random commit.

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@3233 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 9a3ccdd8a000bd3fd79bab61b35e50bd707cfb29

3 files changed, 18 insertions, 17 deletions

diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
index 969daba6..770eb55f 100644
--- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
@@ -383,7 +383,7 @@ class Bitmap_cubical_complex : public T {
     std::vector<std::size_t> bdry = this->get_boundary_of_a_cell(sh);
     if (globalDbg) {
       std::cerr << "std::pair<Simplex_handle, Simplex_handle> endpoints( Simplex_handle sh )\n";
-      std::cerr << "bdry.size() : " << bdry.size() << std::endl;
+      std::cerr << "bdry.size() : " << bdry.size() << "\n";
     }
     // this method returns two first elements from the boundary of sh.
     if (bdry.size() < 2)
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
index 0da1dc20..f66c4b04 100644
--- 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
@@ -31,26 +31,27 @@ int main() {
   // ----------------------------------------------------------------------------
   // 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) {
-      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";
-      }
+	  //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;
-
-  //------------------------------------------------------------------------------
-  // Note that this treshold mean that the points in the distance 1, i.e. corelation
-  // 0 will be connected.
-  //------------------------------------------------------------------------------
-  double threshold = 1.0;
+  
 
   Rips_complex rips_complex_from_points(distances, threshold);
 
diff --git a/src/common/include/gudhi/writing_persistence_to_file.h b/src/common/include/gudhi/writing_persistence_to_file.h
index 53c83533..5767c06e 100644
--- a/src/common/include/gudhi/writing_persistence_to_file.h
+++ b/src/common/include/gudhi/writing_persistence_to_file.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef FILE_WRITER_
-#define FILE_WRITER_
+#ifndef WRITING_PERSISTENCE_TO_FILE_H
+#define WRITING_PERSISTENCE_TO_FILE_H
 
 #include <iostream>
 #include <string>
@@ -141,8 +141,8 @@ private:
 **/ 
 template <typename Filtration_type , typename Coefficient_field>
 void write_persistence_intervals_to_stream( 
-//const std::vector< Persistence_interval_common<Filtration_type,Coefficient_field> >& intervals,
-
+const std::vector< Persistence_interval_common<Filtration_type,Coefficient_field> >& intervals,
+//TODO: change to ranges when it is clear how to do that.
                                           std::ostream& out = std::cout )
 {
 	for ( auto interval : intervals )
@@ -155,4 +155,4 @@ void write_persistence_intervals_to_stream(
 
 }
 
-#endif //FILE_WRITER_
+#endif //WRITING_PERSISTENCE_TO_FILE_H