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-rw-r--r--doc/Rips_complex/COPYRIGHT19
-rw-r--r--doc/Rips_complex/Intro_rips_complex.h158
-rw-r--r--doc/Rips_complex/rips_complex_representation.ipe326
-rw-r--r--doc/Rips_complex/rips_complex_representation.pngbin0 -> 15677 bytes
-rw-r--r--doc/Rips_complex/rips_one_skeleton.ipe326
-rw-r--r--doc/Rips_complex/rips_one_skeleton.pngbin0 -> 47651 bytes
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diff --git a/doc/Rips_complex/COPYRIGHT b/doc/Rips_complex/COPYRIGHT
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--- /dev/null
+++ b/doc/Rips_complex/COPYRIGHT
@@ -0,0 +1,19 @@
+The files of this directory are part of the Gudhi Library. The Gudhi library
+(Geometric Understanding in Higher Dimensions) is a generic C++ library for
+computational topology.
+
+Author(s): Clément Maria, Pawel Dlotko, Vincent Rouvreau
+
+Copyright (C) 2015 INRIA
+
+This program is free software: you can redistribute it and/or modify it under
+the terms of the GNU General Public License as published by the Free Software
+Foundation, either version 3 of the License, or (at your option) any later
+version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along with
+this program. If not, see <http://www.gnu.org/licenses/>.
diff --git a/doc/Rips_complex/Intro_rips_complex.h b/doc/Rips_complex/Intro_rips_complex.h
new file mode 100644
index 00000000..124dfec9
--- /dev/null
+++ b/doc/Rips_complex/Intro_rips_complex.h
@@ -0,0 +1,158 @@
+/* This file is part of the Gudhi Library. The Gudhi library
+ * (Geometric Understanding in Higher Dimensions) is a generic C++
+ * library for computational topology.
+ *
+ * Author(s): Clément Maria, Pawel Dlotko, Vincent Rouvreau
+ *
+ * Copyright (C) 2016 INRIA
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef DOC_RIPS_COMPLEX_INTRO_RIPS_COMPLEX_H_
+#define DOC_RIPS_COMPLEX_INTRO_RIPS_COMPLEX_H_
+
+namespace Gudhi {
+
+namespace rips_complex {
+
+/** \defgroup rips_complex Rips complex
+ *
+ * \author Clément Maria, Pawel Dlotko, Vincent Rouvreau
+ *
+ * @{
+ *
+ * \section ripsdefinition Rips complex definition
+ *
+ * Rips_complex
+ * <a target="_blank" href="https://en.wikipedia.org/wiki/Vietoris%E2%80%93Rips_complex">(Wikipedia)</a> is a
+ * one skeleton graph that allows to construct a
+ * <a target="_blank" href="https://en.wikipedia.org/wiki/Simplicial_complex">simplicial complex</a>
+ * from it.
+ * The input can be a point cloud with a given distance function, or a distance matrix.
+ *
+ * The filtration value of each edge is computed from a user-given distance function, or directly from the distance
+ * matrix.
+ *
+ * All edges that have a filtration value strictly greater than a given threshold value are not inserted into
+ * the complex.
+ *
+ * When creating a simplicial complex from this one skeleton graph, Rips inserts the one skeleton graph into the data
+ * structure, and then expands the simplicial complex when required.
+ *
+ * Vertex name correspond to the index of the point in the given range (aka. the point cloud).
+ *
+ * \image html "rips_complex_representation.png" "Rips-complex one skeleton graph representation"
+ *
+ * On this example, as edges (4,5), (4,6) and (5,6) are in the complex, simplex (4,5,6) is added with the filtration
+ * value set with \f$max(filtration(4,5), filtration(4,6), filtration(5,6))\f$.
+ * And so on for simplex (0,1,2,3).
+ *
+ * If the Rips_complex interfaces are not detailed enough for your need, please refer to
+ * <a href="_persistent_cohomology_2rips_persistence_step_by_step_8cpp-example.html">
+ * rips_persistence_step_by_step.cpp</a> example, where the graph construction over the Simplex_tree is more detailed.
+ *
+ * \section ripspointsdistance Point cloud and distance function
+ *
+ * \subsection ripspointscloudexample Example from a point cloud and a distance function
+ *
+ * This example builds the one skeleton graph from the given points, threshold value, and distance function.
+ * Then it creates a `Simplex_tree` with it.
+ *
+ * Then, it is asked to display information about the simplicial complex.
+ *
+ * \include Rips_complex/example_one_skeleton_rips_from_points.cpp
+ *
+ * When launching (Rips maximal distance between 2 points is 12.0, is expanded until dimension 1 - one skeleton graph
+ * in other words):
+ *
+ * \code $> ./Rips_complex_example_one_skeleton_from_points
+ * \endcode
+ *
+ * the program output is:
+ *
+ * \include Rips_complex/one_skeleton_rips_for_doc.txt
+ *
+ * \subsection ripsoffexample Example from OFF file
+ *
+ * This example builds the Rips_complex from the given points in an OFF file, threshold value, and distance
+ * function.
+ * Then it creates a `Simplex_tree` with it.
+ *
+ *
+ * Then, it is asked to display information about the Rips complex.
+ *
+ * \include Rips_complex/example_rips_complex_from_off_file.cpp
+ *
+ * When launching:
+ *
+ * \code $> ./Rips_complex_example_from_off ../../data/points/alphacomplexdoc.off 12.0 3
+ * \endcode
+ *
+ * the program output is:
+ *
+ * \include Rips_complex/full_skeleton_rips_for_doc.txt
+ *
+ *
+ *
+ * \section ripsdistancematrix Distance matrix
+ *
+ * \subsection ripsdistancematrixexample Example from a distance matrix
+ *
+ * This example builds the one skeleton graph from the given distance matrix and threshold value.
+ * Then it creates a `Simplex_tree` with it.
+ *
+ * Then, it is asked to display information about the simplicial complex.
+ *
+ * \include Rips_complex/example_one_skeleton_rips_from_distance_matrix.cpp
+ *
+ * When launching (Rips maximal distance between 2 points is 1.0, is expanded until dimension 1 - one skeleton graph
+ * with other words):
+ *
+ * \code $> ./Rips_complex_example_one_skeleton_from_distance_matrix
+ * \endcode
+ *
+ * the program output is:
+ *
+ * \include Rips_complex/one_skeleton_rips_for_doc.txt
+ *
+ * \subsection ripscsvdistanceexample Example from a distance matrix read in a csv file
+ *
+ * This example builds the one skeleton graph from the given distance matrix read in a csv file and threshold value.
+ * Then it creates a `Simplex_tree` with it.
+ *
+ *
+ * Then, it is asked to display information about the Rips complex.
+ *
+ * \include Rips_complex/example_rips_complex_from_csv_distance_matrix_file.cpp
+ *
+ * When launching:
+ *
+ * \code $> ./Rips_complex_example_from_csv_distance_matrix ../../data/distance_matrix/full_square_distance_matrix.csv 1.0 3
+ * \endcode
+ *
+ * the program output is:
+ *
+ * \include Rips_complex/full_skeleton_rips_for_doc.txt
+ *
+ * \copyright GNU General Public License v3.
+ * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
+ */
+/** @} */ // end defgroup rips_complex
+
+} // namespace rips_complex
+
+} // namespace Gudhi
+
+#endif // DOC_RIPS_COMPLEX_INTRO_RIPS_COMPLEX_H_
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diff --git a/doc/Rips_complex/rips_one_skeleton.png b/doc/Rips_complex/rips_one_skeleton.png
new file mode 100644
index 00000000..1028770e
--- /dev/null
+++ b/doc/Rips_complex/rips_one_skeleton.png
Binary files differ