The last commit before changing inheritance to templates in the library desing.

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/gudhi_stat@1738 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 9432e8ee5d37fda7e1d82fc8e8b0121a41afa5b9

9 files changed, 128 insertions, 117 deletions

diff --git a/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Topological_data_with_averages.h b/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Topological_data_with_averages.h
index 8585a62c..cc2cd00f 100644
--- a/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Topological_data_with_averages.h
+++ b/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Topological_data_with_averages.h
@@ -24,6 +24,7 @@
 #ifndef Abs_Topological_data_with_averages_H_
 #define Abs_Topological_data_with_averages_H_
 #include <gudhi/abstract_classes/Abs_Topological_data.h>
+#include <vector>
 
 
 namespace Gudhi 
diff --git a/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Topological_data_with_scalar_product.h b/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Topological_data_with_scalar_product.h
index 819b1376..ccda5e63 100644
--- a/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Topological_data_with_scalar_product.h
+++ b/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Topological_data_with_scalar_product.h
@@ -20,11 +20,11 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef Abs_Topological_data_with_scalar_product_H
+#ifndef Abs_Topological_data_with_scalar_product_H_
 #define Abs_Topological_data_with_scalar_product_H_
 
 #include <gudhi/abstract_classes/Abs_Topological_data.h>
-
+#include <vector>
 
 namespace Gudhi 
 {
diff --git a/src/Gudhi_stat/include/gudhi/concretizations/Persistence_heat_maps.h b/src/Gudhi_stat/include/gudhi/concretizations/Persistence_heat_maps.h
index 89254f16..e9175af9 100644
--- a/src/Gudhi_stat/include/gudhi/concretizations/Persistence_heat_maps.h
+++ b/src/Gudhi_stat/include/gudhi/concretizations/Persistence_heat_maps.h
@@ -148,6 +148,17 @@ double arc_tan_of_persistence_of_point( const std::pair< double , double >& poin
 	return atan( point_in_diagram.second - point_in_diagram.first );
 }
 
+class weight_by_setting_maximal_interval_to_have_length_one
+{
+public:
+	weight_by_setting_maximal_interval_to_have_length_one( double len ):letngth_of_maximal_interval(len){}
+	double operator()( const std::pair< double , double >& point_in_diagram )
+	{
+		return (point_in_diagram.second-point_in_diagram.first)/this->letngth_of_maximal_interval;
+	}
+private:
+	double letngth_of_maximal_interval;
+};
 
 
 
diff --git a/src/Gudhi_stat/include/gudhi/concretizations/Persistence_landscape.h b/src/Gudhi_stat/include/gudhi/concretizations/Persistence_landscape.h
index f5f96d34..aa74514e 100644
--- a/src/Gudhi_stat/include/gudhi/concretizations/Persistence_landscape.h
+++ b/src/Gudhi_stat/include/gudhi/concretizations/Persistence_landscape.h
@@ -59,101 +59,6 @@ namespace Gudhi_stat
 
 
 /**
- * Extra functions needed in construction of barcodes.
-**/
-double minus_length( std::pair<double,double> a )
-{
-    return a.first-a.second;
-}
-double birth_plus_deaths( std::pair<double,double> a )
-{
-    return a.first+a.second;
-}
-
-
-
-/**
- * Given two points in R^2, the procedure compute the parameters A and B of the line y = Ax + B that crosses those two points.
-**/
-std::pair<double,double> compute_parameters_of_a_line( std::pair<double,double> p1 , std::pair<double,double> p2 )
-{
-    double a = (p2.second-p1.second)/( p2.first - p1.first );
-    double b = p1.second - a*p1.first;
-    return std::make_pair(a,b);
-}
-
-/**
- * This procedure given two points which lies on the opposide sides of x axis, compute x for which the line connecting those two points crosses x axis.
-**/
-double find_zero_of_a_line_segment_between_those_two_points ( std::pair<double,double> p1, std::pair<double,double> p2 )
-{
-    if ( p1.first == p2.first )return p1.first;
-    if ( p1.second*p2.second > 0 )
-    {
-        std::ostringstream errMessage;
-        errMessage <<"In function find_zero_of_a_line_segment_between_those_two_points the agguments are: (" << p1.first << "," << p1.second << ") and (" << p2.first << "," << p2.second << "). There is no zero in line between those two points. Program terminated.";
-        std::string errMessageStr = errMessage.str();
-        const char* err = errMessageStr.c_str();
-        throw(err);
-    }
-    //we assume here, that x \in [ p1.first, p2.first ] and p1 and p2 are points between which we will put the line segment
-    double a = (p2.second - p1.second)/(p2.first - p1.first);
-    double b = p1.second - a*p1.first;
-    //cerr << "Line crossing points : (" << p1.first << "," << p1.second << ") oraz (" << p2.first << "," << p2.second << ") : \n";
-    //cerr << "a : " << a << " , b : " << b << " , x : " << x << endl;
-    return -b/a;
-}
-
-
-
-
-/**
- * Lexicographical ordering of points	.
-**/
-bool compare_points_sorting( std::pair<double,double> f, std::pair<double,double> s )
-{
-    if ( f.first < s.first )
-    {
-        return true;
-    }
-    else
-    {//f.first >= s.first
-        if ( f.first > s.first )
-        {
-            return false;
-        }
-        else
-        {//f.first == s.first
-            if ( f.second > s.second )
-            {
-                return true;
-            }
-            else
-            {
-                return false;
-            }
-        }
-    }
-}
-
-
-
-/**
- * This procedure takes two points in R^2 and a double value x. It conputes the line pasing through those two points and return the value of that linear function at x.
-**/
-double function_value ( std::pair<double,double> p1, std::pair<double,double> p2 , double x )
-{
-    //we assume here, that x \in [ p1.first, p2.first ] and p1 and p2 are points between which we will put the line segment
-    double a = (p2.second - p1.second)/(p2.first - p1.first);
-    double b = p1.second - a*p1.first;
-    return (a*x+b);
-}
-
-
-
-
-
-/**
  * A clas implementing persistence landascpes data structures. For theroretical desciritpion, please consult a paper ''Statistical topological data analysis using persistence landscapes'' by Peter Bubenik.
  * For details of algorithms, please consult ''A persistence landscapes toolbox for topological statistics'' by Peter Bubenik and Pawel Dlotko.
  * Persistence landscapes allow vertorization, computations of distances, computations of projections to Real, computations of averages and scalar products. Therefore they implement suitable interfaces.
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 8afab347..988c9f16 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
@@ -42,7 +42,7 @@
 #include <gudhi/abstract_classes/Abs_Real_valued_topological_data.h>
 #include <gudhi/abstract_classes/Abs_Topological_data_with_scalar_product.h>
 #include <gudhi/concretizations/read_persitence_from_file.h>
-#include <gudhi/common_gudhi_stat.h>	
+#include <gudhi/common_gudhi_stat.h>
 
 
 
@@ -54,23 +54,6 @@ namespace Gudhi
 namespace Gudhi_stat
 {
 
-/**
- * Given two points in R^2, the procedure compute the parameters A and B of the line y = Ax + B that crosses those two points.
-**/
-std::pair<double,double> compute_parameters_of_a_line( std::pair<double,double> p1 , std::pair<double,double> p2 )
-{
-    double a = (p2.second-p1.second)/( p2.first - p1.first );
-    double b = p1.second - a*p1.first;
-    return std::make_pair(a,b);
-}
-
-struct greater
-{
-    template<class T>
-    bool operator()(T const &a, T const &b) const { return a > b; }
-};
-
-
 class Persistence_landscape_on_grid  :
 								public Abs_Vectorized_topological_data ,
 								public Abs_Topological_data_with_distances,
@@ -994,7 +977,7 @@ void Persistence_landscape_on_grid::set_up_values_of_landscapes( const std::vect
 	//and now we need to sort the valuesL
 	for ( size_t pt = 0 ; pt != this->values_of_landscapes.size() ; ++pt )
 	{
-		std::sort( this->values_of_landscapes[pt].begin() , this->values_of_landscapes[pt].end() , greater() );	
+		std::sort( this->values_of_landscapes[pt].begin() , this->values_of_landscapes[pt].end() , greater_landscapes_on_grid() );	
 	}
 }//set_up_values_of_landscapes
 
diff --git a/src/Gudhi_stat/include/gudhi/concretizations/Vector_distances_in_diagram.h b/src/Gudhi_stat/include/gudhi/concretizations/Vector_distances_in_diagram.h
index 951d8717..bb350040 100644
--- a/src/Gudhi_stat/include/gudhi/concretizations/Vector_distances_in_diagram.h
+++ b/src/Gudhi_stat/include/gudhi/concretizations/Vector_distances_in_diagram.h
@@ -31,7 +31,6 @@
 #include <limits>
 
 
-
 #include <gudhi/abstract_classes/Abs_Vectorized_topological_data.h>
 #include <gudhi/abstract_classes/Abs_Topological_data_with_averages.h>
 #include <gudhi/abstract_classes/Abs_Topological_data_with_distances.h>
diff --git a/src/Gudhi_stat/include/gudhi/concretizations/read_persitence_from_file.h b/src/Gudhi_stat/include/gudhi/concretizations/read_persitence_from_file.h
index 03446289..519c44fa 100644
--- a/src/Gudhi_stat/include/gudhi/concretizations/read_persitence_from_file.h
+++ b/src/Gudhi_stat/include/gudhi/concretizations/read_persitence_from_file.h
@@ -34,6 +34,114 @@ namespace Gudhi
 {
 namespace Gudhi_stat
 {
+			
+	
+/**
+ * This procedure reads birth-death dagta from a file. We assume that in the file, there may be one type of string 'inf' or 'Inf'. If the second parameter of the program is set to -1,
+ * then those vales are ignored. If the second parameter of this program is set to a positive value, then the infinite intervals will be substituted by that number.
+**/ 
+std::vector< std::pair< double,double > > read_file_names_that_may_contain_inf_string( char* filename , double what_to_substitute_for_infinite_bar = -1 )
+{
+	
+	bool dbg = true;
+	
+	if ( !( access( filename, F_OK ) != -1 ) )
+	{
+		cerr << "The file : " << filename << " do not exist. The program will now terminate \n";
+		throw "The file from which you are trying to read do not exist. The program will now terminate \n";
+	}
+	
+	std::string line;
+    std::vector< std::pair<double,double> > barcode;
+
+	std::ifstream in;
+    in.open( filename );
+    while (!in.eof())
+    {
+        getline(in,line);        
+        if ( !(line.length() == 0 || line[0] == '#') )
+        {
+			std::stringstream lineSS;
+            lineSS << line;
+            double beginn, endd;
+			if ( (line.find("inf") != std::string::npos) || (line.find("Inf") != std::string::npos) )
+			{
+				if ( dbg )
+				{
+					std::cerr << "This line: " << line << " contains infinite interval. We will skip it. \n";
+				}
+				if ( what_to_substitute_for_infinite_bar != -1 )
+				{
+					lineSS >> beginn;
+					endd = what_to_substitute_for_infinite_bar;
+				}
+				else
+				{
+					continue;
+				}
+			}
+			else
+			{           				       
+				lineSS >> beginn;
+				lineSS >> endd;
+			}
+            if ( beginn > endd )
+            {
+                double b = beginn;
+                beginn = endd;
+                endd = b;
+            }  
+            if ( dbg )
+			{
+				std::cerr << "Getting an interval : " << beginn << "," << endd << std::endl;
+			}          
+			barcode.push_back( std::make_pair( beginn , endd ) );			
+        }
+	}
+	return barcode;    
+}//readFileNames	
+	
+	
+/**
+ * This procedure reads names of files which are stored in a file. 
+**/ 
+std::vector< std::string > readFileNames( char* filenameWithFilenames )
+{
+    bool dbg = false;
+    
+    if ( !( access( filenameWithFilenames, F_OK ) != -1 ) )
+	{
+		cerr << "The file : " << filename << " do not exist. The program will now terminate \n";
+		throw "The file from which you are trying to read do not exist. The program will now terminate \n";
+	}
+
+    std::vector< std::string > result;
+    std::ifstream in;
+    in.open( filenameWithFilenames );
+    std::string line;
+    while (!in.eof())
+    {
+        getline(in,line);
+        line.erase( std::remove_if( line.begin(), line.end(), ::isspace) , line.end() );
+
+        if (dbg){std::cerr << "line : " << line << std::endl;}
+
+        if ( (line.length() == 0) || (line[0] == '#') )
+        {
+            //in this case we have a file name. First we should remove all the white spaces.
+            if ( dbg ){std::cerr << "This is a line with comment, it will be ignored n";}
+        }
+        else
+        {
+            result.push_back( line.c_str() );
+            if (dbg){std::cerr << "Line after removing white spaces : " << line << std::endl;}
+        }
+	}
+    in.close();
+
+    return result;
+}//readFileNames
+
 
 /**
  * This method reads persistence from standalone file. The format of the file is as follows:
diff --git a/src/Gudhi_stat/utilities/CMakeLists.txt b/src/Gudhi_stat/utilities/CMakeLists.txt
index d75acc43..4fc11b57 100644
--- a/src/Gudhi_stat/utilities/CMakeLists.txt
+++ b/src/Gudhi_stat/utilities/CMakeLists.txt
@@ -100,4 +100,7 @@ add_executable ( persistence_vectors/plot_persistence_vectors persistence_vector
 target_link_libraries(persistence_vectors/plot_persistence_vectors ${Boost_SYSTEM_LIBRARY})
 
 
+#some stat libraries:
+#add_executable ( permutation_test permutation_test.cpp )
+#target_link_libraries(permutation_test ${Boost_SYSTEM_LIBRARY})
 
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 8e309b11..657dd2d4 100644
--- a/src/Gudhi_stat/utilities/persistence_vectors/create_persistence_vectors.cpp
+++ b/src/Gudhi_stat/utilities/persistence_vectors/create_persistence_vectors.cpp
@@ -46,6 +46,7 @@ int main( int argc , char** argv )
 	for ( size_t i = 0 ; i != filenames.size() ; ++i )
 	{
 		std::cerr << "Creatign persistence vectors based on a file : " << filenames[i] << std::endl;
+		//std::vector< std::pair< double , double > > persistence_pairs = read_gudhi_file( filenames[i] , size_t dimension = 0 )
 		Vector_distances_in_diagram< euclidean_distance<double> > l( filenames[i] , -1 );				
 		std::stringstream ss;
 		ss << filenames[i] << ".vect";