3 files changed, 86 insertions, 11 deletions
diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h
index 3b3d9248..c60ed15a 100644
--- a/src/common/doc/file_formats.h
+++ b/src/common/doc/file_formats.h
@@ -57,10 +57,10 @@ namespace Gudhi {
 
  \section FileFormatsIsoCuboid Iso-cuboid
 
- Such a file describes an iso-oriented cuboid with diagonal opposite vertices (min_hx, min_hy, min_hz,...) and (max_hx, max_hy, max_hz, ...). The format is:<br>
+ Such a file describes an iso-oriented cuboid with diagonal opposite vertices (min_x, min_y, min_z,...) and (max_x, max_y, max_z, ...). The format is:<br>
  \verbatim
-   min_hx min_hy [min_hz ...]
-   max_hx max_hy [max_hz ...]
+   min_x min_y [min_z ...]
+   max_x max_y [max_z ...]
  \endverbatim
 
  Here is a simple sample file in the 3D case:
@@ -68,6 +68,57 @@ namespace Gudhi {
    -1. -1. -1.
    1. 1. 1.
  \endverbatim
+
+
+ \section FileFormatsPerseus Perseus
+
+ This file format is the format used by the Perseus software
+ (http://www.sas.upenn.edu/~vnanda/perseus/) by Vidit Nanda.
+ The first line contains a number d begin the dimension of the
+ bitmap (2 in the example below). Next d lines are the numbers of top dimensional cubes in each dimensions (3 and 3
+ in the example below). Next, in lexicographical order, the filtration of top dimensional cubes is given (1 4 6 8
+ 20 4 7 6 5 in the example below).
+ 
+ \image html "exampleBitmap.png" "Example of a input data."
+ 
+ The input file for the following complex is:
+ \verbatim
+ 2
+ 3
+ 3
+ 1
+ 4
+ 6
+ 8
+ 20
+ 4
+ 7
+ 6
+ 5
+ \endverbatim
+
+ To indicate periodic boundary conditions in a
+ given direction, then number of top dimensional cells in this direction have to be multiplied by -1. For instance:
+
+ \verbatim
+ 2
+ -3
+ 3
+ 1
+ 4
+ 6
+ 8
+ 20
+ 4
+ 7
+ 6
+ 5
+ \endverbatim
+
+ Indicate that we have imposed periodic boundary conditions in the direction x, but not in the direction y.
+
+ Other sample files can be found in the `data/bitmap` folder.
+
 */
 }  // namespace Gudhi
 
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 34d3893d..148ee670 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -99,7 +99,7 @@
   <tr>
     <td width="25%">
       <b>Author:</b> Mathieu Carri&egrave;re<br>
-      <b>Introduced in:</b> GUDHI 2.0.1<br>
+      <b>Introduced in:</b> GUDHI 2.1.0<br>
       <b>Copyright:</b> GPL v3<br>
     </td>
     <td width="75%">
@@ -170,6 +170,7 @@
 </table>
  
  \section Toolbox Toolbox
+ 
  \subsection BottleneckDistanceToolbox Bottleneck distance
  \image html "perturb_pd.png" "Bottleneck distance is the length of the longest edge"
 <table border="0">
@@ -229,7 +230,25 @@
     <b>User manual:</b> \ref persistent_cohomology - <b>Reference manual:</b> Gudhi::persistent_cohomology::Persistent_cohomology
     </td>
  </tr>
+</table> 
+ \subsection PersistenceRepresentationsToolbox Persistence representations
+ \image html "average_landscape.png" "Persistence representations"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> Pawel Dlotko<br>
+      <b>Introduced in:</b> GUDHI 2.1.0<br>
+      <b>Copyright:</b> GPL v3<br>      
+    </td>
+    <td width="75%">
+    It contains 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.<br>
+    <b>User manual:</b> \ref Persistence_representations
+    </td>
+ </tr>
 </table>
+ 
 */
 
 /*! \page installation GUDHI installation
@@ -328,7 +347,7 @@ make doxygen
  * \li <a href="_bottleneck_distance_2bottleneck_basic_example_8cpp-example.html">
  * Bottleneck_distance/bottleneck_basic_example.cpp</a>
  * \li <a href="_bottleneck_distance_2bottleneck_read_file_8cpp-example.html">
- * Bottleneck_distance/bottleneck_read_file.cpp</a>
+ * Bottleneck_distance/bottleneck_distance.cpp</a>
  * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html">
  * Spatial_searching/example_spatial_searching.cpp</a>
  * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html">
@@ -411,9 +430,9 @@ make doxygen
  * \li <a href="_alpha_complex_2weighted_alpha_complex_3d_persistence_8cpp-example.html">
  * Alpha_complex/weighted_alpha_complex_3d_persistence.cpp</a>
  * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_8cpp-example.html">
- * Bitmap_cubical_complex/Bitmap_cubical_complex.cpp</a>
+ * Bitmap_cubical_complex/cubical_complex_persistence.cpp</a>
  * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_periodic_boundary_conditions_8cpp-example.html">
- * Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp</a>
+ * Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp</a>
  * \li <a href="_bitmap_cubical_complex_2_random_bitmap_cubical_complex_8cpp-example.html">
  * Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp</a>
  * \li <a href="_simplex_tree_2simple_simplex_tree_8cpp-example.html">
@@ -491,9 +510,9 @@ make doxygen
  * @example Alpha_complex/weighted_alpha_complex_3d_persistence.cpp
  * @example Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp
  * @example Bottleneck_distance/bottleneck_basic_example.cpp
- * @example Bottleneck_distance/bottleneck_read_file.cpp
- * @example Bitmap_cubical_complex/Bitmap_cubical_complex.cpp
- * @example Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp
+ * @example Bottleneck_distance/bottleneck_distance.cpp
+ * @example Bitmap_cubical_complex/cubical_complex_persistence.cpp
+ * @example Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp
  * @example Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp
  * @example common/example_CGAL_3D_points_off_reader.cpp
  * @example common/example_CGAL_points_off_reader.cpp
@@ -532,4 +551,4 @@ make doxygen
  * @example Witness_complex/weak_witness_persistence.cpp
  * @example Witness_complex/strong_witness_persistence.cpp
  */
-
+ 
diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h
index f6e2ab5a..c556155e 100644
--- a/src/common/include/gudhi/distance_functions.h
+++ b/src/common/include/gudhi/distance_functions.h
@@ -26,6 +26,7 @@
 #include <cmath>  // for std::sqrt
 #include <type_traits>  // for std::decay
 #include <iterator>  // for std::begin, std::end
+#include <utility>
 
 namespace Gudhi {
 
@@ -48,6 +49,10 @@ class Euclidean_distance {
     }
     return std::sqrt(dist);
   }
+  template< typename T >
+  T operator() (const std::pair< T, T >& f, const std::pair< T, T >& s) {
+    return  sqrt((f.first-s.first)*(f.first-s.first) + (f.second-s.second)*(f.second-s.second));
+  }
 };
 
 }  // namespace Gudhi