Add doc, example renamed

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cechcomplex_vincent@3254 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 666bacd07c711b89167c87155c21fe88688e2e68

10 files changed, 791 insertions, 12 deletions

diff --git a/src/Cech_complex/doc/COPYRIGHT b/src/Cech_complex/doc/COPYRIGHT
new file mode 100644
index 00000000..594b7d03
--- /dev/null
+++ b/src/Cech_complex/doc/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/src/Cech_complex/doc/Intro_cech_complex.h b/src/Cech_complex/doc/Intro_cech_complex.h
index e69de29b..f2052763 100644
--- a/src/Cech_complex/doc/Intro_cech_complex.h
+++ b/src/Cech_complex/doc/Intro_cech_complex.h
@@ -0,0 +1,92 @@
+/*    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):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2018  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_CECH_COMPLEX_INTRO_CECH_COMPLEX_H_
+#define DOC_CECH_COMPLEX_INTRO_CECH_COMPLEX_H_
+
+namespace Gudhi {
+
+namespace cech_complex {
+
+/**  \defgroup cech_complex Cech complex
+ * 
+ * \author    Clément Maria, Pawel Dlotko, Vincent Rouvreau
+ * 
+ * @{
+ * 
+ * \section cechdefinition Cech complex definition
+ * 
+ * Cech_complex
+ * <a target="_blank" href="https://en.wikipedia.org/wiki/%C4%8Cech_cohomology">(Wikipedia)</a> is a
+ * proximity 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.
+ * 
+ * The filtration value of each edge is computed from a user-given distance function.
+ * 
+ * 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 proximity graph, Cech inserts the proximity 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 "cech_complex_representation.png" "Cech complex proximity 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 Cech_complex interfaces are not detailed enough for your need, please refer to
+ * <a href="_persistent_cohomology_2cech_persistence_step_by_step_8cpp-example.html">
+ * cech_persistence_step_by_step.cpp</a> example, where the graph construction over the Simplex_tree is more detailed.
+ *
+ * \section cechpointsdistance Point cloud and distance function
+ * 
+ * \subsection cechpointscloudexample Example from a point cloud and a distance function
+ * 
+ * This example builds the proximity 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 Cech_complex/cech_complex_example_from_points.cpp
+ * 
+ * When launching (Cech maximal distance between 2 points is 7.1, is expanded until dimension 2):
+ * 
+ * \code $> ./Cech_complex_example_from_points
+ * \endcode
+ *
+ * the program output is:
+ * 
+ * \include Cech_complex/cech_complex_example_from_points_for_doc.txt
+ * 
+ */
+/** @} */  // end defgroup cech_complex
+
+}  // namespace cech_complex
+
+}  // namespace Gudhi
+
+#endif  // DOC_CECH_COMPLEX_INTRO_CECH_COMPLEX_H_
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+<symbolsize name="tiny" value="1.1"/>
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+<arrowsize name="small" value="5"/>
+<arrowsize name="tiny" value="3"/>
+<color name="red" value="1 0 0"/>
+<color name="green" value="0 1 0"/>
+<color name="blue" value="0 0 1"/>
+<color name="yellow" value="1 1 0"/>
+<color name="orange" value="1 0.647 0"/>
+<color name="gold" value="1 0.843 0"/>
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+<textstyle name="item" begin="\begin{itemize}\item{}" end="\end{itemize}"/>
+<gridsize name="4 pts" value="4"/>
+<gridsize name="8 pts (~3 mm)" value="8"/>
+<gridsize name="16 pts (~6 mm)" value="16"/>
+<gridsize name="32 pts (~12 mm)" value="32"/>
+<gridsize name="10 pts (~3.5 mm)" value="10"/>
+<gridsize name="20 pts (~7 mm)" value="20"/>
+<gridsize name="14 pts (~5 mm)" value="14"/>
+<gridsize name="28 pts (~10 mm)" value="28"/>
+<gridsize name="56 pts (~20 mm)" value="56"/>
+<anglesize name="90 deg" value="90"/>
+<anglesize name="60 deg" value="60"/>
+<anglesize name="45 deg" value="45"/>
+<anglesize name="30 deg" value="30"/>
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+</path>
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+</ipe>
diff --git a/src/Cech_complex/doc/cech_one_skeleton.png b/src/Cech_complex/doc/cech_one_skeleton.png
new file mode 100644
index 00000000..1028770e
--- /dev/null
+++ b/src/Cech_complex/doc/cech_one_skeleton.png
diff --git a/src/Cech_complex/example/CMakeLists.txt b/src/Cech_complex/example/CMakeLists.txt
index 8097871f..ac32ff95 100644
--- a/src/Cech_complex/example/CMakeLists.txt
+++ b/src/Cech_complex/example/CMakeLists.txt
@@ -7,8 +7,8 @@ if (TBB_FOUND)
   target_link_libraries(Cech_complex_example_step_by_step ${TBB_LIBRARIES})
 endif()
 
-add_executable ( Cech_complex_example_one_skeleton_from_points example_one_skeleton_cech_from_points.cpp)
+add_executable ( Cech_complex_example_from_points cech_complex_example_from_points.cpp)
 if (TBB_FOUND)
-  target_link_libraries(Cech_complex_example_one_skeleton_from_points ${TBB_LIBRARIES})
+  target_link_libraries(Cech_complex_example_from_points ${TBB_LIBRARIES})
 endif()
-add_test(NAME Cech_complex_example_one_skeleton_from_points COMMAND $<TARGET_FILE:Cech_complex_example_one_skeleton_from_points>)
+add_test(NAME Cech_complex_example_from_points COMMAND $<TARGET_FILE:Cech_complex_example_from_points>)
diff --git a/src/Cech_complex/example/example_one_skeleton_cech_from_points.cpp b/src/Cech_complex/example/cech_complex_example_from_points.cpp
index 73679716..882849c3 100644
--- a/src/Cech_complex/example/example_one_skeleton_cech_from_points.cpp
+++ b/src/Cech_complex/example/cech_complex_example_from_points.cpp
@@ -28,7 +28,6 @@
 #include <string>
 #include <vector>
 #include <array>
-#include <limits>  // for std::numeric_limits
 
 int main() {
   // Type definitions
@@ -47,15 +46,16 @@ int main() {
   points.push_back({9.0, 17.0});
 
   // ----------------------------------------------------------------------------
-  // Init of a Rips complex from points
+  // Init of a Cech complex from points
   // ----------------------------------------------------------------------------
-  Filtration_value threshold = 12.0;
+  // 7.1 is a magic number to force one blocker, and one non-blocker
+  Filtration_value threshold = 7.1;
   Cech_complex cech_complex_from_points(points, threshold, Gudhi::Euclidean_distance());
 
   Simplex_tree stree;
-  cech_complex_from_points.create_complex(stree, 3);
+  cech_complex_from_points.create_complex(stree, 2);
   // ----------------------------------------------------------------------------
-  // Display information about the one skeleton Rips complex
+  // Display information about the one skeleton Cech complex
   // ----------------------------------------------------------------------------
   std::cout << "Cech complex is of dimension " << stree.dimension() <<
                " - " << stree.num_simplices() << " simplices - " <<
diff --git a/src/Cech_complex/example/cech_complex_example_from_points_for_doc.txt b/src/Cech_complex/example/cech_complex_example_from_points_for_doc.txt
new file mode 100644
index 00000000..684e120b
--- /dev/null
+++ b/src/Cech_complex/example/cech_complex_example_from_points_for_doc.txt
@@ -0,0 +1,16 @@
+Cech complex is of dimension 2 - 14 simplices - 7 vertices.
+Iterator on Cech complex simplices in the filtration order, with [filtration value]:
+   ( 0 ) -> [0] 
+   ( 1 ) -> [0] 
+   ( 2 ) -> [0] 
+   ( 3 ) -> [0] 
+   ( 4 ) -> [0] 
+   ( 5 ) -> [0] 
+   ( 6 ) -> [0] 
+   ( 3 2 ) -> [5] 
+   ( 5 4 ) -> [5.38516] 
+   ( 2 0 ) -> [5.83095] 
+   ( 1 0 ) -> [6.08276] 
+   ( 3 1 ) -> [6.32456] 
+   ( 2 1 ) -> [6.7082] 
+   ( 3 2 1 ) -> [7.07107] 
diff --git a/src/Cech_complex/include/gudhi/Cech_complex_blocker.h b/src/Cech_complex/include/gudhi/Cech_complex_blocker.h
index f8738be0..fb52f712 100644
--- a/src/Cech_complex/include/gudhi/Cech_complex_blocker.h
+++ b/src/Cech_complex/include/gudhi/Cech_complex_blocker.h
@@ -80,12 +80,12 @@ class Cech_blocker {
 #endif  // DEBUG_TRACES
     }
     Min_sphere ms(cc_ptr_->dimension(), points.begin(),points.end());
-    Filtration_value radius = std::sqrt(ms.squared_radius());
+    Filtration_value diameter = 2 * std::sqrt(ms.squared_radius());
 #ifdef DEBUG_TRACES
-    std::cout << "radius = " << radius << " - " << (radius > cc_ptr_->threshold()) << std::endl;
+    std::cout << "diameter = " << diameter << " - " << (diameter > cc_ptr_->threshold()) << std::endl;
 #endif  // DEBUG_TRACES
-    simplicial_complex_.assign_filtration(sh, radius);
-    return (radius > cc_ptr_->threshold());
+    simplicial_complex_.assign_filtration(sh, diameter);
+    return (diameter > cc_ptr_->threshold());
   }
 
   /** \internal \brief Cech complex blocker constructor. */