From 1d611ca664d78d3b0b53264c52b04a8396383140 Mon Sep 17 00:00:00 2001
From: pdlotko <pdlotko@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Mon, 25 Sep 2017 20:14:45 +0000
Subject: Adding all that is needed for Rips complex construction from
 correlation matrix. Moduo the fact that I cannot see the doc (althoug make
 doxygen do not create any errors), this is ready for review.

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@2712 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: e8e7acceaf2be6f17baa3d77c85e207a74a4fb33
---
 src/Rips_complex/doc/Intro_rips_complex.h          | 23 ++++++++++++++++++++++
 src/Rips_complex/example/CMakeLists.txt            |  4 ++++
 ...eleton_rips_from_correlation_matrix_for_doc.txt | 17 ++++++++++++++++
 3 files changed, 44 insertions(+)
 create mode 100644 src/Rips_complex/example/one_skeleton_rips_from_correlation_matrix_for_doc.txt

(limited to 'src/Rips_complex')

diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h
index 124dfec9..401b689b 100644
--- a/src/Rips_complex/doc/Intro_rips_complex.h
+++ b/src/Rips_complex/doc/Intro_rips_complex.h
@@ -146,6 +146,29 @@ namespace rips_complex {
  * 
  * \include Rips_complex/full_skeleton_rips_for_doc.txt
  * 
+ * 
+ * \section ripscorrelationematrix Correlation matrix
+ * 
+ * Analogously to the case of distance matrix, Rips complexes can be also constructed based on correlation matrix. 
+ * Given a correlation matrix M, comportment-wise 1-M is a distance matrix.
+ * This example builds the one skeleton graph from the given corelation 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_correlation_matrix.cpp
+ * 
+ * When launching:
+ * 
+ * \code $> ./example_one_skeleton_from_correlation_matrix
+ * \endcode
+ *
+ * the program output is:
+ * 
+ * \include Rips_complex/one_skeleton_rips_from_correlation_matrix_for_doc.txt
+ * 
+ * All the other constructions discussed for Rips complex for distance matrix can be also performed for Rips complexes construction from correlation matrices.
+ * 
  * \copyright GNU General Public License v3.                         
  * \verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
  */
diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt
index 2940f164..f58ab455 100644
--- a/src/Rips_complex/example/CMakeLists.txt
+++ b/src/Rips_complex/example/CMakeLists.txt
@@ -9,12 +9,16 @@ add_executable ( Rips_complex_example_one_skeleton_from_points example_one_skele
 # Distance matrix
 add_executable ( Rips_complex_example_one_skeleton_from_distance_matrix example_one_skeleton_rips_from_distance_matrix.cpp )
 
+add_executable ( example_one_skeleton_rips_from_correlation_matrix example_one_skeleton_rips_from_correlation_matrix.cpp )
+
+
 add_executable ( Rips_complex_example_from_csv_distance_matrix example_rips_complex_from_csv_distance_matrix_file.cpp )
 
 if (TBB_FOUND)
   target_link_libraries(Rips_complex_example_from_off ${TBB_LIBRARIES})
   target_link_libraries(Rips_complex_example_one_skeleton_from_points ${TBB_LIBRARIES})
   target_link_libraries(Rips_complex_example_one_skeleton_from_distance_matrix ${TBB_LIBRARIES})
+  target_link_libraries(example_one_skeleton_rips_from_correlation_matrix ${TBB_LIBRARIES})
   target_link_libraries(Rips_complex_example_from_csv_distance_matrix ${TBB_LIBRARIES})
 endif()
 
diff --git a/src/Rips_complex/example/one_skeleton_rips_from_correlation_matrix_for_doc.txt b/src/Rips_complex/example/one_skeleton_rips_from_correlation_matrix_for_doc.txt
new file mode 100644
index 00000000..640d7083
--- /dev/null
+++ b/src/Rips_complex/example/one_skeleton_rips_from_correlation_matrix_for_doc.txt
@@ -0,0 +1,17 @@
+Rips complex is of dimension 1 - 15 simplices - 5 vertices.
+Iterator on Rips complex simplices in the filtration order, with [filtration value]:
+   ( 0 ) -> [0] 
+   ( 1 ) -> [0] 
+   ( 2 ) -> [0] 
+   ( 3 ) -> [0] 
+   ( 4 ) -> [0] 
+   ( 4 0 ) -> [0.11] 
+   ( 2 1 ) -> [0.26] 
+   ( 3 2 ) -> [0.28] 
+   ( 4 3 ) -> [0.3] 
+   ( 4 1 ) -> [0.39] 
+   ( 2 0 ) -> [0.77] 
+   ( 1 0 ) -> [0.94] 
+   ( 4 2 ) -> [0.97] 
+   ( 3 0 ) -> [0.99] 
+   ( 3 1 ) -> [0.99] 
-- 
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