Fix #20: Add OFF section in file format and all documents target to it instead of geomview.org documentation. Modify data/points/alphacomplexdoc.off in dimension 3 to be used as an example for OFF section in file format.

10 files changed, 88 insertions, 33 deletions

diff --git a/data/points/alphacomplexdoc.off b/data/points/alphacomplexdoc.off
index bb790193..a90db49a 100644
--- a/data/points/alphacomplexdoc.off
+++ b/data/points/alphacomplexdoc.off
@@ -1,10 +1,12 @@
-nOFF
-2 7 0 0
-1.0 1.0
-7.0 0.0
-4.0 6.0
-9.0 6.0
-0.0 14.0
-2.0 19.0
-9.0 17.0
-
+# Default is 3 dimension
+OFF
+# 7 vertices - 0 face - 0 edge
+7 0 0
+# Point set:
+1.0 1.0  0.0
+7.0 0.0  0.0
+4.0 6.0  0.0
+9.0 6.0  0.0
+0.0 14.0 0.0
+2.0 19.0 0.0
+9.0 17.0 0.0
diff --git a/src/Alpha_complex/utilities/alphacomplex.md b/src/Alpha_complex/utilities/alphacomplex.md
index b77656ff..fcd16a3b 100644
--- a/src/Alpha_complex/utilities/alphacomplex.md
+++ b/src/Alpha_complex/utilities/alphacomplex.md
@@ -33,7 +33,7 @@ a prime number).
 

 where

 `<input OFF file>` is the path to the input point cloud in

-[nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html).

+[nOFF ASCII format]({{ site.officialurl }}/doc/latest/fileformats.html#FileFormatsOFF).

 

 **Allowed options**

 

@@ -87,7 +87,7 @@ a prime number).
 ```

 

 where `<input OFF file>` is the path to the input point cloud in

-[nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html).

+[nOFF ASCII format]({{ site.officialurl }}/doc/latest/fileformats.html#FileFormatsOFF).

 

 **Allowed options**

 

diff --git a/src/Doxyfile.in b/src/Doxyfile.in
index 54a438d4..5b1b8ecc 100644
--- a/src/Doxyfile.in
+++ b/src/Doxyfile.in
@@ -821,7 +821,8 @@ EXCLUDE_SYMBOLS        =
 
 EXAMPLE_PATH           = biblio/    \
 	                     example/   \
-	                     utilities/
+	                     utilities/   \
+	                     data/
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
diff --git a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h
index bc8aecc3..e72d63dd 100644
--- a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h
+++ b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h
@@ -37,8 +37,7 @@ namespace cover_complex {
  * neato (from <a target="_blank" href="http://www.graphviz.org/">graphviz</a>),
  * <a target="_blank" href="http://www.geomview.org/">geomview</a>,
  * <a target="_blank" href="https://github.com/MLWave/kepler-mapper">KeplerMapper</a>.
- * Input point clouds are assumed to be
- * <a target="_blank" href="http://www.geomview.org/docs/html/OFF.html">OFF files</a>.
+ * Input point clouds are assumed to be \ref FileFormatsOFF "OFF files"
  *
  * \section covers Covers
  *
diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h
index 23214e25..235296d3 100644
--- a/src/common/doc/file_formats.h
+++ b/src/common/doc/file_formats.h
@@ -29,6 +29,32 @@ namespace Gudhi {
 
  \tableofcontents
 
+ \section FileFormatsOFF OFF file format
+
+ OFF files must be conform to format described here: http://www.geomview.org/docs/html/OFF.html
+
+ OFF files are mainly used as point cloud inputs. Here is an example of 7 points in a 3-dimensional space. As edges and
+ faces are not used for point set, there is no need to specify them (just set their numbers to 0):
+
+ \include points/alphacomplexdoc.off
+
+ For dimensions bigger than 3, the dimension can be set like here:
+ \verbatim
+  # Dimension is no more 3
+  nOFF
+  # dimension 4 - 7 vertices - 0 face - 0 edge
+  4 7 0 0
+  # Point set:
+  1.0 1.0  0.0 0.0
+  7.0 0.0  0.0 0.0
+  4.0 6.0  0.0 0.0
+  9.0 6.0  0.0 0.0
+  0.0 14.0 0.0 0.0
+  2.0 19.0 0.0 0.0
+  9.0 17.0 0.0 0.0
+ \endverbatim
+
+
  \section FileFormatsPers Persistence Diagram
 
  Such a file, whose extension is usually `.pers`, contains a list of persistence intervals.<br>
diff --git a/src/common/example/vectordoubleoffreader_result.txt b/src/common/example/vectordoubleoffreader_result.txt
index 1deb8dbd..b399425a 100644
--- a/src/common/example/vectordoubleoffreader_result.txt
+++ b/src/common/example/vectordoubleoffreader_result.txt
@@ -1,7 +1,7 @@
-Point[0] = 1 1 
-Point[1] = 7 0 
-Point[2] = 4 6 
-Point[3] = 9 6 
-Point[4] = 0 14 
-Point[5] = 2 19 
-Point[6] = 9 17 
+Point[0] = 1 1 0 
+Point[1] = 7 0 0 
+Point[2] = 4 6 0 
+Point[3] = 9 6 0 
+Point[4] = 0 14 0 
+Point[5] = 2 19 0 
+Point[6] = 9 17 0 
diff --git a/src/common/include/gudhi/Off_reader.h b/src/common/include/gudhi/Off_reader.h
index 05a1e145..fc951fe7 100644
--- a/src/common/include/gudhi/Off_reader.h
+++ b/src/common/include/gudhi/Off_reader.h
@@ -37,8 +37,7 @@ namespace Gudhi {
 
 /** \brief OFF file reader top class visitor. 
  * 
- * OFF file must be conform to format described here : 
- * http://www.geomview.org/docs/html/OFF.html
+ * OFF file must be conform to \ref FileFormatsOFF
  */
 class Off_reader {
  public:
diff --git a/src/common/test/test_points_off_reader.cpp b/src/common/test/test_points_off_reader.cpp
index ba3bab71..e4b76ed7 100644
--- a/src/common/test/test_points_off_reader.cpp
+++ b/src/common/test/test_points_off_reader.cpp
@@ -44,19 +44,19 @@ BOOST_AUTO_TEST_CASE( points_doc_test )
   BOOST_CHECK(point_cloud.size() == 7);
 
   std::vector<Point_d> expected_points;
-  std::vector<double> point = {1.0, 1.0};
+  std::vector<double> point = {1.0, 1.0, 0.0};
   expected_points.push_back(Point_d(point.begin(), point.end()));
-  point = {7.0, 0.0};
+  point = {7.0, 0.0, 0.0};
   expected_points.push_back(Point_d(point.begin(), point.end()));
-  point = {4.0, 6.0};
+  point = {4.0, 6.0, 0.0};
   expected_points.push_back(Point_d(point.begin(), point.end()));
-  point = {9.0, 6.0};
+  point = {9.0, 6.0, 0.0};
   expected_points.push_back(Point_d(point.begin(), point.end()));
-  point = {0.0, 14.0};
+  point = {0.0, 14.0, 0.0};
   expected_points.push_back(Point_d(point.begin(), point.end()));
-  point = {2.0, 19.0};
+  point = {2.0, 19.0, 0.0};
   expected_points.push_back(Point_d(point.begin(), point.end()));
-  point = {9.0, 17.0};
+  point = {9.0, 17.0, 0.0};
   expected_points.push_back(Point_d(point.begin(), point.end()));
 
   BOOST_CHECK(point_cloud == expected_points);
diff --git a/src/cython/doc/fileformats.rst b/src/cython/doc/fileformats.rst
index e205cc8b..345dfdba 100644
--- a/src/cython/doc/fileformats.rst
+++ b/src/cython/doc/fileformats.rst
@@ -5,6 +5,35 @@
 File formats
 ############
 
+OFF file format
+***************
+
+OFF files must be conform to format described here:
+http://www.geomview.org/docs/html/OFF.html
+
+OFF files are mainly used as point cloud inputs. Here is an example of 7 points
+in a 3-dimensional space. As edges and faces are not used for point set, there
+is no need to specify them (just set their numbers to 0):
+
+.. literalinclude:: ../../data/points/alphacomplexdoc.off
+
+.. centered:: ../../points/alphacomplexdoc.off
+
+For dimensions bigger than 3, the dimension can be set like here::
+
+    # Dimension is no more 3
+    nOFF
+    # dimension 4 - 7 vertices - 0 face - 0 edge
+    4 7 0 0
+    # Point set:
+    1.0 1.0  0.0 0.0
+    7.0 0.0  0.0 0.0
+    4.0 6.0  0.0 0.0
+    9.0 6.0  0.0 0.0
+    0.0 14.0 0.0 0.0
+    2.0 19.0 0.0 0.0
+    9.0 17.0 0.0 0.0
+
 Persistence Diagram
 *******************
 
diff --git a/src/cython/doc/nerve_gic_complex_user.rst b/src/cython/doc/nerve_gic_complex_user.rst
index 94a2b246..9101f45d 100644
--- a/src/cython/doc/nerve_gic_complex_user.rst
+++ b/src/cython/doc/nerve_gic_complex_user.rst
@@ -13,8 +13,7 @@ Visualizations of the simplicial complexes can be done with either
 neato (from `graphviz <http://www.graphviz.org/>`_),
 `geomview <http://www.geomview.org/>`_,
 `KeplerMapper <https://github.com/MLWave/kepler-mapper>`_.
-Input point clouds are assumed to be
-`OFF files <http://www.geomview.org/docs/html/OFF.html>`_.
+Input point clouds are assumed to be OFF files (cf. :doc:`fileformats`).
 
 Covers
 ------