From ca2ad986b9925ab7006597f0f7045f7be47a42b2 Mon Sep 17 00:00:00 2001
From: pdlotko <pdlotko@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 7 Apr 2017 09:10:52 +0000
Subject: Answers to Marc's comments

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/gudhi_stat@2317 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: f941a6b20210282408d0ef95b84daa973add2513
---
 src/common/doc/main_page.h | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

(limited to 'src/common/doc')

diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index e6f29fa8..55673f60 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -151,6 +151,23 @@
     </td>
  </tr>
 </table>
+</table>
+ \subsection Gudhi_stat Gudhi statistical sublibrary
+ \image html "average_landscape.png" "Gudhi statistical sublibrary"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> Pawel Dlotko<br>
+      <b>Introduced in:</b> GUDHI 2.0.0<br>
+      <b>Copyright:</b> GPL v3<br>      
+    </td>
+    <td width="75%">
+    This is a statistical library for gudhi. It contain implementation of various representations of persistence diagrams; diagrams themselves, persistence landscapes (rigorous and grid version), 
+    persistence heath maps, vectors and others. It implements basic functionalities which are neccessary to use persistence in statistics and machine learning. 
+    <b>User manual:</b> \ref gudhi_stat - <b>Reference manual:</b> Gudhi::Gudhi_stat
+    </td>
+ </tr>
+</table>
  
  \section Toolbox Toolbox
  \subsection BottleneckDistanceToolbox Bottleneck distance
-- 
cgit v1.2.3


From aecf253b150fcaf0a9e2a41686de7dfea91fa4d8 Mon Sep 17 00:00:00 2001
From: pdlotko <pdlotko@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 13 Apr 2017 12:42:19 +0000
Subject: Answer to Vincent's comments. At the moment I need to discuss how to
 correct the doc. At the moment make doxygen generate some errors.

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/gudhi_stat@2342 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 4bb5c3b30bca852045fb414eacf59936975a3855
---
 .../Persistence_landscape.h                        |  6 ++--
 .../Persistence_landscape_on_grid.h                |  6 ++--
 src/Gudhi_stat/utilities/Landscape_bootstrap.cpp   |  2 +-
 .../create_persistence_heat_maps.cpp               |  2 +-
 ...aps_weighted_by_arctan_of_their_persistence.cpp |  2 +-
 ...eat_maps_weighted_by_distance_from_diagonal.cpp |  2 +-
 ..._weighted_by_squared_distance_from_diagonal.cpp |  2 +-
 .../persistence_heat_maps/create_pssk.cpp          |  2 +-
 ...te_birth_death_range_in_persistence_diagram.cpp |  2 +-
 .../compute_bottleneck_distance.cpp                |  2 +-
 .../compute_number_of_dominant_intervals.cpp       |  2 +-
 .../plot_histogram_of_intervals_lengths.cpp        |  2 +-
 .../plot_persistence_Betti_numbers.cpp             |  2 +-
 .../plot_persistence_intervals.cpp                 |  2 +-
 .../persistence_landscapes/create_landscapes.cpp   |  2 +-
 .../create_landscapes_on_grid.cpp                  |  2 +-
 .../create_persistence_vectors.cpp                 |  2 +-
 src/common/doc/main_page.h                         | 34 ++++++++++++----------
 18 files changed, 39 insertions(+), 37 deletions(-)

(limited to 'src/common/doc')

diff --git a/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_landscape.h b/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_landscape.h
index 681f5d8d..925d784f 100644
--- a/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_landscape.h
+++ b/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_landscape.h
@@ -270,7 +270,7 @@ public:
     }
 
 	/**
-	 *\private Computations of a L^i norm of landscape, where i is the input parameter.
+	 *\private Computations of a \f$L^i\f$ norm of landscape, where i is the input parameter.
 	**/
     double compute_norm_of_landscape( double i )
     {
@@ -291,14 +291,14 @@ public:
     double operator()(unsigned level,double x)const{return this->compute_value_at_a_given_point(level,x);}
 
 	/**
-	 *\private Computations of L^{\infty} distance between two landscapes.
+	 *\private Computations of \f$L^{\infty}\f$ distance between two landscapes.
 	**/
     friend double compute_max_norm_distance_of_landscapes( const Persistence_landscape& first, const Persistence_landscape& second );
     //friend double compute_max_norm_distance_of_landscapes( const Persistence_landscape& first, const Persistence_landscape& second , unsigned& nrOfLand , double&x , double& y1, double& y2 );
 
 
 	/**
-	 *\private Computations of L^{p} distance between two landscapes. p is the parameter of the procedure.
+	 *\private Computations of \f$L^{p}\f$ distance between two landscapes. p is the parameter of the procedure.
 	**/
     friend double compute_distance_of_landscapes( const Persistence_landscape& first, const Persistence_landscape& second , double p );
 
diff --git a/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_landscape_on_grid.h b/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_landscape_on_grid.h
index 1f4cb3ff..3103172d 100644
--- a/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_landscape_on_grid.h
+++ b/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_landscape_on_grid.h
@@ -595,7 +595,7 @@ public:
 	}
 
 	/**
-	 * Computations of a L^i norm of landscape, where i is the input parameter.
+	 * Computations of a \f$L^i\f$ norm of landscape, where i is the input parameter.
 	**/
     double compute_norm_of_landscape( double i )const
     {
@@ -618,7 +618,7 @@ public:
     double operator()(unsigned level,double x)const{return this->compute_value_at_a_given_point(level,x);}
 
 	/**
-	 * Computations of L^{\infty} distance between two landscapes.
+	 * Computations of \f$L^{\infty}\f$ distance between two landscapes.
 	**/
     friend double compute_max_norm_distance_of_landscapes( const Persistence_landscape_on_grid& first, const Persistence_landscape_on_grid& second );
     //friend double compute_max_norm_distance_of_landscapes( const Persistence_landscape_on_grid& first, const Persistence_landscape_on_grid& second , unsigned& nrOfLand , double&x , double& y1, double& y2 );
@@ -765,7 +765,7 @@ public:
 	
 	
 	/**
-	 * Computations of L^{p} distance between two landscapes on a grid. p is the parameter of the procedure.
+	 * Computations of \f$L^{p}\f$ distance between two landscapes on a grid. p is the parameter of the procedure.
 	 * FIXME: Note that, due to the grid representation, the method below may give non--accurate results in case when the landscape P and Q the difference of which we want to compute
 	 * are interxsecting. This is a consequence of a general way they are computed. In the future, an integral of absolute value of a difference of P and Q will be given as a separated
 	 * function to fix that inaccuracy. 
diff --git a/src/Gudhi_stat/utilities/Landscape_bootstrap.cpp b/src/Gudhi_stat/utilities/Landscape_bootstrap.cpp
index d67bb820..9bd6c89e 100644
--- a/src/Gudhi_stat/utilities/Landscape_bootstrap.cpp
+++ b/src/Gudhi_stat/utilities/Landscape_bootstrap.cpp
@@ -38,7 +38,7 @@
 using Persistence_landscape = Gudhi::Gudhi_stat::Persistence_landscape;
 
 typedef int Vertex_handle;
-typedef double Filtration_value;
+//typedef double Filtration_value;
 
 
 //if this variable is -1, then the infinite interals are ignored. If not, they infinite values are replaced with what_to_replace_infinite_intervals_with:
diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp
index d9c7aded..e99b829a 100644
--- a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp
+++ b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp
@@ -57,7 +57,7 @@ int main( int argc , char** argv )
 	
 	unsigned dimension = std::numeric_limits<unsigned>::max();
 	int dim = atoi( argv[5] );	 
-	if ( (dim != -1) && (dim >= 0) )
+	if ( dim >= 0 )
 	{
 		dimension = (unsigned)dim;
 	}
diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp
index 7cb7eeb7..b98fc3f7 100644
--- a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp
+++ b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp
@@ -58,7 +58,7 @@ int main( int argc , char** argv )
 	
 	unsigned dimension = std::numeric_limits<unsigned>::max();
 	int dim = atoi( argv[5] );	 
-	if ( (dim != -1) && (dim >= 0) )
+	if ( dim >= 0 )
 	{
 		dimension = (unsigned)dim;
 	}
diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp
index 3242e106..ecef449a 100644
--- a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp
+++ b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp
@@ -57,7 +57,7 @@ int main( int argc , char** argv )
 	
 	unsigned dimension = std::numeric_limits<unsigned>::max();
 	int dim = atoi( argv[5] );	 
-	if ( (dim != -1) && (dim >= 0) )
+	if ( dim >= 0 )
 	{
 		dimension = (unsigned)dim;
 	}
diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp
index 27846a99..59966855 100644
--- a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp
+++ b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp
@@ -57,7 +57,7 @@ int main( int argc , char** argv )
 
 	unsigned dimension = std::numeric_limits<unsigned>::max();
 	int dim = atoi( argv[5] );	 
-	if ( (dim != -1) && (dim >= 0) )
+	if ( dim >= 0 )
 	{
 		dimension = (unsigned)dim;
 	}
diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/create_pssk.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/create_pssk.cpp
index 404a4be3..78989ccc 100644
--- a/src/Gudhi_stat/utilities/persistence_heat_maps/create_pssk.cpp
+++ b/src/Gudhi_stat/utilities/persistence_heat_maps/create_pssk.cpp
@@ -57,7 +57,7 @@ int main( int argc , char** argv )
 	
 	unsigned dimension = std::numeric_limits<unsigned>::max();
 	int dim = atoi( argv[5] );	 
-	if ( (dim != -1) && (dim >= 0) )
+	if ( dim >= 0 )
 	{
 		dimension = (unsigned)dim;
 	}
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 426a9b7b..a3e19400 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
@@ -45,7 +45,7 @@ int main( int argc , char** argv )
 	
 	int dim = atoi( argv[1] );
 	unsigned dimension = std::numeric_limits<unsigned>::max();
-	if ( (dim != -1) && (dim >= 0) )
+	if ( dim >= 0 )
 	{
 		dimension = (unsigned)dim;
 	}
diff --git a/src/Gudhi_stat/utilities/persistence_intervals/compute_bottleneck_distance.cpp b/src/Gudhi_stat/utilities/persistence_intervals/compute_bottleneck_distance.cpp
index 6f0ba635..d8b533cf 100644
--- a/src/Gudhi_stat/utilities/persistence_intervals/compute_bottleneck_distance.cpp
+++ b/src/Gudhi_stat/utilities/persistence_intervals/compute_bottleneck_distance.cpp
@@ -48,7 +48,7 @@ int main( int argc , char** argv )
 
 	int dim = atoi(argv[1]);
 	unsigned dimension = std::numeric_limits<unsigned>::max();
-	if ( (dim != -1) && (dim >= 0) )
+	if ( dim >= 0 )
 	{
 		dimension = (unsigned)dim;
 	}
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 0a7f7c2b..281902fe 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
@@ -43,7 +43,7 @@ int main( int argc , char** argv )
 	}
 	int dim = atoi( argv[2] );
 	unsigned dimension = std::numeric_limits<unsigned>::max();
-	if ( (dim != -1) && (dim >= 0) )
+	if ( dim >= 0 )
 	{
 		dimension = (unsigned)dim;
 	}
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 11876a0d..acfb0eed 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
@@ -48,7 +48,7 @@ int main( int argc , char** argv )
 	{
 		dim = atoi( argv[2] );
 	} 
-	if ( (dim != -1) && (dim >= 0) )
+	if ( dim >= 0 )
 	{
 		dimension = (unsigned)dim;
 	}
diff --git a/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp b/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp
index 09c6cc22..21ba06f4 100644
--- a/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp
+++ b/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp
@@ -48,7 +48,7 @@ int main( int argc , char** argv )
 	{
 		dim = atoi( argv[2] );
 	} 
-	if ( (dim != -1) && (dim >= 0) )
+	if ( dim >= 0 )
 	{
 		dimension = (unsigned)dim;
 	}
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 4315abb9..95c0cf1f 100644
--- a/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_intervals.cpp
+++ b/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_intervals.cpp
@@ -51,7 +51,7 @@ int main( int argc , char** argv )
 	{
 		dim = atoi( argv[2] );
 	} 
-	if ( (dim != -1) && (dim >= 0) )
+	if ( dim >= 0 )
 	{
 		dimension = (unsigned)dim;
 	}
diff --git a/src/Gudhi_stat/utilities/persistence_landscapes/create_landscapes.cpp b/src/Gudhi_stat/utilities/persistence_landscapes/create_landscapes.cpp
index f36e313a..040ccc95 100644
--- a/src/Gudhi_stat/utilities/persistence_landscapes/create_landscapes.cpp
+++ b/src/Gudhi_stat/utilities/persistence_landscapes/create_landscapes.cpp
@@ -40,7 +40,7 @@ int main( int argc , char** argv )
 	std::vector< const char* > filenames;
 	int dim = atoi(argv[1]);
 	unsigned dimension = std::numeric_limits<unsigned>::max();
-	if ( (dim != -1) && (dim >= 0) )
+	if ( dim >= 0 )
 	{
 		dimension = (unsigned)dim;
 	}
diff --git a/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp
index eb534bf1..6dbb70c4 100644
--- a/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp
+++ b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp
@@ -52,7 +52,7 @@ int main( int argc , char** argv )
 	double max_ = atof( argv[3] );
 	int dim = atoi( argv[4] );
 	unsigned dimension = std::numeric_limits<unsigned>::max();
-	if ( (dim != -1) && (dim >= 0) )
+	if ( dim >= 0 )
 	{
 		dimension = (unsigned)dim;
 	}
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 40f5e81f..7f0492c6 100644
--- a/src/Gudhi_stat/utilities/persistence_vectors/create_persistence_vectors.cpp
+++ b/src/Gudhi_stat/utilities/persistence_vectors/create_persistence_vectors.cpp
@@ -39,7 +39,7 @@ int main( int argc , char** argv )
 	std::cout << "The remaining parameters are the names of files with persistence diagrams. \n";
 	int dim = atoi( argv[1] );
 	unsigned dimension = std::numeric_limits<unsigned>::max();
-	if ( (dim != -1) && (dim >= 0) )
+	if ( dim >= 0 )
 	{
 		dimension = (unsigned)dim;
 	}
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 55673f60..f3816238 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -151,22 +151,6 @@
     </td>
  </tr>
 </table>
-</table>
- \subsection Gudhi_stat Gudhi statistical sublibrary
- \image html "average_landscape.png" "Gudhi statistical sublibrary"
-<table border="0">
-  <tr>
-    <td width="25%">
-      <b>Author:</b> Pawel Dlotko<br>
-      <b>Introduced in:</b> GUDHI 2.0.0<br>
-      <b>Copyright:</b> GPL v3<br>      
-    </td>
-    <td width="75%">
-    This is a statistical library for gudhi. It contain implementation of various representations of persistence diagrams; diagrams themselves, persistence landscapes (rigorous and grid version), 
-    persistence heath maps, vectors and others. It implements basic functionalities which are neccessary to use persistence in statistics and machine learning. 
-    <b>User manual:</b> \ref gudhi_stat - <b>Reference manual:</b> Gudhi::Gudhi_stat
-    </td>
- </tr>
 </table>
  
  \section Toolbox Toolbox
@@ -227,9 +211,27 @@
     \cite DBLP:journals/corr/abs-1208-5018 and the Compressed Annotation Matrix implementation of
     \cite DBLP:conf/esa/BoissonnatDM13 .<br>
     <b>User manual:</b> \ref persistent_cohomology - <b>Reference manual:</b> Gudhi::persistent_cohomology::Persistent_cohomology
+    </td>
+ </tr>
+</table> 
+ \subsection Gudhi_stat_sublibrary Gudhi statistical sublibrary
+ \image html "average_landscape.png" "Gudhi statistical sublibrary"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> Pawel Dlotko<br>
+      <b>Introduced in:</b> GUDHI 2.0.0<br>
+      <b>Copyright:</b> GPL v3<br>      
+    </td>
+    <td width="75%">
+    This is a statistical library for gudhi. It contain implementation of various representations of persistence diagrams; diagrams themselves, persistence landscapes (rigorous and grid version), 
+    persistence heath maps, vectors and others. It implements basic functionalities which are neccessary to use persistence in statistics and machine learning. 
+    <b>User manual:</b> \ref Gudhi_stat 
+    
     </td>
  </tr>
 </table>
+ 
 */
 
 /*! \page installation GUDHI installation
-- 
cgit v1.2.3