Add iso-cuboid file format

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2882 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: ad82867ef7523c4a03fdb89054e5bd7b8d40f7da

3 files changed, 20 insertions, 4 deletions

diff --git a/src/Alpha_complex/utilities/README b/src/Alpha_complex/utilities/README
index abb17bf7..67ea1875 100644
--- a/src/Alpha_complex/utilities/README
+++ b/src/Alpha_complex/utilities/README
@@ -48,9 +48,10 @@ This program computes the persistent homology with coefficient field Z/pZ of the
 where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p` must be a prime number).
 
 **Usage**
-`periodic_alpha_complex_3d_persistence <input OFF file> <p> <min_persistence>`
+`periodic_alpha_complex_3d_persistence <input OFF file> <cuboid file> <p> <min_persistence>`
 where
 `<input OFF file>` is the path to the input point cloud in OFF format.
+`<cuboid file>` is the path to the file describing the periodic domain. It must be in the format described [here](http://gudhi.gforge.inria.fr/doc/latest/fileformats.html#FileFormatsIsoCuboid).
 `<p>` is the characteristic p of the coefficient field *Z/pZ* for computing homology. It must be a stricly positive integer.
 `<min_persistence>` is the minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.
 
diff --git a/src/Bottleneck_distance/utilities/README b/src/Bottleneck_distance/utilities/README
index cfdccf0b..d9fdd252 100644
--- a/src/Bottleneck_distance/utilities/README
+++ b/src/Bottleneck_distance/utilities/README
@@ -5,6 +5,6 @@ This program computes the Bottleneck distance between two persistence diagram fi
 

 Usage:

 `bottleneck_read_file_example <file_1.pers> <file_2.pers> [<tolerance>]`

-

-<file_1.pers> and <file_2.pers> must be in the format described [here](http://gudhi.gforge.inria.fr/doc/latest/fileformats.html#FileFormatsPers).

-<tolerance> is an error bound on the bottleneck distance (set by default to the smallest positive double value).

+where

+`<file_1.pers>` and `<file_2.pers>` must be in the format described [here](http://gudhi.gforge.inria.fr/doc/latest/fileformats.html#FileFormatsPers).

+`<tolerance>` is an error bound on the bottleneck distance (set by default to the smallest positive double value).

diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h
index d715aa4d..3b3d9248 100644
--- a/src/common/doc/file_formats.h
+++ b/src/common/doc/file_formats.h
@@ -53,6 +53,21 @@ namespace Gudhi {
  Such files can be generated with `Gudhi::persistent_cohomology::Persistent_cohomology::output_diagram()` and read with
  `Gudhi::read_persistence_intervals_and_dimension()`, `Gudhi::read_persistence_intervals_grouped_by_dimension()` or
  `Gudhi::read_persistence_intervals_in_dimension()`.
+ 
+
+ \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>
+ \verbatim
+   min_hx min_hy [min_hz ...]
+   max_hx max_hy [max_hz ...]
+ \endverbatim
+
+ Here is a simple sample file in the 3D case:
+ \verbatim
+   -1. -1. -1.
+   1. 1. 1.
+ \endverbatim
 */
 }  // namespace Gudhi