From 82c0652b06949b0b002781688565d7ecf30f04fe Mon Sep 17 00:00:00 2001
From: pdlotko <pdlotko@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 8 Feb 2018 10:37:21 +0000
Subject: Fixed comments from Marc and Vincent.

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@3234 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 8b5e08c38cd05512ba8b2824f13a62d35f39bac3
---
 ...e_one_skeleton_rips_from_correlation_matrix.cpp | 10 +++---
 .../rips_correlation_matrix_persistence.cpp        | 40 +++++++++++-----------
 2 files changed, 25 insertions(+), 25 deletions(-)

(limited to 'src/Rips_complex')

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 f66c4b04..a34ce15c 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
@@ -40,11 +40,11 @@ int main() {
 		  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];
+      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];
+    }    
   }
 
   //-----------------------------------------------------------------------------
diff --git a/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp b/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp
index 3fe0edb0..95bce491 100644
--- a/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp
+++ b/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp
@@ -24,7 +24,7 @@
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Persistent_cohomology.h>
 #include <gudhi/reader_utils.h>
-#include <gudhi/file_writer.h>
+#include <gudhi/writing_persistence_to_file.h>
 
 #include <boost/program_options.hpp>
 
@@ -57,28 +57,23 @@ int main(int argc, char* argv[]) {
   Correlation_matrix correlations =
       Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file);
 
+  Filtration_value threshold = 0;
+
   // 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";
+      //Here we make sure that the values of corelations lie between -1 and 1. 
+      //If not, we throw an exception.
+      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";
       }
+      if ( correlations[i][j] > threshold ) threshold = correlations[i][j];
     }
   }
 
-  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 - 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
@@ -95,10 +90,16 @@ int main(int argc, char* argv[]) {
   Persistent_cohomology pcoh(simplex_tree);
   // initializes the coefficient field for homology
   pcoh.init_coefficients(p);
-  // compute persistence
+  //compute persistence
   pcoh.compute_persistent_cohomology(min_persistence);
-
-  // invert the persistence diagram
+    
+  
+  //invert the persistence diagram. The reason for this procedure is the following:
+  //The input to the program is a corelation matrix M. When processing it, it is 
+  //turned into 1-M and the obtained persistence intervals are in '1-M' units.
+  //Below we reverse every (birth,death) pair into (1-birth, 1-death) pair
+  //so that the input and the output to the program is expressed in the same
+  //units. 
   auto pairs = pcoh.get_persistent_pairs();
   std::vector<intervals_common> processed_persistence_intervals;
   processed_persistence_intervals.reserve(pairs.size());
@@ -118,8 +119,7 @@ int main(int argc, char* argv[]) {
     write_persistence_intervals_to_stream(processed_persistence_intervals);
   } else {
     std::ofstream out(filediag);
-    write_persistence_intervals_to_stream(processed_persistence_intervals, out);
-    out.close();
+    write_persistence_intervals_to_stream(processed_persistence_intervals, out);    
   }
   return 0;
 }
-- 
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