Add warnings for rips persistence from correlation matrix (points under the diagonal).

Use range instead of vector in write_persistence_intervals_to_stream


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@3326 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: ea0fdc32c91f1927c5a9f2a3864360895ce8128a

5 files changed, 93 insertions, 137 deletions

diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h
index 3f02206b..496c4218 100644
--- a/src/Rips_complex/doc/Intro_rips_complex.h
+++ b/src/Rips_complex/doc/Intro_rips_complex.h
@@ -170,6 +170,9 @@ namespace rips_complex {
  * All the other constructions discussed for Rips complex for distance matrix can be also performed for Rips complexes
  * construction from correlation matrices.
  * 
+ * @warning As persistence diagrams points will be under the diagonal, bottleneck distance and persistence graphical
+ * tool will not work properly, this is a known issue.
+ *
  */
 /** @} */  // end defgroup rips_complex
 
diff --git a/src/Rips_complex/utilities/ripscomplex.md b/src/Rips_complex/utilities/ripscomplex.md
index 3f064e67..857e6293 100644
--- a/src/Rips_complex/utilities/ripscomplex.md
+++ b/src/Rips_complex/utilities/ripscomplex.md
@@ -68,3 +68,8 @@ Please refer to data/correlation_matrix/lower_triangular_correlation_matrix.csv
 **Example**
 
 `rips_correlation_matrix_persistence data/distance_matrix/full_square_distance_matrix.csv -r 15 -d 3 -p 3 -m 0`
+
+**Warning**
+
+As persistence diagrams points will be under the diagonal, bottleneck distance and persistence graphical tool will not work
+properly, this is a known issue.
diff --git a/src/common/include/gudhi/writing_persistence_to_file.h b/src/common/include/gudhi/writing_persistence_to_file.h
index 5457cf48..5020b5fb 100644
--- a/src/common/include/gudhi/writing_persistence_to_file.h
+++ b/src/common/include/gudhi/writing_persistence_to_file.h
@@ -29,150 +29,88 @@
 
 namespace Gudhi {
 
-
 /**
-* This is a class to store persistence intervals. Its main purpose is to 
+* This is a class to store persistence intervals. Its main purpose is to
 * exchange data in between different packages and provide unified way
-* of writing a collection of persistence intervals to file. 
+* of writing a collection of persistence intervals to file.
 **/
-template <typename Filtration_type , typename Coefficient_field>
-class Persistence_interval_common
-{
-public:	
-    /**
-     * Constructor taking as an input birth and death of the pair. 
-    **/ 
-	Persistence_interval_common( Filtration_type birth , Filtration_type death ):
-	birth_(birth),death_(death),dimension_(std::numeric_limits<unsigned>::max),
-	arith_element_(std::numeric_limits<Coefficient_field>::max() ){} 
-	
-    /**
-     * Constructor taking as an input birth, death and dimension of the pair. 
-    **/ 	
-	Persistence_interval_common( Filtration_type birth , Filtration_type death,
-	unsigned dim ):
-	birth_(birth),death_(death),dimension_(dim),
-	arith_element_(std::numeric_limits<Coefficient_field>::max()){}
-	
-	/**
-     * Constructor taking as an input birth, death, dimension of the pair as well
-     * as the number p such that this interval is present over Z_p field. 
-    **/ 
-	Persistence_interval_common( Filtration_type birth , Filtration_type death,
-	unsigned dim , Coefficient_field field ):
-	birth_(birth),death_(death),dimension_(dim),
-	arith_element_(field){}
-	
-	/**
-	 * Operator to compare two persistence pairs. During the comparision all the 
-	 * fields: birth, death, dimensiona and arith_element_ are taken into account 
-	 * and they all have to be equal for two pairs to be equal.
-	**/ 
-	inline bool operator == ( const Persistence_interval_common &i2)
-	{
-		return ( 
-		        (this->birth_ == i2.birth_) && (this->death_ == i2.death_) && 
-		        (this->dimension_ == i2.dimension_) && (this->arith_element_ == i2.arith_element_)
-		       );
-	}
-	
-	/**
-	 * Check if two persistence paris are not equal. 
-	**/ 
-	inline bool operator != ( const Persistence_interval_common &i2)
-	{
-		return (!((*this)==i2));
-	}
-	
-	
-	/**
-	 * Operator to compare objects of a type Persistence_interval_common. 
-	 * One intervals is smaller than the other if it has lower persistence. 
-	 * Note that this operator do not take Arith_element into account when doing comparisions.
-	**/ 
-	inline bool operator < ( const Persistence_interval_common &i2)
-	{		
-		return 	fabs( this->death_-this->birth_ ) < fabs( i2.death_-i2.birth_ );
-		//if ( this->birth_ < i2.birth_ )
-		//{
-		//	return true;
-		//}
-		//else
-		//{
-		//	if ( this->birth_ > i2.birth_ )
-		//	{
-		//		return false;
-		//	}
-		//	else
-		//	{
-		//		//in this case this->birth_ == i2.birth_
-		//		if ( this->death_ > i2.death_ )
-		//		{
-		//			return true;
-		//		}
-		//		else
-		//		{
-		//			if ( this->death_ < i2.death_ )
-		//			{
-		//				return false;
-		//			}
-		//			else
-		//			{
-		//				//in this case this->death_ == i2.death_
-		//				if ( this->dimension_ < i2.dimension_ )
-		//				{
-		//					return true;
-		//				}
-		//				else
-		//				{
-		//					//in this case this->dimension >= i2.dimension
-		//					return false;
-		//				}
-		//			}
-		//		}
-		//	}
-		//}
-	}
-	
-	friend std::ostream& operator<<(std::ostream& out, const Persistence_interval_common& it)
-	{
-		if ( it.arith_element_ != std::numeric_limits<Coefficient_field>::max() ) 
-		{
-			out << it.arith_element_ << "  ";	
-		}		
-		if ( it.dimension_ != std::numeric_limits<unsigned>::max() )
-		{
-			out << it.dimension_ << " ";
-		}				
-		out << it.birth_ << " " << it.death_ << " ";				
-		return out;
-	}
-	
-private:
-	Filtration_type birth_;
-	Filtration_type death_;
-	unsigned dimension_;
-	Coefficient_field arith_element_;
-};//Persistence_interval_common
+template <typename Filtration_type, typename Coefficient_field>
+class Persistence_interval_common {
+ public:
+  /**
+   * Constructor taking as an input birth and death of the pair.
+  **/
+  Persistence_interval_common(Filtration_type birth, Filtration_type death)
+      : birth_(birth),
+        death_(death),
+        dimension_(std::numeric_limits<unsigned>::max),
+        arith_element_(std::numeric_limits<Coefficient_field>::max()) {}
 
+  /**
+   * Constructor taking as an input birth, death and dimension of the pair.
+  **/
+  Persistence_interval_common(Filtration_type birth, Filtration_type death, unsigned dim)
+      : birth_(birth), death_(death), dimension_(dim), arith_element_(std::numeric_limits<Coefficient_field>::max()) {}
 
-/**
- * This function write a vector<Persistence_interval_common> to a stream
-**/ 
-template <typename Filtration_type , typename Coefficient_field>
-void write_persistence_intervals_to_stream( 
-const std::vector< Persistence_interval_common<Filtration_type,Coefficient_field> >& intervals,
-//TODO: change to ranges when it is clear how to do that.
-                                          std::ostream& out = std::cout )
-{
-	for ( auto interval : intervals )
-	{
-		out << interval << "\n";
-	}
-}//write_persistence_intervals_to_stream
+  /**
+* Constructor taking as an input birth, death, dimension of the pair as well
+* as the number p such that this interval is present over Z_p field.
+**/
+  Persistence_interval_common(Filtration_type birth, Filtration_type death, unsigned dim, Coefficient_field field)
+      : birth_(birth), death_(death), dimension_(dim), arith_element_(field) {}
+
+  /**
+   * Operator to compare two persistence pairs. During the comparision all the
+   * fields: birth, death, dimensiona and arith_element_ are taken into account
+   * and they all have to be equal for two pairs to be equal.
+  **/
+  inline bool operator==(const Persistence_interval_common& i2) {
+    return ((this->birth_ == i2.birth_) && (this->death_ == i2.death_) && (this->dimension_ == i2.dimension_) &&
+            (this->arith_element_ == i2.arith_element_));
+  }
+
+  /**
+   * Check if two persistence paris are not equal.
+  **/
+  inline bool operator!=(const Persistence_interval_common& i2) { return (!((*this) == i2)); }
 
+  /**
+   * Operator to compare objects of a type Persistence_interval_common.
+   * One intervals is smaller than the other if it has lower persistence.
+   * Note that this operator do not take Arith_element into account when doing comparisions.
+  **/
+  inline bool operator<(const Persistence_interval_common& i2) {
+    return fabs(this->death_ - this->birth_) < fabs(i2.death_ - i2.birth_);
+  }
 
+  friend std::ostream& operator<<(std::ostream& out, const Persistence_interval_common& it) {
+    if (it.arith_element_ != std::numeric_limits<Coefficient_field>::max()) {
+      out << it.arith_element_ << "  ";
+    }
+    if (it.dimension_ != std::numeric_limits<unsigned>::max()) {
+      out << it.dimension_ << " ";
+    }
+    out << it.birth_ << " " << it.death_ << " ";
+    return out;
+  }
 
+ private:
+  Filtration_type birth_;
+  Filtration_type death_;
+  unsigned dimension_;
+  Coefficient_field arith_element_;
+};
+
+/**
+ * This function write a vector<Persistence_interval_common> to a stream
+**/
+template <typename Persistence_interval_range>
+void write_persistence_intervals_to_stream(const Persistence_interval_range& intervals,
+                                           std::ostream& out = std::cout) {
+  for (auto interval : intervals) {
+    out << interval << "\n";
+  }
+}
 }
 
-#endif //WRITING_PERSISTENCE_TO_FILE_H
+#endif  // WRITING_PERSISTENCE_TO_FILE_H
diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst
index b80ff7fe..7738aef0 100644
--- a/src/cython/doc/rips_complex_user.rst
+++ b/src/cython/doc/rips_complex_user.rst
@@ -305,3 +305,8 @@ until dimension 1 - one skeleton graph in other words), the output is:
     [2, 4] -> 0.97
     [0, 3] -> 0.99
     [1, 3] -> 0.99
+
+.. note::
+    As persistence diagrams points will be under the diagonal,
+    bottleneck distance and persistence graphical tool will not work properly,
+    this is a known issue.
diff --git a/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
index ad990fdc..aa82ef71 100755
--- a/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
+++ b/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
@@ -50,6 +50,11 @@ if not (-1. < args.min_edge_correlation < 1.):
     sys.exit(1)
 
 print("#####################################################################")
+print("Caution: as persistence diagrams points will be under the diagonal,")
+print("bottleneck distance and persistence graphical tool will not work")
+print("properly, this is a known issue.")
+
+print("#####################################################################")
 print("RipsComplex creation from correlation matrix read in a csv file")
 
 message = "RipsComplex with min_edge_correlation=" + repr(args.min_edge_correlation)