Merge add_utils_in_gudhi_v2 branch after 2nd round of review

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3041 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: ad134cc2b6756e20afc8d9db9e40c5af87d09f9d

2 files changed, 58 insertions, 9 deletions

diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h
index 3b3d9248..d06b81f5 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 +68,55 @@ 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.
+
 */
 }  // namespace Gudhi
 
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 34d3893d..72ef191d 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -328,7 +328,7 @@ 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 +411,9 @@ 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 +491,9 @@ 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