a few more changes

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@2823 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: d12b2413620003883e82b3022f8d933aa05e2856

1 files changed, 50 insertions, 6 deletions

diff --git a/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp b/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp
index 41cf915a..6f12dada 100644
--- a/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp
@@ -24,6 +24,7 @@
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Persistent_cohomology.h>
 #include <gudhi/reader_utils.h>
+#include <gudhi/file_writer.h>
 
 #include <boost/program_options.hpp>
 
@@ -38,6 +39,7 @@ 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>>;
+using intervals_common = Gudhi::Persistence_interval_common< double , int >;
 
 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);
@@ -66,6 +68,13 @@ int main(int argc, char* argv[]) {
     }
   }
 
+  //If the treshold, being minimal corelation is in the range [0,1], 
+  //change it to 1-threshold
+  if ( ( threshold>=0 ) && ( threshold<=1 ) )
+  {
+	  threshold = 1-threshold;
+  }
+  
   Rips_complex rips_complex_from_file(correlations, threshold);
 
   // Construct the Rips complex in a Simplex Tree
@@ -82,15 +91,34 @@ int main(int argc, char* argv[]) {
   Persistent_cohomology pcoh(simplex_tree);
   // initializes the coefficient field for homology
   pcoh.init_coefficients(p);
-
+  //compute persistence
   pcoh.compute_persistent_cohomology(min_persistence);
-
-  // Output the diagram in filediag
+    
+  
+  //invert the persistence diagram 
+  auto pairs = pcoh.get_persistent_pairs();
+  std::vector< intervals_common > processed_persistence_intervals;
+  processed_persistence_intervals.reserve( pairs.size() );
+  for (auto pair :pairs )
+  {
+	  double birth = 1-simplex_tree.filtration( get<0>(pair) );
+	  double death = 1-simplex_tree.filtration( get<1>(pair) );
+	  unsigned dimension = (unsigned)simplex_tree.dimension( get<0>(pair) );
+	  int field = get<2>(pair);
+	  processed_persistence_intervals.push_back(
+	  intervals_common(birth, death,dimension,field)
+	  );
+  }	  
+  
+  //sort the processed intervals:
+  std::sort( processed_persistence_intervals.begin() , processed_persistence_intervals.end() );
+
+  //and write them to a file 
   if (filediag.empty()) {
-    pcoh.output_diagram();
+    write_persistence_intervals_to_stream(processed_persistence_intervals);
   } else {
     std::ofstream out(filediag);
-    pcoh.output_diagram(out);
+    write_persistence_intervals_to_stream(processed_persistence_intervals,out);
     out.close();
   }
   return 0;
@@ -103,6 +131,9 @@ void program_options(int argc, char* argv[], std::string& csv_matrix_file, std::
   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 ';'.");
+  hidden.add_options()
+      ("input-file", po::value<std::string>(&csv_matrix_file),
+       "Name of file containing a corelation 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")(
@@ -118,6 +149,19 @@ void program_options(int argc, char* argv[], std::string& csv_matrix_file, std::
       "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");
+  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")
+      ("min-edge-corelation,c",
+       po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
+       "Minimal corelation 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);
@@ -132,7 +176,7 @@ void program_options(int argc, char* argv[], std::string& csv_matrix_file, std::
   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 << "of a Rips complex defined on a corelation 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";