.602647,24	));
-	pbns.push_back(make_pair<double,double>(	0.605044,25	));
-	pbns.push_back(make_pair<double,double>(	0.621962,24	));
-	pbns.push_back(make_pair<double,double>(	0.629449,23	));
-	pbns.push_back(make_pair<double,double>(	0.636719,22	));
-	pbns.push_back(make_pair<double,double>(	0.64957,21	));
-	pbns.push_back(make_pair<double,double>(	0.650781,22	));
-	pbns.push_back(make_pair<double,double>(	0.654951,23	));
-	pbns.push_back(make_pair<double,double>(	0.683489,24	));
-	pbns.push_back(make_pair<double,double>(	0.687172,23	));
-	pbns.push_back(make_pair<double,double>(	0.69703,22	));
-	pbns.push_back(make_pair<double,double>(	0.701174,21	));
-	pbns.push_back(make_pair<double,double>(	0.717623,22	));
-	pbns.push_back(make_pair<double,double>(	0.722023,21	));
-	pbns.push_back(make_pair<double,double>(	0.722298,20	));
-	pbns.push_back(make_pair<double,double>(	0.725347,19	));
-	pbns.push_back(make_pair<double,double>(	0.73071,18	));
-	pbns.push_back(make_pair<double,double>(	0.758355,17	));
-	pbns.push_back(make_pair<double,double>(	0.770913,18	));
-	pbns.push_back(make_pair<double,double>(	0.790833,17	));
-	pbns.push_back(make_pair<double,double>(	0.821211,16	));
-	pbns.push_back(make_pair<double,double>(	0.849305,17	));
-	pbns.push_back(make_pair<double,double>(	0.853669,16	));
-	pbns.push_back(make_pair<double,double>(	0.866659,15	));
-	pbns.push_back(make_pair<double,double>(	0.872896,16	));
-	pbns.push_back(make_pair<double,double>(	0.889597,15	));
-	pbns.push_back(make_pair<double,double>(	0.900231,14	));
-	pbns.push_back(make_pair<double,double>(	0.903847,13	));
-	pbns.push_back(make_pair<double,double>(	0.906299,12	));
-	pbns.push_back(make_pair<double,double>(	0.910852,11	));
-	pbns.push_back(make_pair<double,double>(	0.93453,10	));
-	pbns.push_back(make_pair<double,double>(	0.944757,9	));
-	pbns.push_back(make_pair<double,double>(	0.947812,8	));
-	pbns.push_back(make_pair<double,double>(	0.959154,7	));
-	pbns.push_back(make_pair<double,double>(	0.975654,6	));
-	pbns.push_back(make_pair<double,double>(	0.976719,5	));
-	pbns.push_back(make_pair<double,double>(	0.977343,4	));
-	pbns.push_back(make_pair<double,double>(	0.980129,3	));
-	pbns.push_back(make_pair<double,double>(	0.987842,2	));
-	pbns.push_back(make_pair<double,double>(	0.990127,1	));
-	pbns.push_back(make_pair<double,double>(	0.994537,0	));
+	pbns.push_back(std::make_pair<double,double>(	0.0290362,1	));
+	pbns.push_back(std::make_pair<double,double>(	0.0307676,2	));
+	pbns.push_back(std::make_pair<double,double>(	0.0366312,3	));
+	pbns.push_back(std::make_pair<double,double>(	0.0544614,4	));
+	pbns.push_back(std::make_pair<double,double>(	0.0920033,5	));
+	pbns.push_back(std::make_pair<double,double>(	0.104599,6	));
+	pbns.push_back(std::make_pair<double,double>(	0.114718,7	));
+	pbns.push_back(std::make_pair<double,double>(	0.117379,8	));
+	pbns.push_back(std::make_pair<double,double>(	0.123493,9	));
+	pbns.push_back(std::make_pair<double,double>(	0.133638,10	));
+	pbns.push_back(std::make_pair<double,double>(	0.137798,9	));
+	pbns.push_back(std::make_pair<double,double>(	0.149798,10	));
+	pbns.push_back(std::make_pair<double,double>(	0.155421,11	));
+	pbns.push_back(std::make_pair<double,double>(	0.158443,12	));
+	pbns.push_back(std::make_pair<double,double>(	0.176956,13	));
+	pbns.push_back(std::make_pair<double,double>(	0.183234,12	));
+	pbns.push_back(std::make_pair<double,double>(	0.191069,13	));
+	pbns.push_back(std::make_pair<double,double>(	0.191333,14	));
+	pbns.push_back(std::make_pair<double,double>(	0.191836,15	));
+	pbns.push_back(std::make_pair<double,double>(	0.192675,16	));
+	pbns.push_back(std::make_pair<double,double>(	0.208564,17	));
+	pbns.push_back(std::make_pair<double,double>(	0.218425,18	));
+	pbns.push_back(std::make_pair<double,double>(	0.219902,17	));
+	pbns.push_back(std::make_pair<double,double>(	0.23233,16	));
+	pbns.push_back(std::make_pair<double,double>(	0.234558,17	));
+	pbns.push_back(std::make_pair<double,double>(	0.237166,16	));
+	pbns.push_back(std::make_pair<double,double>(	0.247352,17	));
+	pbns.push_back(std::make_pair<double,double>(	0.267421,18	));
+	pbns.push_back(std::make_pair<double,double>(	0.268093,19	));
+	pbns.push_back(std::make_pair<double,double>(	0.278734,18	));
+	pbns.push_back(std::make_pair<double,double>(	0.284722,19	));
+	pbns.push_back(std::make_pair<double,double>(	0.284998,20	));
+	pbns.push_back(std::make_pair<double,double>(	0.294069,21	));
+	pbns.push_back(std::make_pair<double,double>(	0.306293,22	));
+	pbns.push_back(std::make_pair<double,double>(	0.322361,21	));
+	pbns.push_back(std::make_pair<double,double>(	0.323152,22	));
+	pbns.push_back(std::make_pair<double,double>(	0.371021,23	));
+	pbns.push_back(std::make_pair<double,double>(	0.372395,24	));
+	pbns.push_back(std::make_pair<double,double>(	0.387744,25	));
+	pbns.push_back(std::make_pair<double,double>(	0.435537,26	));
+	pbns.push_back(std::make_pair<double,double>(	0.462911,25	));
+	pbns.push_back(std::make_pair<double,double>(	0.483569,26	));
+	pbns.push_back(std::make_pair<double,double>(	0.489209,25	));
+	pbns.push_back(std::make_pair<double,double>(	0.517115,24	));
+	pbns.push_back(std::make_pair<double,double>(	0.522197,23	));
+	pbns.push_back(std::make_pair<double,double>(	0.532665,22	));
+	pbns.push_back(std::make_pair<double,double>(	0.545262,23	));
+	pbns.push_back(std::make_pair<double,double>(	0.587227,22	));
+	pbns.push_back(std::make_pair<double,double>(	0.593036,23	));
+	pbns.push_back(std::make_pair<double,double>(	0.602647,24	));
+	pbns.push_back(std::make_pair<double,double>(	0.605044,25	));
+	pbns.push_back(std::make_pair<double,double>(	0.621962,24	));
+	pbns.push_back(std::make_pair<double,double>(	0.629449,23	));
+	pbns.push_back(std::make_pair<double,double>(	0.636719,22	));
+	pbns.push_back(std::make_pair<double,double>(	0.64957,21	));
+	pbns.push_back(std::make_pair<double,double>(	0.650781,22	));
+	pbns.push_back(std::make_pair<double,double>(	0.654951,23	));
+	pbns.push_back(std::make_pair<double,double>(	0.683489,24	));
+	pbns.push_back(std::make_pair<double,double>(	0.687172,23	));
+	pbns.push_back(std::make_pair<double,double>(	0.69703,22	));
+	pbns.push_back(std::make_pair<double,double>(	0.701174,21	));
+	pbns.push_back(std::make_pair<double,double>(	0.717623,22	));
+	pbns.push_back(std::make_pair<double,double>(	0.722023,21	));
+	pbns.push_back(std::make_pair<double,double>(	0.722298,20	));
+	pbns.push_back(std::make_pair<double,double>(	0.725347,19	));
+	pbns.push_back(std::make_pair<double,double>(	0.73071,18	));
+	pbns.push_back(std::make_pair<double,double>(	0.758355,17	));
+	pbns.push_back(std::make_pair<double,double>(	0.770913,18	));
+	pbns.push_back(std::make_pair<double,double>(	0.790833,17	));
+	pbns.push_back(std::make_pair<double,double>(	0.821211,16	));
+	pbns.push_back(std::make_pair<double,double>(	0.849305,17	));
+	pbns.push_back(std::make_pair<double,double>(	0.853669,16	));
+	pbns.push_back(std::make_pair<double,double>(	0.866659,15	));
+	pbns.push_back(std::make_pair<double,double>(	0.872896,16	));
+	pbns.push_back(std::make_pair<double,double>(	0.889597,15	));
+	pbns.push_back(std::make_pair<double,double>(	0.900231,14	));
+	pbns.push_back(std::make_pair<double,double>(	0.903847,13	));
+	pbns.push_back(std::make_pair<double,double>(	0.906299,12	));
+	pbns.push_back(std::make_pair<double,double>(	0.910852,11	));
+	pbns.push_back(std::make_pair<double,double>(	0.93453,10	));
+	pbns.push_back(std::make_pair<double,double>(	0.944757,9	));
+	pbns.push_back(std::make_pair<double,double>(	0.947812,8	));
+	pbns.push_back(std::make_pair<double,double>(	0.959154,7	));
+	pbns.push_back(std::make_pair<double,double>(	0.975654,6	));
+	pbns.push_back(std::make_pair<double,double>(	0.976719,5	));
+	pbns.push_back(std::make_pair<double,double>(	0.977343,4	));
+	pbns.push_back(std::make_pair<double,double>(	0.980129,3	));
+	pbns.push_back(std::make_pair<double,double>(	0.987842,2	));
+	pbns.push_back(std::make_pair<double,double>(	0.990127,1	));
+	pbns.push_back(std::make_pair<double,double>(	0.994537,0	));
 
 
 
@@ -308,7 +307,7 @@ BOOST_AUTO_TEST_CASE(check_compute_persistent_betti_numbers)
 	std::vector< std::pair< double , size_t > > pbns_new = p.compute_persistent_betti_numbers();	
 	for ( size_t i = 0 ; i != pbns.size() ; ++i )
 	{
-		//cout << pbns_new[i].first << "," << pbns_new[i].second << endl;
+		//cout << pbns_new[i].first << "," << pbns_new[i].second << std::endl;
 		BOOST_CHECK( fabs ( pbns[i].first - pbns_new[i].first ) <= epsilon );		
 		BOOST_CHECK( fabs ( pbns[i].second - pbns_new[i].second ) <= epsilon );
 	}
@@ -334,7 +333,7 @@ BOOST_AUTO_TEST_CASE(check_k_n_n)
 		
 	for ( size_t i = 0 ; i != knn.size() ; ++i )
 	{
-		//cout << knn[i] << endl;
+		//cout << knn[i] << std::endl;
 		BOOST_CHECK( fabs ( knn[i] - knn_template[i] ) <= 0.000005 );
 	}
 }
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 2e24f932..84b01f3e 100644
--- a/src/Gudhi_stat/test/persistence_lanscapes_on_grid_test.cpp
+++ b/src/Gudhi_stat/test/persistence_lanscapes_on_grid_test.cpp
@@ -38,7 +38,6 @@ using namespace Gudhi::Gudhi_stat;
 
 double epsilon = 0.0000005;
 
-using namespace std;
 
 
 	
diff --git a/src/Gudhi_stat/test/persistence_lanscapes_test.cpp b/src/Gudhi_stat/test/persistence_lanscapes_test.cpp
index 30ebdba3..dd010174 100644
--- a/src/Gudhi_stat/test/persistence_lanscapes_test.cpp
+++ b/src/Gudhi_stat/test/persistence_lanscapes_test.cpp
@@ -38,7 +38,6 @@ using namespace Gudhi::Gudhi_stat;
 
 double epsilon = 0.0000005;
 
-using namespace std;
 
 	
 
diff --git a/src/Gudhi_stat/test/vector_representation_test.cpp b/src/Gudhi_stat/test/vector_representation_test.cpp
index b38c5147..dd84fc33 100644
--- a/src/Gudhi_stat/test/vector_representation_test.cpp
+++ b/src/Gudhi_stat/test/vector_representation_test.cpp
@@ -37,7 +37,6 @@
 using namespace Gudhi;
 using namespace Gudhi::Gudhi_stat;
 
-using namespace std;
 
 
 
diff --git a/src/Gudhi_stat/utilities/Hausdorff_bootstrap.cpp b/src/Gudhi_stat/utilities/Hausdorff_bootstrap.cpp
index 9b8f539d..a4eb73b8 100644
--- a/src/Gudhi_stat/utilities/Hausdorff_bootstrap.cpp
+++ b/src/Gudhi_stat/utilities/Hausdorff_bootstrap.cpp
@@ -26,7 +26,7 @@
 #include <gudhi/read_persitence_from_file.h>
 #include <gudhi/concretizations/Vector_distances_in_diagram.h>
 
-using namespace std;
+
 using namespace Gudhi;
 using namespace Gudhi::Gudhi_stat;
 
diff --git a/src/Gudhi_stat/utilities/Landscape_bootstrap.cpp b/src/Gudhi_stat/utilities/Landscape_bootstrap.cpp
index f9757020..1cf4de94 100644
--- a/src/Gudhi_stat/utilities/Landscape_bootstrap.cpp
+++ b/src/Gudhi_stat/utilities/Landscape_bootstrap.cpp
@@ -35,7 +35,6 @@
 
 
 
-using namespace std;
 using namespace Gudhi;
 using namespace Gudhi::Gudhi_stat;
 using namespace Gudhi::persistent_cohomology;
diff --git a/src/Gudhi_stat/utilities/Multiplicative_bootstrap.cpp b/src/Gudhi_stat/utilities/Multiplicative_bootstrap.cpp
index abcb3f55..9981d5c4 100644
--- a/src/Gudhi_stat/utilities/Multiplicative_bootstrap.cpp
+++ b/src/Gudhi_stat/utilities/Multiplicative_bootstrap.cpp
@@ -26,7 +26,6 @@
 #include <gudhi/read_persitence_from_file.h>
 #include <gudhi/concretizations/Vector_distances_in_diagram.h>
 
-using namespace std;
 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 809802d7..dfbe3129 100644
--- a/src/Gudhi_stat/utilities/permutation_test.cpp
+++ b/src/Gudhi_stat/utilities/permutation_test.cpp
@@ -26,7 +26,6 @@
 #include <iostream>
 #include <cstring>
 
-using namespace std;
 using namespace Gudhi;
 using namespace Gudhi::Gudhi_stat;
 
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 d73165b7..46711d27 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
@@ -34,20 +34,18 @@
 using namespace Gudhi;
 using namespace Gudhi::Gudhi_stat;
 
-using namespace std;
-
 
 int main( int argc , char** argv )
 {
 	//std::cout << "This program compute minimum birth and the maximum death time for a collection of persistence intervals \n";
 	//if ( argc != 2 )
 	//{
-	//	cout << "To run this program, please provide the name of a file with persistence diagram \n";
+	//	std::cout << "To run this program, please provide the name of a file with persistence diagram \n";
 	//	return 1;
 	//}
 	//Persistence_intervals p( argv[1] );
 	//std::pair<double,double> min_max_ = p.min_max();
-	//cout << "Birth-death range : min: " <<  min_max_.first << ", max: " << min_max_.second << endl;
+	//std::cout << "Birth-death range : min: " <<  min_max_.first << ", max: " << min_max_.second << endl;
 	
 	std::vector< const char* > filenames;
 	for ( int i = 1 ; i < argc ; ++i )
@@ -66,6 +64,6 @@ int main( int argc , char** argv )
 		if ( min_max_.first < min_ )min_ = min_max_.first;
 		if ( min_max_.second > max_ )max_ = min_max_.second;
 	}
-	cout << "Birth-death range : min: " <<  min_ << ", max: " << max_ << endl;
+	std::cout << "Birth-death range : min: " <<  min_ << ", max: " << max_ << std::endl;
 	return 0;
 }
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 d4949932..8c263705 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
@@ -32,24 +32,22 @@
 using namespace Gudhi;
 using namespace Gudhi::Gudhi_stat;
 
-using namespace std;
-
 
 int main( int argc , char** argv )
 {
 	std::cout << "This program compute the dominant intervals. A number of intervals to be displayed is a parameter of this program. \n";
 	if ( argc != 3 )
 	{
-		cout << "To run this program, please provide the name of a file with persistence diagram and number of dominant intervals you would like to get \n";
+		std::cout << "To run this program, please provide the name of a file with persistence diagram and number of dominant intervals you would like to get \n";
 		return 1;
 	}
 
 	Persistence_intervals p( argv[1] );
 	std::vector< std::pair<double,double> > dominant_intervals = p.dominant_intervals( atoi( argv[2] ) );
-	cout << "Here are the dominant intervals : " << endl;
+	std::cout << "Here are the dominant intervals : " << std::endl;
 	for ( size_t i = 0 ; i != dominant_intervals.size() ; ++i )
 	{
-		cout << " " << dominant_intervals[i].first<< "," << dominant_intervals[i].second  << " "<< endl;
+		std::cout << " " << dominant_intervals[i].first<< "," << dominant_intervals[i].second  << " "<< std::endl;
 	}
 	
 	return 0;
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 96e6fa47..f21afdd2 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
@@ -32,15 +32,13 @@
 using namespace Gudhi;
 using namespace Gudhi::Gudhi_stat;
 
-using namespace std;
-
 
 int main( int argc , char** argv )
 {
 	std::cout << "This program compute a histogram of barcode's length. A number of bins in the histogram is a parameter of this program. \n";
 	if ( argc != 3 )
 	{
-		cout << "To run this program, please provide the name of a file with persistence diagram and number of dominant intervals you would like to get \n";
+		std::cout << "To run this program, please provide the name of a file with persistence diagram and number of dominant intervals you would like to get \n";
 		return 1;
 	}
 
@@ -50,7 +48,7 @@ int main( int argc , char** argv )
 	
 	std::stringstream gnuplot_script;
 	gnuplot_script << argv[1] << "_Gnuplot_script";
-	ofstream out;
+	std::ofstream out;
 	out.open( gnuplot_script.str().c_str() );
 	
 	out << "set style data histogram" << std::endl;
@@ -61,7 +59,7 @@ int main( int argc , char** argv )
 	{
 		out << histogram[i]  << std::endl;
 	}		
-	out << endl;
+	out << std::endl;
 	std::cout << "To vizualize, open gnuplot and type: load \'" << gnuplot_script.str().c_str() << "\'" <<  std::endl;	
 	out.close();	
 	return 0;
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 e4efdf79..d12c4605 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
@@ -32,15 +32,13 @@
 using namespace Gudhi;
 using namespace Gudhi::Gudhi_stat;
 
-using namespace std;
-
 
 int main( int argc , char** argv )
 {
 	std::cout << "This program compute a plot of persistence Betti numbers. The input parameter is a file with persistence intervals. \n";
 	if ( argc != 2 )
 	{
-		cout << "To run this program, please provide the name of a file with persistence diagram and number of dominant intervals you would like to get \n";
+		std::cout << "To run this program, please provide the name of a file with persistence diagram and number of dominant intervals you would like to get \n";
 		return 1;
 	}
 	
@@ -48,7 +46,7 @@ int main( int argc , char** argv )
 	
 	std::stringstream gnuplot_script;
 	gnuplot_script << argv[1] << "_Gnuplot_script";
-	ofstream out;
+	std::ofstream out;
 	out.open( gnuplot_script.str().c_str() );
 	
 	Persistence_intervals p( argv[1] );
@@ -68,22 +66,22 @@ int main( int argc , char** argv )
 	yRangeEnd += yRangeEnd/100;
 	
 	
-	out << "set xrange [" << xRangeBegin << " : " << xRangeEnd << "]" << endl;
-    out << "set yrange [" << yRangeBegin << " : " << yRangeEnd << "]" << endl;	
+	out << "set xrange [" << xRangeBegin << " : " << xRangeEnd << "]" << std::endl;
+    out << "set yrange [" << yRangeBegin << " : " << yRangeEnd << "]" << std::endl;	
 	out << "plot '-' using 1:2 notitle with lp " << std::endl;    
 	double previous_y = 0;
 	for ( size_t i = 0 ; i != pbns.size() ; ++i )
 	{
-		out << pbns[i].first << " " << previous_y << endl;
+		out << pbns[i].first << " " << previous_y << std::endl;
 		out << pbns[i].first << " " << pbns[i].second << std::endl;
 		previous_y = pbns[i].second;
 	}		
-	out << endl;
+	out << std::endl;
 	out.close();
 	
 	//for ( size_t i = 0 ; i != pbns.size() ; ++i )
 	//{
-	//	cout << pbns[i].first << " " << pbns[i].second << std::endl;
+	//	std::cout << pbns[i].first << " " << pbns[i].second << std::endl;
 	//}	
 	
 	std::cout << "To vizualize, open gnuplot and type: load \'" << gnuplot_script.str().c_str() << "\'" << std::endl;
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 2c398742..d2e49ef3 100644
--- a/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_intervals.cpp
+++ b/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_intervals.cpp
@@ -36,14 +36,12 @@ using namespace Gudhi::Gudhi_stat;
 
 double epsilon = 0.0000005;
 
-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";
+		std::cout << "To run this program, please provide the name of a file with persistence diagram \n";
 		return 1;
 	}