1 files changed, 76 insertions, 7 deletions

diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h
index c145b271..d06b81f5 100644
--- a/src/common/doc/file_formats.h
+++ b/src/common/doc/file_formats.h
@@ -2,7 +2,7 @@
 *    (Geometric Understanding in Higher Dimensions) is a generic C++
 *    library for computational topology.
 *
-*    Author(s):       Clément Jamin
+*    Author(s):       Clément Jamin
 *
 *    Copyright (C) 2017  INRIA
 *
@@ -26,7 +26,7 @@
 namespace Gudhi {
 
 /*! \page fileformats File formats
- 
+
  \tableofcontents
 
  \section FileFormatsPers Persistence Diagram
@@ -34,20 +34,89 @@ namespace Gudhi {
  Such a file, whose extension is usually `.pers`, contains a list of persistence intervals.<br>
  Lines starting with `#` are ignored (comments).<br>
  Other lines might contain 2, 3 or 4 values (the number of values on each line must be the same for all lines):
- \code{.unparsed}
+ \verbatim
    [[field] dimension] birth death
- \endcode
+ \endverbatim
 
  Here is a simple sample file:
- \code{.unparsed}
-   # Beautiful persistence diagram
+ \verbatim
+   # Persistence diagram example
    2 2.7 3.7
    2 9.6 14.
+   # Some comments
    3 34.2 34.974
    4 3. inf
- \endcode
+ \endverbatim
 
  Other sample files can be found in the `data/persistence_diagram` folder.
+
+ 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_x, min_y, min_z,...) and (max_x, max_y, max_z, ...). The format is:<br>
+ \verbatim
+   min_x min_y [min_z ...]
+   max_x max_y [max_z ...]
+ \endverbatim
+
+ Here is a simple sample file in the 3D case:
+ \verbatim
+   -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