Merge rips_complex_from_correlation_matrix branch

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3328 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: a0d98d884fc06a6528e3362d6ed627cd964f527a

3 files changed, 105 insertions, 0 deletions

diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt
index 2940f164..fcb1eaee 100644
--- a/src/Rips_complex/example/CMakeLists.txt
+++ b/src/Rips_complex/example/CMakeLists.txt
@@ -11,17 +11,23 @@ add_executable ( Rips_complex_example_one_skeleton_from_distance_matrix example_
 
 add_executable ( Rips_complex_example_from_csv_distance_matrix example_rips_complex_from_csv_distance_matrix_file.cpp )
 
+# Correlation matrix
+add_executable (  Rips_complex_example_one_skeleton_rips_from_correlation_matrix example_one_skeleton_rips_from_correlation_matrix.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(Rips_complex_example_from_csv_distance_matrix ${TBB_LIBRARIES})
+  target_link_libraries(Rips_complex_example_one_skeleton_rips_from_correlation_matrix ${TBB_LIBRARIES})
 endif()
 
 add_test(NAME Rips_complex_example_one_skeleton_from_points
     COMMAND $<TARGET_FILE:Rips_complex_example_one_skeleton_from_points>)
 add_test(NAME Rips_complex_example_one_skeleton_from_distance_matrix
     COMMAND $<TARGET_FILE:Rips_complex_example_one_skeleton_from_distance_matrix>)
+add_test(NAME Rips_complex_example_one_skeleton_rips_from_correlation_matrix
+    COMMAND $<TARGET_FILE:Rips_complex_example_one_skeleton_rips_from_correlation_matrix>)
 
 add_test(NAME Rips_complex_example_from_off_doc_12_1 COMMAND $<TARGET_FILE:Rips_complex_example_from_off>
     "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "12.0" "1" "${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt")
@@ -57,3 +63,4 @@ install(TARGETS Rips_complex_example_from_off DESTINATION bin)
 install(TARGETS Rips_complex_example_one_skeleton_from_points DESTINATION bin)
 install(TARGETS Rips_complex_example_one_skeleton_from_distance_matrix DESTINATION bin)
 install(TARGETS Rips_complex_example_from_csv_distance_matrix DESTINATION bin)
+install(TARGETS Rips_complex_example_one_skeleton_rips_from_correlation_matrix DESTINATION bin)
diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_correlation_matrix.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_correlation_matrix.cpp
new file mode 100644
index 00000000..1343f24d
--- /dev/null
+++ b/src/Rips_complex/example/example_one_skeleton_rips_from_correlation_matrix.cpp
@@ -0,0 +1,81 @@
+#include <gudhi/Rips_complex.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/distance_functions.h>
+
+#include <iostream>
+#include <string>
+#include <vector>
+#include <limits>  // for std::numeric_limits
+
+int main() {
+  // Type definitions
+  using Simplex_tree = Gudhi::Simplex_tree<>;
+  using Filtration_value = Simplex_tree::Filtration_value;
+  using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
+  using Distance_matrix = std::vector<std::vector<Filtration_value>>;
+
+  // User defined correlation matrix is:
+  // |1	    0.06	0.23	0.01	0.89|
+  // |0.06	1	    0.74	0.01	0.61|
+  // |0.23	0.74	1	    0.72	0.03|
+  // |0.01	0.01	0.72	1	    0.7 |
+  // |0.89	0.61	0.03	0.7	    1   |
+
+  Distance_matrix correlations;
+  correlations.push_back({});
+  correlations.push_back({0.06});
+  correlations.push_back({0.23, 0.74});
+  correlations.push_back({0.01, 0.01, 0.72});
+  correlations.push_back({0.89, 0.61, 0.03, 0.7});
+
+  // ----------------------------------------------------------------------------
+  // Convert correlation matrix to a distance matrix:
+  // ----------------------------------------------------------------------------
+  double threshold = 0;
+  for (size_t i = 0; i != correlations.size(); ++i) {
+    for (size_t j = 0; j != correlations[i].size(); ++j) {
+      // Here we check if our data comes from corelation matrix.
+      if ((correlations[i][j] < -1) || (correlations[i][j] > 1)) {
+        std::cerr << "The input matrix is not a correlation matrix. The program will now terminate.\n";
+        throw "The input matrix is not a correlation matrix. The program will now terminate.\n";
+      }
+      correlations[i][j] = 1 - correlations[i][j];
+      // Here we make sure that we will get the treshold value equal to maximal
+      // distance in the matrix.
+      if (correlations[i][j] > threshold) threshold = correlations[i][j];
+    }
+  }
+
+  //-----------------------------------------------------------------------------
+  // Now the correlation matrix is a distance matrix and can be processed further.
+  //-----------------------------------------------------------------------------
+  Distance_matrix distances = correlations;
+
+  Rips_complex rips_complex_from_points(distances, threshold);
+
+  Simplex_tree stree;
+  rips_complex_from_points.create_complex(stree, 1);
+  // ----------------------------------------------------------------------------
+  // Display information about the one skeleton Rips complex. Note that
+  // the filtration displayed here comes from the distance matrix computed
+  // above, which is 1 - initial correlation matrix. Only this way, we obtain
+  // a complex with filtration. If a correlation matrix is used instead, we would
+  // have a reverse filtration (i.e. filtration of boundary of each simplex S
+  // is greater or equal to the filtration of S).
+  // ----------------------------------------------------------------------------
+  std::cout << "Rips complex is of dimension " << stree.dimension() << " - " << stree.num_simplices() << " simplices - "
+            << stree.num_vertices() << " vertices." << std::endl;
+
+  std::cout << "Iterator on Rips complex simplices in the filtration order, with [filtration value]:" << std::endl;
+  for (auto f_simplex : stree.filtration_simplex_range()) {
+    std::cout << "   ( ";
+    for (auto vertex : stree.simplex_vertex_range(f_simplex)) {
+      std::cout << vertex << " ";
+    }
+    std::cout << ") -> "
+              << "[" << stree.filtration(f_simplex) << "] ";
+    std::cout << std::endl;
+  }
+
+  return 0;
+}
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]