Move some utils + update doc so that utilities are shown as examples

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2756 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: a707d174a382da7efad3d12a73bb66d2c90da599

7 files changed, 41 insertions, 44 deletions

diff --git a/src/Doxyfile b/src/Doxyfile
index 7f5975eb..7b506e42 100644
--- a/src/Doxyfile
+++ b/src/Doxyfile
@@ -819,7 +819,8 @@ EXCLUDE_SYMBOLS        =
 # command).
 
 EXAMPLE_PATH           = biblio/ \
-	example/
+	example/ \
+	utilities/
 
 # 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/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
index e17e5926..576a1af8 100644
--- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
+++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
@@ -143,8 +143,8 @@ namespace persistent_cohomology {
 
 We provide several example files: run these examples with -h for details on their use, and read the README file.
 
-\li <a href="_persistent_cohomology_2rips_persistence_8cpp-example.html">
-Persistent_cohomology/rips_persistence.cpp</a> computes the Rips complex of a point cloud and outputs its persistence
+\li <a href="_rips_complex_2rips_persistence_8cpp-example.html">
+Rips_complex/rips_persistence.cpp</a> computes the Rips complex of a point cloud and outputs its persistence
 diagram.
 \code $> ./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3 \endcode
 \code The complex contains 177838 simplices 
@@ -158,12 +158,12 @@ diagram.
 Persistent_cohomology/rips_multifield_persistence.cpp</a> computes the Rips complex of a point cloud and outputs its
 persistence diagram with a family of field coefficients.
 
-\li <a href="_persistent_cohomology_2rips_distance_matrix_persistence_8cpp-example.html">
-Persistent_cohomology/rips_distance_matrix_persistence.cpp</a> computes the Rips complex of a distance matrix and
+\li <a href="_rips_complex_2rips_distance_matrix_persistence_8cpp-example.html">
+Rips_complex/rips_distance_matrix_persistence.cpp</a> computes the Rips complex of a distance matrix and
 outputs its persistence diagram.
 
-\li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html">
-Persistent_cohomology/alpha_complex_3d_persistence.cpp</a> computes the persistent homology with
+\li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html">
+Alpha_complex/alpha_complex_3d_persistence.cpp</a> computes the persistent homology with
 \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file.
 \code $> ./alpha_complex_3d_persistence ../../data/points/tore3D_300.off 2 0.45 \endcode
 \code Simplex_tree dim: 3
@@ -194,8 +194,8 @@ and a weights file.
 2  1 0.0934117 1.00003
 2  2 0.56444 1.03938 \endcode
 
-\li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
-Persistent_cohomology/alpha_complex_persistence.cpp</a> computes the persistent homology with
+\li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html">
+Alpha_complex/alpha_complex_persistence.cpp</a> computes the persistent homology with
 \f$\mathbb{Z}/p\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file.
 \code $> ./alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off \endcode
 \code Alpha complex is of dimension 3 - 9273 simplices - 300 vertices.
@@ -205,8 +205,8 @@ Simplex_tree dim: 3
 2  1 0.0934117 1.00003 
 2  2 0.56444 1.03938 \endcode
 
-\li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
-Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a> computes the persistent homology with
+\li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
+Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> computes the persistent homology with
 \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the periodic alpha complex on points sampling from an OFF file.
 \code $> ./periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off 3 1.0 \endcode
 \code Periodic Delaunay computed.
diff --git a/src/Persistent_cohomology/utilities/CMakeLists.txt b/src/Rips_complex/utilities/CMakeLists.txt
index 9a506b3f..baa571fa 100644
--- a/src/Persistent_cohomology/utilities/CMakeLists.txt
+++ b/src/Rips_complex/utilities/CMakeLists.txt
@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 2.6)
-project(Persistent_cohomology_utilities)
+project(Rips_complex_utilities)
 
 add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp)
 target_link_libraries(rips_distance_matrix_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
@@ -12,9 +12,9 @@ if (TBB_FOUND)
   target_link_libraries(rips_persistence ${TBB_LIBRARIES})
 endif()
 
-add_test(NAME Persistent_cohomology_example_from_rips_distance_matrix COMMAND $<TARGET_FILE:rips_distance_matrix_persistence>
+add_test(NAME Rips_complex_utility_from_rips_distance_matrix COMMAND $<TARGET_FILE:rips_distance_matrix_persistence>
     "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" "-r" "1.0" "-d" "3" "-p" "3" "-m" "0")
-add_test(NAME Persistent_cohomology_example_from_rips_on_tore_3D COMMAND $<TARGET_FILE:rips_persistence>
+add_test(NAME Rips_complex_utility_from_rips_on_tore_3D COMMAND $<TARGET_FILE:rips_persistence>
     "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3")
 
 install(TARGETS rips_distance_matrix_persistence DESTINATION bin)
diff --git a/src/Persistent_cohomology/utilities/README b/src/Rips_complex/utilities/README
index eecee7ee..ddb7860f 100644
--- a/src/Persistent_cohomology/utilities/README
+++ b/src/Rips_complex/utilities/README
@@ -1,4 +1,4 @@
-# Persistent_cohomology #
+# Rips_complex #
 
 ## `rips_persistence` ##
 This program computes the persistent homology with coefficient field *Z/pZ* of a Rips complex defined on a set of input points. The output diagram contains one bar per line, written with the convention:
diff --git a/src/Persistent_cohomology/utilities/rips_distance_matrix_persistence.cpp b/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp
index d38808c7..d38808c7 100644
--- a/src/Persistent_cohomology/utilities/rips_distance_matrix_persistence.cpp
+++ b/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp
diff --git a/src/Persistent_cohomology/utilities/rips_persistence.cpp b/src/Rips_complex/utilities/rips_persistence.cpp
index d504798b..d504798b 100644
--- a/src/Persistent_cohomology/utilities/rips_persistence.cpp
+++ b/src/Rips_complex/utilities/rips_persistence.cpp
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index cee0c28b..466236ad 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -271,8 +271,8 @@ make doxygen
  * 
  * The following examples/utilities require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms
  * Library</a> (CGAL \cite cgal:eb-15b) and will not be built if CGAL is not installed:
- * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html">
- * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html">
+ * Alpha_complex/alpha_complex_3d_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2exact_alpha_complex_3d_persistence_8cpp-example.html">
  * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2weighted_alpha_complex_3d_persistence_8cpp-example.html">
@@ -289,10 +289,10 @@ make doxygen
  * Alpha_complex/Alpha_complex_from_off.cpp</a>
  * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
  * Alpha_complex/Alpha_complex_from_points.cpp</a>
- * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
- * Persistent_cohomology/alpha_complex_persistence.cpp</a>
- * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
- * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html">
+ * Alpha_complex/alpha_complex_persistence.cpp</a>
+ * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
+ * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
  * Persistent_cohomology/custom_persistence_sort.cpp</a>
  * 
@@ -329,12 +329,12 @@ make doxygen
  * Alpha_complex/Alpha_complex_from_off.cpp</a>
  * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
  * Alpha_complex/Alpha_complex_from_points.cpp</a>
+ * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html">
+ * Alpha_complex/alpha_complex_persistence.cpp</a>
+ * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
+ * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a>
  * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html">
  * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a>
- * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
- * Persistent_cohomology/alpha_complex_persistence.cpp</a>
- * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
- * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
  * Persistent_cohomology/custom_persistence_sort.cpp</a>
  * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html">
@@ -364,26 +364,24 @@ make doxygen
  * Alpha_complex/Alpha_complex_from_off.cpp</a>
  * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
  * Alpha_complex/Alpha_complex_from_points.cpp</a>
+ * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html">
+ * Alpha_complex/alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html">
+ * Alpha_complex/alpha_complex_persistence.cpp</a>
+ * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
+ * Alpha_complex/periodic_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>
  * \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>
  * \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="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html">
- * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a>
- * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
- * Persistent_cohomology/alpha_complex_persistence.cpp</a>
  * \li <a href="_simplex_tree_2simple_simplex_tree_8cpp-example.html">
  * Simplex_tree/simple_simplex_tree.cpp</a>
  * \li <a href="_simplex_tree_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html">
  * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a>
  * \li <a href="_simplex_tree_2simplex_tree_from_cliques_of_graph_8cpp-example.html">
  * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp</a>
- * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html">
- * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a>
- * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
- * Persistent_cohomology/alpha_complex_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2rips_persistence_via_boundary_matrix_8cpp-example.html">
  * Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp</a>
  * \li <a href="_persistent_cohomology_2persistence_from_file_8cpp-example.html">
@@ -392,26 +390,24 @@ make doxygen
  * Persistent_cohomology/persistence_from_simple_simplex_tree.cpp</a>
  * \li <a href="_persistent_cohomology_2plain_homology_8cpp-example.html">
  * Persistent_cohomology/plain_homology.cpp</a>
- * \li <a href="_persistent_cohomology_2rips_distance_matrix_persistence_8cpp-example.html">
- * Persistent_cohomology/rips_distance_matrix_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html">
  * Persistent_cohomology/rips_multifield_persistence.cpp</a>
- * \li <a href="_persistent_cohomology_2rips_persistence_8cpp-example.html">
- * Persistent_cohomology/rips_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2rips_persistence_step_by_step_8cpp-example.html">
  * Persistent_cohomology/rips_persistence_step_by_step.cpp</a>
  * \li <a href="_persistent_cohomology_2exact_alpha_complex_3d_persistence_8cpp-example.html">
  * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2weighted_alpha_complex_3d_persistence_8cpp-example.html">
  * Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp</a>
- * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
- * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
  * Persistent_cohomology/custom_persistence_sort.cpp</a>
  * \li <a href="_rips_complex_2example_one_skeleton_rips_from_points_8cpp-example.html">
  * Rips_complex/example_one_skeleton_rips_from_points.cpp</a>
  * \li <a href="_rips_complex_2example_rips_complex_from_off_file_8cpp-example.html">
  * Rips_complex/example_rips_complex_from_off_file.cpp</a>
+ * \li <a href="_rips_complex_2rips_distance_matrix_persistence_8cpp-example.html">
+ * Rips_complex/rips_distance_matrix_persistence.cpp</a>
+ * \li <a href="_rips_complex_2rips_persistence_8cpp-example.html">
+ * Rips_complex/rips_persistence.cpp</a>
  * 
  * \section Contributions Bug reports and contributions
  * Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to:
@@ -436,6 +432,9 @@ make doxygen
 /*! @file Examples
  * @example Alpha_complex/Alpha_complex_from_off.cpp
  * @example Alpha_complex/Alpha_complex_from_points.cpp
+ * @example Alpha_complex/alpha_complex_3d_persistence.cpp
+ * @example Alpha_complex/alpha_complex_persistence.cpp
+ * @example Alpha_complex/periodic_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_example.cpp
@@ -446,22 +445,19 @@ make doxygen
  * @example common/example_CGAL_points_off_reader.cpp
  * @example Contraction/Garland_heckbert.cpp
  * @example Contraction/Rips_contraction.cpp
- * @example Persistent_cohomology/alpha_complex_3d_persistence.cpp
- * @example Persistent_cohomology/alpha_complex_persistence.cpp
  * @example Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp
  * @example Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp
  * @example Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp
- * @example Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp
  * @example Persistent_cohomology/persistence_from_file.cpp
  * @example Persistent_cohomology/persistence_from_simple_simplex_tree.cpp
  * @example Persistent_cohomology/plain_homology.cpp
  * @example Persistent_cohomology/rips_multifield_persistence.cpp
- * @example Persistent_cohomology/rips_distance_matrix_persistence.cpp
- * @example Persistent_cohomology/rips_persistence.cpp
  * @example Persistent_cohomology/custom_persistence_sort.cpp
  * @example Persistent_cohomology/rips_persistence_step_by_step.cpp
  * @example Rips_complex/example_one_skeleton_rips_from_points.cpp
  * @example Rips_complex/example_rips_complex_from_off_file.cpp
+ * @example Rips_complex/rips_persistence.cpp
+ * @example Rips_complex/rips_distance_matrix_persistence.cpp
  * @example Simplex_tree/mini_simplex_tree.cpp
  * @example Simplex_tree/simple_simplex_tree.cpp
  * @example Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp