Fix to Marc's comments.

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/gudhi_stat@1841 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c5be190621dcbb43433c027c78e782916cc6ae93

12 files changed, 66 insertions, 42 deletions

diff --git a/src/Gudhi_stat/utilities/Hausdorff_bootstrap.cpp b/src/Gudhi_stat/utilities/Hausdorff_bootstrap.cpp
index 16c9b085..9b8f539d 100644
--- a/src/Gudhi_stat/utilities/Hausdorff_bootstrap.cpp
+++ b/src/Gudhi_stat/utilities/Hausdorff_bootstrap.cpp
@@ -23,7 +23,7 @@
 
 #include <gudhi/Hausdorff_distances.h>
 #include <gudhi/bootstrap.h>
-#include <gudhi/concretizations/read_persitence_from_file.h>
+#include <gudhi/read_persitence_from_file.h>
 #include <gudhi/concretizations/Vector_distances_in_diagram.h>
 
 using namespace std;
diff --git a/src/Gudhi_stat/utilities/Landscape_bootstrap.cpp b/src/Gudhi_stat/utilities/Landscape_bootstrap.cpp
index 5b3d0609..f9757020 100644
--- a/src/Gudhi_stat/utilities/Landscape_bootstrap.cpp
+++ b/src/Gudhi_stat/utilities/Landscape_bootstrap.cpp
@@ -24,7 +24,7 @@
 #include <gudhi/Hausdorff_distances.h>
 #include <gudhi/bootstrap.h>
 #include <gudhi/concretizations/Persistence_landscape.h>
-#include <gudhi/concretizations/read_persitence_from_file.h>
+#include <gudhi/read_persitence_from_file.h>
 #include <gudhi/concretizations/Vector_distances_in_diagram.h>
 //persistence part:
 #include <gudhi/reader_utils.h>
diff --git a/src/Gudhi_stat/utilities/Multiplicative_bootstrap.cpp b/src/Gudhi_stat/utilities/Multiplicative_bootstrap.cpp
index d968b460..abcb3f55 100644
--- a/src/Gudhi_stat/utilities/Multiplicative_bootstrap.cpp
+++ b/src/Gudhi_stat/utilities/Multiplicative_bootstrap.cpp
@@ -23,7 +23,7 @@
 
 #include <gudhi/Hausdorff_distances.h>
 #include <gudhi/multiplicative_bootstrap.h>
-#include <gudhi/concretizations/read_persitence_from_file.h>
+#include <gudhi/read_persitence_from_file.h>
 #include <gudhi/concretizations/Vector_distances_in_diagram.h>
 
 using namespace std;
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 efe4ec3d..631057af 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
@@ -44,7 +44,13 @@ int main( int argc , char** argv )
 		return 1;
 	}
 	
-	int p = atoi( argv[1] );
+	int pp = atoi( argv[1] );
+	double p = std::numeric_limits<double>::max();
+	if ( pp != -1 )
+	{
+		p = pp;
+	}
+	
 
 	std::vector< const char* > filenames;
 	for ( int i = 2 ; i < argc ; ++i )
@@ -80,17 +86,17 @@ int main( int argc , char** argv )
 	}
 	
 	//and now output the result to the screen and a file:
-	ofstream out;
+	std::ofstream out;
 	out.open( "distance" );
 	for ( size_t i = 0 ; i != distance.size() ; ++i )
 	{
 		for ( size_t j = 0 ; j != distance.size() ; ++j )
 		{
-			cout << distance[i][j] << " ";
+			std::cout << distance[i][j] << " ";
 			out << distance[i][j] << " ";
 		}
-		cout << endl;
-		out << endl;
+		std::cout << std::endl;
+		out << std::endl;
 	}
 	out.close();
 		
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 4caf30af..46edbc28 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
@@ -71,17 +71,17 @@ int main( int argc , char** argv )
 	}
 	
 	//and now output the result to the screen and a file:
-	ofstream out;
+	std::ofstream out;
 	out.open( "scalar_product" );
 	for ( size_t i = 0 ; i != scalar_product.size() ; ++i )
 	{
 		for ( size_t j = 0 ; j != scalar_product.size() ; ++j )
 		{
-			cout << scalar_product[i][j] << " ";
+			std::cout << scalar_product[i][j] << " ";
 			out << scalar_product[i][j] << " ";
 		}
-		cout << endl;
-		out << endl;
+		std::cout << std::endl;
+		out << std::endl;
 	}
 	out.close();
 		
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 5f961332..2c398742 100644
--- a/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_intervals.cpp
+++ b/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_intervals.cpp
@@ -24,7 +24,7 @@
 
 #include <gudhi/reader_utils.h>
 #include <gudhi/concretizations/Persistence_intervals.h>
-#include <gudhi/concretizations/read_persitence_from_file.h>
+#include <gudhi/read_persitence_from_file.h>
 
 #include <iostream>
 
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 e3c3a33e..937a902e 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
@@ -43,7 +43,13 @@ int main( int argc , char** argv )
 		return 1;
 	}
 	
-	int p = atoi( argv[1] );
+	int pp = atoi( argv[1] );
+	double p = std::numeric_limits<double>::max();
+	if ( pp != -1 )
+	{
+		p = pp;
+	}
+	
 
 	std::vector< const char* > filenames;
 	for ( int i = 2 ; i < argc ; ++i )
@@ -75,23 +81,23 @@ int main( int argc , char** argv )
 	{
 		for ( size_t j = i ; j != landscaspes.size() ; ++j )
 		{			
-			distance[i][j] = distance[j][i] = compute_discance_of_landscapes( landscaspes[i], landscaspes[j] , p ) ;
+			distance[i][j] = distance[j][i] = compute_distance_of_landscapes( landscaspes[i], landscaspes[j] , p ) ;
 			
 		}
 	}
 	
 	//and now output the result to the screen and a file:
-	ofstream out;
+	std::ofstream out;
 	out.open( "distance" );
 	for ( size_t i = 0 ; i != distance.size() ; ++i )
 	{
 		for ( size_t j = 0 ; j != distance.size() ; ++j )
 		{
-			cout << distance[i][j] << " ";
+			std::cout << distance[i][j] << " ";
 			out << distance[i][j] << " ";
 		}
-		cout << endl;
-		out << endl;
+		std::cout << std::endl;
+		out << std::endl;
 	}
 	out.close();
 		
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 ef9de9c7..39772b9b 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
@@ -71,17 +71,17 @@ int main( int argc , char** argv )
 	}
 	
 	//and now output the result to the screen and a file:
-	ofstream out;
+	std::ofstream out;
 	out.open( "scalar_product" );
 	for ( size_t i = 0 ; i != scalar_product.size() ; ++i )
 	{
 		for ( size_t j = 0 ; j != scalar_product.size() ; ++j )
 		{
-			cout << scalar_product[i][j] << " ";
+			std::cout << scalar_product[i][j] << " ";
 			out << scalar_product[i][j] << " ";
 		}
-		cout << endl;
-		out << endl;
+		std::cout << std::endl;
+		out << std::endl;
 	}
 	out.close();
 		
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 ace5066a..58c5ec47 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
@@ -43,7 +43,13 @@ int main( int argc , char** argv )
 		return 1;
 	}
 	
-	int p = atoi( argv[1] );
+	int pp = atoi( argv[1] );
+	double p = std::numeric_limits<double>::max();
+	if ( pp != -1 )
+	{
+		p = pp;
+	}
+	
 
 	std::vector< const char* > filenames;
 	for ( int i = 2 ; i < argc ; ++i )
@@ -74,22 +80,22 @@ int main( int argc , char** argv )
 	{
 		for ( size_t j = i ; j != landscaspes.size() ; ++j )
 		{
-			distance[i][j] = distance[j][i] = compute_discance_of_landscapes_on_grid( landscaspes[i], landscaspes[j] , p ) ;
+			distance[i][j] = distance[j][i] = compute_distance_of_landscapes_on_grid( landscaspes[i], landscaspes[j] , p ) ;
 		}
 	}
 	
 	//and now output the result to the screen and a file:
-	ofstream out;
+	std::ofstream out;
 	out.open( "distance" );
 	for ( size_t i = 0 ; i != distance.size() ; ++i )
 	{
 		for ( size_t j = 0 ; j != distance.size() ; ++j )
 		{
-			cout << distance[i][j] << " ";
+			std::cout << distance[i][j] << " ";
 			out << distance[i][j] << " ";
 		}
-		cout << endl;
-		out << endl;
+		std::cout << std::endl;
+		out << std::endl;
 	}
 	out.close();
 		
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 a039a97a..e1a4788f 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
@@ -71,17 +71,17 @@ int main( int argc , char** argv )
 	}
 	
 	//and now output the result to the screen and a file:
-	ofstream out;
+	std::ofstream out;
 	out.open( "scalar_product" );
 	for ( size_t i = 0 ; i != scalar_product.size() ; ++i )
 	{
 		for ( size_t j = 0 ; j != scalar_product.size() ; ++j )
 		{
-			cout << scalar_product[i][j] << " ";
+			std::cout << scalar_product[i][j] << " ";
 			out << scalar_product[i][j] << " ";
 		}
-		cout << endl;
-		out << endl;
+		std::cout << std::endl;
+		out << std::endl;
 	}
 	out.close();
 		
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 7b7faef0..2ca5989e 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
@@ -43,7 +43,13 @@ int main( int argc , char** argv )
 		return 1;
 	}
 	
-	int p = atoi( argv[1] );
+	int pp = atoi( argv[1] );
+	double p = std::numeric_limits<double>::max();
+	if ( pp != -1 )
+	{
+		p = pp;
+	}
+	
 
 	std::vector< const char* > filenames;
 	for ( int i = 2 ; i < argc ; ++i )
@@ -80,17 +86,17 @@ int main( int argc , char** argv )
 	}
 	
 	//and now output the result to the screen and a file:
-	ofstream out;
+	std::ofstream out;
 	out.open( "distance" );
 	for ( size_t i = 0 ; i != distance.size() ; ++i )
 	{
 		for ( size_t j = 0 ; j != distance.size() ; ++j )
 		{
-			cout << distance[i][j] << " ";
+			std::cout << distance[i][j] << " ";
 			out << distance[i][j] << " ";
 		}
-		cout << endl;
-		out << endl;
+		std::cout << std::endl;
+		out << std::endl;
 	}
 	out.close();
 		
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 74172712..78c6ab91 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
@@ -70,17 +70,17 @@ int main( int argc , char** argv )
 	}
 	
 	//and now output the result to the screen and a file:
-	ofstream out;
+	std::ofstream out;
 	out.open( "scalar_product" );
 	for ( size_t i = 0 ; i != scalar_product.size() ; ++i )
 	{
 		for ( size_t j = 0 ; j != scalar_product.size() ; ++j )
 		{
-			cout << scalar_product[i][j] << " ";
+			std::cout << scalar_product[i][j] << " ";
 			out << scalar_product[i][j] << " ";
 		}
-		cout << endl;
-		out << endl;
+		std::cout << std::endl;
+		out << std::endl;
 	}
 	out.close();	
 	return 0;