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

3 files changed, 178 insertions, 1 deletions

diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
index e17e5926..1fe048bc 100644
--- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
+++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
@@ -160,7 +160,18 @@ 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
-outputs its persistence diagram.
+outputs its persistence diagram. The file should contain lower diagonal distance matrix with semicolons as separators.
+The code do not check if it is dealing with a distance matrix. It is the user responsibility to provide a valid input.
+Please refer to data/distance_matrix/lower_triangular_distance_matrix.csv for an example of a file. 
+
+\li <a href="_persistent_cohomology_2rips_correlation_matrix_persistence_8cpp-example.html">
+Persistent_cohomology/rips_correlation_matrix_persistence.cpp</a>
+computes the Rips complex of a correlation matrix and
+outputs its persistence diagram. Note that no check is performed if
+the matrix given as the input is a correlation matrix. 
+It is the user responsibility to ensure that this is the case. The
+input is to be given either as a lower triangular matrix. 
+Please refer to data/distance_matrix/lower_triangular_correlation_matrix.csv for an example of a file. 
 
 \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
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index f47de4c3..8a21d038 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -8,6 +8,9 @@ add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simp
 add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp)
 target_link_libraries(rips_distance_matrix_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
+add_executable(rips_correlation_matrix_persistence rips_correlation_matrix_persistence.cpp)
+target_link_libraries(rips_correlation_matrix_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
 add_executable(rips_persistence rips_persistence.cpp)
 target_link_libraries(rips_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
@@ -24,6 +27,7 @@ if (TBB_FOUND)
   target_link_libraries(plain_homology ${TBB_LIBRARIES})
   target_link_libraries(persistence_from_simple_simplex_tree ${TBB_LIBRARIES})
   target_link_libraries(rips_distance_matrix_persistence ${TBB_LIBRARIES})
+  target_link_libraries(rips_correlation_matrix_persistence ${TBB_LIBRARIES})
   target_link_libraries(rips_persistence ${TBB_LIBRARIES})
   target_link_libraries(rips_persistence_step_by_step ${TBB_LIBRARIES})
   target_link_libraries(rips_persistence_via_boundary_matrix ${TBB_LIBRARIES})
@@ -35,6 +39,8 @@ add_test(NAME Persistent_cohomology_example_from_simple_simplex_tree COMMAND $<T
     "1" "0")
 add_test(NAME Persistent_cohomology_example_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(rips_distance_matrix ${CMAKE_CURRENT_BINARY_DIR}/rips_distance_matrix_persistence
+    ${CMAKE_SOURCE_DIR}/data/distance_matrix/full_correlation_matrix.csv.csv -r 1.0 -d 3 -p 3 -m 0)
 add_test(NAME Persistent_cohomology_example_from_rips_on_tore_3D COMMAND $<TARGET_FILE:rips_persistence>
     "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3")
 add_test(NAME Persistent_cohomology_example_from_rips_step_by_step_on_tore_3D COMMAND $<TARGET_FILE:rips_persistence_step_by_step>
diff --git a/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp b/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp
new file mode 100644
index 00000000..6f2891fe
--- /dev/null
+++ b/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp
@@ -0,0 +1,160 @@
+/*    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):       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/>.
+ */
+
+#include <gudhi/Rips_complex.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/reader_utils.h>
+
+#include <boost/program_options.hpp>
+
+#include <string>
+#include <vector>
+#include <limits>  // infinity
+
+
+// Types definition
+using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
+using Filtration_value = Simplex_tree::Filtration_value;
+using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
+using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp >;
+using Correlation_matrix = std::vector<std::vector<Filtration_value>>;
+
+void program_options(int argc, char * argv[]
+                     , std::string & csv_matrix_file
+                     , std::string & filediag
+                     , Filtration_value & threshold
+                     , int & dim_max
+                     , int & p
+                     , Filtration_value & min_persistence);
+
+int main(int argc, char * argv[]) {
+  std::string csv_matrix_file;
+  std::string filediag;
+  Filtration_value threshold;
+  int dim_max;
+  int p;
+  Filtration_value min_persistence;
+
+  program_options(argc, argv, csv_matrix_file, filediag, threshold, dim_max, p, min_persistence);
+
+  Correlation_matrix correlations = Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file);
+  
+  //Given a correlation matrix M, we compute component-wise M'[i,j] = 1-M[i,j] to get a distance matrix:
+  for ( size_t i = 0 ; i != correlations.size() ; ++i )
+  {
+	  for ( size_t j = 0 ; j != correlations[i].size() ; ++j )
+	  {
+		  correlations[i][j] = 1-correlations[i][j];
+		  if ( correlations[i][j] < 0 )
+		  {
+			  std::cerr << "The input matrix is not a correlation matrix. \n";
+			  throw "The input matrix is not a correlation matrix. \n";
+		  }		  
+	  }
+  } 
+  
+  Rips_complex rips_complex_from_file(correlations, threshold);
+
+  // Construct the Rips complex in a Simplex Tree
+  Simplex_tree simplex_tree;
+
+  rips_complex_from_file.create_complex(simplex_tree, dim_max);
+  std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
+  std::cout << "   and has dimension " << simplex_tree.dimension() << " \n";
+
+  // Sort the simplices in the order of the filtration
+  simplex_tree.initialize_filtration();
+
+  // Compute the persistence diagram of the complex
+  Persistent_cohomology pcoh(simplex_tree);
+  // initializes the coefficient field for homology
+  pcoh.init_coefficients(p);
+
+  pcoh.compute_persistent_cohomology(min_persistence);
+
+  // Output the diagram in filediag
+  if (filediag.empty()) {
+    pcoh.output_diagram();
+  } else {
+    std::ofstream out(filediag);
+    pcoh.output_diagram(out);
+    out.close();
+  }
+  return 0;
+}
+
+void program_options(int argc, char * argv[]
+                     , std::string & csv_matrix_file
+                     , std::string & filediag
+                     , Filtration_value & threshold
+                     , int & dim_max
+                     , int & p
+                     , Filtration_value & min_persistence) {
+  namespace po = boost::program_options;
+  po::options_description hidden("Hidden options");
+  hidden.add_options()
+      ("input-file", po::value<std::string>(&csv_matrix_file),
+       "Name of file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'.");
+
+  po::options_description visible("Allowed options", 100);
+  visible.add_options()
+      ("help,h", "produce help message")
+      ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
+       "Name of file in which the persistence diagram is written. Default print in std::cout")
+      ("max-edge-length,r",
+       po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
+       "Maximal length of an edge for the Rips complex construction.")
+      ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
+       "Maximal dimension of the Rips complex we want to compute.")
+      ("field-charac,p", po::value<int>(&p)->default_value(11),
+       "Characteristic p of the coefficient field Z/pZ for computing homology.")
+      ("min-persistence,m", po::value<Filtration_value>(&min_persistence),
+       "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals");
+
+  po::positional_options_description pos;
+  pos.add("input-file", 1);
+
+  po::options_description all;
+  all.add(visible).add(hidden);
+
+  po::variables_map vm;
+  po::store(po::command_line_parser(argc, argv).
+            options(all).positional(pos).run(), vm);
+  po::notify(vm);
+
+  if (vm.count("help") || !vm.count("input-file")) {
+    std::cout << std::endl;
+    std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
+    std::cout << "of a Rips complex defined on a set of distance matrix.\n \n";
+    std::cout << "The output diagram contains one bar per line, written with the convention: \n";
+    std::cout << "   p   dim b d \n";
+    std::cout << "where dim is the dimension of the homological feature,\n";
+    std::cout << "b and d are respectively the birth and death of the feature and \n";
+    std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
+
+    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
+    std::cout << visible << std::endl;
+    std::abort();
+  }
+}