Adding a code that use Clement's procedure to read files. Correcting some samll errors. Now the code is ready.

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_representation_integration@2610 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: b2947d1c484d661eca6c32fe5386461e741b76f9

1 files changed, 72 insertions, 120 deletions

diff --git a/src/Persistence_representations/include/gudhi/read_persistence_from_file.h b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h
index ad3d4e83..770da15b 100644
--- a/src/Persistence_representations/include/gudhi/read_persistence_from_file.h
+++ b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h
@@ -30,6 +30,7 @@
 #include <algorithm>
 #include <string>
 #include <utility>
+#include <gudhi/reader_utils.h>
 
 namespace Gudhi {
 namespace Persistence_representations {
@@ -49,130 +50,81 @@ namespace Persistence_representations {
  * The procedure returns vector of persistence pairs.
 **/
 std::vector<std::pair<double, double> > read_persistence_intervals_in_one_dimension_from_file(
-    std::string const& filename, int dimension = -1, double what_to_substitute_for_infinite_bar = -1) {
+    std::string const& filename, int dimension = -1, double what_to_substitute_for_infinite_bar = -1) {  
   bool dbg = false;
-  std::ifstream in;
-  in.open(filename);
-  // checking if the file exist:
-  if (!in.good()) {
-    std::cerr << "The file : " << filename << " do not exist. The program will now terminate \n";
-    throw "The persistence landscape file do not exist. The program will now terminate \n";
-  }
 
   std::string line;
-  std::vector<std::pair<double, double> > barcode;
-
-  int number_of_entries_per_line = -1;
-
-  while (!in.eof()) {
-    getline(in, line);
-    if (dbg) std::cerr << "Reading line : " << line << std::endl;
-    if (!(line.length() == 0 || line[0] == '#')) {
-      // If we do not know how many entries per line we have, we check it in below.
-      if (number_of_entries_per_line == -1) {
-        number_of_entries_per_line = 0;
-        std::string line_copy(line);
-        if (line_copy.find("inf") != std::string::npos) {
-          size_t np = line_copy.find("inf");
-          // replace symbols 'inf' in line_copy with white spaces:
-          line_copy[np] = ' ';
-          line_copy[np + 1] = ' ';
-          line_copy[np + 2] = ' ';
-          number_of_entries_per_line = 1;
-        }
-        // check how many entries we have in the line.
-        std::stringstream ss(line_copy);
-        double number;
-        std::vector<double> this_line;
-        while (ss >> number) {
-          this_line.push_back(number);
-        }
-        number_of_entries_per_line += static_cast<int>(this_line.size());
-        if (dbg) {
-          std::cerr << "number_of_entries_per_line : " << number_of_entries_per_line
-                    << ". This number was obtained by analyzing this line : " << line << std::endl;
-        }
-        if ((number_of_entries_per_line < 2) || (number_of_entries_per_line > 4)) {
-          std::cerr << "The input file you have provided have wrong number of numerical entries per line. The program "
-                       "will now terminate. \n";
-          throw "Wrong number of numerical entries per line in the input file. The program will now terminate. \n";
-        }
-      }
-      // In case there is an 'inf' string in this line, we are dealing with this situation in below.
-      if (line.find("inf") != std::string::npos) {
-        if (dbg) {
-          std::cerr << "This line: " << line << " contains infinite interval. \n";
-        }
-        // first we substitute inf by white spaces:
-        size_t np = line.find("inf");
-        line[np] = ' ';
-        line[np + 1] = ' ';
-        line[np + 2] = ' ';
-        if (what_to_substitute_for_infinite_bar != -1) {
-          double beginn, field, dim;
-          std::stringstream lineSS(line);
-          if (number_of_entries_per_line == 4) lineSS >> field;
-          if (number_of_entries_per_line >= 3) {
-            lineSS >> dim;
-          } else {
-            dim = dimension;
-          }
-          lineSS >> beginn;
-          if (dim == dimension) {
-            if (beginn > what_to_substitute_for_infinite_bar) {
-              barcode.push_back(std::make_pair(what_to_substitute_for_infinite_bar, beginn));
-            } else {
-              barcode.push_back(std::make_pair(beginn, what_to_substitute_for_infinite_bar));
-            }
-            if (dbg) {
-              std::cerr << "this is the line that is going to the output : " << beginn << " , "
-                        << what_to_substitute_for_infinite_bar << std::endl;
-            }
-          }
-        } else {
-          // this is a line with infinity. Since the variable what_to_substitute_for_infinite_bar have not been set up,
-          // it means that this line will be skipped.
-          if (dbg) {
-            std::cerr << "We will skip it \n";
-          }
-        }
-        continue;
-      } else {
-        // Then, we read the content of the line. We know that it do not contain 'inf' substring.
-        std::stringstream lineSS(line);
-        double beginn, endd, field, dim;
-        if (number_of_entries_per_line == 4) lineSS >> field;
-        if (number_of_entries_per_line >= 3) {
-          lineSS >> dim;
-        } else {
-          dim = dimension;
-        }
-        lineSS >> beginn;
-        lineSS >> endd;
-        if (beginn > endd) {
-          std::swap(beginn, endd);
-        }
-        if (dim == dimension) {
-          barcode.push_back(std::make_pair(beginn, endd));
-          if (dbg) {
-            std::cerr << "This is a line that is going to the output : " << beginn << " , " << endd << std::endl;
-          }
-        } else {
-          if ((number_of_entries_per_line == 3) && (dimension == -1)) {
-            barcode.push_back(std::make_pair(beginn, endd));
-          }
-        }
-      }
-    } else {
-      if (dbg) {
-        std::cerr << "This is a comment line \n";
-      }
-    }
+  std::vector<std::pair<double, double> > barcode_initial = read_persistence_intervals_in_dimension(filename,(int)dimension);
+  std::vector<std::pair<double, double> > final_barcode;
+  final_barcode.reserve( barcode_initial.size() );
+  
+  if ( dbg ) 
+  {
+	  std::cerr << "Here are the intervals that we read from the file : \n";
+	  for ( size_t i = 0 ; i != barcode_initial.size() ; ++i )
+	  {
+		  std::cout << barcode_initial[i].first << " " << barcode_initial[i].second << std::endl;
+	  }
+	  getchar();
   }
-  in.close();
-  if (dbg) std::cerr << "End of reading \n";
-
-  return barcode;
+  
+  for ( size_t i = 0 ; i != barcode_initial.size() ; ++i )
+  {
+	   if ( dbg )
+	   {
+		   std::cout << "COnsidering interval : " << barcode_initial[i].first << " " << barcode_initial[i].second << std::endl;
+	   }
+	   // if ( barcode_initial[i].first == barcode_initial[i].second )
+	   //{
+	   //		if ( dbg )std::cout << "It has zero length \n";
+	   //		continue;//zero length intervals are not relevant, so we skip all of them.
+	   //}
+	
+		if ( barcode_initial[i].first > barcode_initial[i].second )//note that in this case barcode_initial[i].second != std::numeric_limits<double>::infinity()
+		{
+			if ( dbg )std::cout << "Swap and enter \n";
+			//swap them to make sure that birth < death
+			final_barcode.push_back( std::pair<double,double>( barcode_initial[i].second , barcode_initial[i].first ) );
+			continue;
+		}
+		else
+		{
+			if ( barcode_initial[i].second != std::numeric_limits<double>::infinity() )
+			{
+				if ( dbg )std::cout << "Simply enters\n";
+				//in this case, due to the previous conditions we know that barcode_initial[i].first < barcode_initial[i].second, so we put them as they are
+				final_barcode.push_back( std::pair<double,double>( barcode_initial[i].first , barcode_initial[i].second ) );
+			}
+		}
+	
+		if ( (barcode_initial[i].second == std::numeric_limits<double>::infinity() ) && ( what_to_substitute_for_infinite_bar != -1 ) )
+		{								
+			if ( barcode_initial[i].first < what_to_substitute_for_infinite_bar )//if only birth < death.
+			{ 
+				final_barcode.push_back( std::pair<double,double>( barcode_initial[i].first , what_to_substitute_for_infinite_bar ) );
+			}
+		}
+		else
+		{
+			//if the variable what_to_substitute_for_infinite_bar is not set, then we ignore all the infinite bars. 
+		}		
+  }
+  
+    
+  if ( dbg ) 
+  {
+	  std::cerr << "Here are the final bars that we are sending further : \n";
+	  for ( size_t i = 0 ; i != final_barcode.size() ; ++i )
+	  {
+		  std::cout << final_barcode[i].first << " " << final_barcode[i].second << std::endl;
+	  }
+	  std::cerr << "final_barcode.size() : " << final_barcode.size() << std::endl;
+	  getchar();
+  }
+  
+  
+  
+  return final_barcode;  
 }  // read_persistence_intervals_in_one_dimension_from_file
 
 }  // namespace Persistence_representations