Answer to Vincent's comments.

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@2859 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 1a049ce98ccf893fc6af6c2631e508d3a9dc6c09

1 files changed, 26 insertions, 37 deletions

diff --git a/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp b/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp
index 94d5b8d4..676ef793 100644
--- a/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp
@@ -42,17 +42,17 @@ 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);
+                     Filtration_value& correlation_min, 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;
+  Filtration_value correlation_min;
   int dim_max;
   int p;
   Filtration_value min_persistence;
 
-  program_options(argc, argv, csv_matrix_file, filediag, threshold, dim_max, p, min_persistence);
+  program_options(argc, argv, csv_matrix_file, filediag, correlation_min, dim_max, p, min_persistence);
 
   Correlation_matrix correlations =
       Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file);
@@ -68,13 +68,19 @@ int main(int argc, char* argv[]) {
     }
   }
 
-  // If the threshold, being minimal correlation is in the range [0,1],
-  // change it to 1-threshold
-  if ( ( threshold>=0 ) && ( threshold<=1 ) )
+  Filtration_value threshold;
+  //If the correlation_min, being minimal corelation is in the range [0,1],
+  //change it to 1-correlation_min
+  if ( ( correlation_min>=0 ) && ( correlation_min<=1 ) )
   {
-	  threshold = 1-threshold;
+	  threshold = 1-correlation_min;
   }
-  
+  else
+  {
+	  std::cout << "Wrong value of the treshold corelation (should be between 0 and 1). The program will now terminate.\n";
+	  return 1;
+  }
+
   Rips_complex rips_complex_from_file(correlations, threshold);
 
   // Construct the Rips complex in a Simplex Tree
@@ -93,9 +99,9 @@ int main(int argc, char* argv[]) {
   pcoh.init_coefficients(p);
   //compute persistence
   pcoh.compute_persistent_cohomology(min_persistence);
-    
-  
-  // invert the persistence diagram
+
+
+  //invert the persistence diagram
   auto pairs = pcoh.get_persistent_pairs();
   std::vector< intervals_common > processed_persistence_intervals;
   processed_persistence_intervals.reserve( pairs.size() );
@@ -108,12 +114,12 @@ int main(int argc, char* argv[]) {
 	  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 
+  //and write them to a file
   if (filediag.empty()) {
     write_persistence_intervals_to_stream(processed_persistence_intervals);
   } else {
@@ -125,37 +131,20 @@ int main(int argc, char* argv[]) {
 }
 
 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) {
+                     Filtration_value& correlation_min, 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 correlation 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 correlation matrix. Can be square or lower triangular matrix. Separator is ';'.");
-
+       "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")(
-  //     "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");
   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-correlation,c",
-       po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
-       "Minimal correlation of an edge for the Rips complex construction.")
+      ("min-edge-corelation,c",
+       po::value<Filtration_value>(&correlation_min)->default_value(0),
+       "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),
@@ -176,7 +165,7 @@ 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 correlation 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";