Merge of persistence_representations_fix_reading branch + clang format files

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3116 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0bae116ddc294d46e347d61fecc6e76b1e13f053

7 files changed, 127 insertions, 149 deletions

diff --git a/src/Persistence_representations/include/gudhi/PSSK.h b/src/Persistence_representations/include/gudhi/PSSK.h
index e2d4225e..630f5623 100644
--- a/src/Persistence_representations/include/gudhi/PSSK.h
+++ b/src/Persistence_representations/include/gudhi/PSSK.h
@@ -121,10 +121,10 @@ void PSSK::construct(const std::vector<std::pair<double, double> >& intervals_,
 
   for (size_t pt_nr = 0; pt_nr != intervals_.size(); ++pt_nr) {
     // compute the value of intervals_[pt_nr] in the grid:
-    int x_grid = static_cast<int>((intervals_[pt_nr].first - this->min_) /
-                                  (this->max_ - this->min_) * number_of_pixels);
-    int y_grid = static_cast<int>((intervals_[pt_nr].second - this->min_) /
-                                  (this->max_ - this->min_) * number_of_pixels);
+    int x_grid =
+        static_cast<int>((intervals_[pt_nr].first - this->min_) / (this->max_ - this->min_) * number_of_pixels);
+    int y_grid =
+        static_cast<int>((intervals_[pt_nr].second - this->min_) / (this->max_ - this->min_) * number_of_pixels);
 
     if (dbg) {
       std::cerr << "point : " << intervals_[pt_nr].first << " , " << intervals_[pt_nr].second << std::endl;
diff --git a/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h b/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h
index 04dd78ad..fb741642 100644
--- a/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h
+++ b/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h
@@ -582,10 +582,10 @@ void Persistence_heat_maps<Scalling_of_kernels>::construct(const std::vector<std
 
   for (size_t pt_nr = 0; pt_nr != intervals_.size(); ++pt_nr) {
     // compute the value of intervals_[pt_nr] in the grid:
-    int x_grid = static_cast<int>((intervals_[pt_nr].first - this->min_) /
-                                  (this->max_ - this->min_) * number_of_pixels);
-    int y_grid = static_cast<int>((intervals_[pt_nr].second - this->min_) /
-                                  (this->max_ - this->min_) * number_of_pixels);
+    int x_grid =
+        static_cast<int>((intervals_[pt_nr].first - this->min_) / (this->max_ - this->min_) * number_of_pixels);
+    int y_grid =
+        static_cast<int>((intervals_[pt_nr].second - this->min_) / (this->max_ - this->min_) * number_of_pixels);
 
     if (dbg) {
       std::cerr << "point : " << intervals_[pt_nr].first << " , " << intervals_[pt_nr].second << std::endl;
@@ -797,8 +797,7 @@ void Persistence_heat_maps<Scalling_of_kernels>::load_from_file(const char* file
 
   std::string temp;
   std::getline(in, temp);
-
-  while (!in.eof()) {
+  while (in.good()) {
     std::getline(in, temp);
     std::stringstream lineSS;
     lineSS << temp;
diff --git a/src/Persistence_representations/include/gudhi/Persistence_intervals.h b/src/Persistence_representations/include/gudhi/Persistence_intervals.h
index 525d58a3..a3f963cf 100644
--- a/src/Persistence_representations/include/gudhi/Persistence_intervals.h
+++ b/src/Persistence_representations/include/gudhi/Persistence_intervals.h
@@ -402,9 +402,8 @@ std::vector<double> Persistence_intervals::characteristic_function_of_diagram(do
     }
 
     for (size_t pos = beginIt; pos != endIt; ++pos) {
-      result[pos] +=
-          ((x_max - x_min) / static_cast<double>(number_of_bins)) *
-           (this->intervals[i].second - this->intervals[i].first);
+      result[pos] += ((x_max - x_min) / static_cast<double>(number_of_bins)) *
+                     (this->intervals[i].second - this->intervals[i].first);
     }
     if (dbg) {
       std::cerr << "Result at this stage \n";
diff --git a/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h b/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h
index d5ab04b4..e476d28a 100644
--- a/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h
+++ b/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h
@@ -26,7 +26,6 @@
 #include <gudhi/Persistence_intervals.h>
 #include <gudhi/Bottleneck.h>
 
-
 #include <limits>
 
 namespace Gudhi {
diff --git a/src/Persistence_representations/include/gudhi/Persistence_landscape.h b/src/Persistence_representations/include/gudhi/Persistence_landscape.h
index 5c300112..2d83dcc3 100644
--- a/src/Persistence_representations/include/gudhi/Persistence_landscape.h
+++ b/src/Persistence_representations/include/gudhi/Persistence_landscape.h
@@ -79,14 +79,16 @@ class Persistence_landscape {
   /**
   * Constructor that takes as an input a vector of birth-death pairs.
   **/
-  Persistence_landscape(const std::vector<std::pair<double, double> >& p, size_t number_of_levels = std::numeric_limits<size_t>::max() );
+  Persistence_landscape(const std::vector<std::pair<double, double> >& p,
+                        size_t number_of_levels = std::numeric_limits<size_t>::max());
 
   /**
        * Constructor that reads persistence intervals from file and creates persistence landscape. The format of the
     *input file is the following: in each line we put birth-death pair. Last line is assumed
        * to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read.
       **/
-  Persistence_landscape(const char* filename, size_t dimension = std::numeric_limits<unsigned>::max() , size_t number_of_levels = std::numeric_limits<size_t>::max() );
+  Persistence_landscape(const char* filename, size_t dimension = std::numeric_limits<unsigned>::max(),
+                        size_t number_of_levels = std::numeric_limits<size_t>::max());
 
   /**
    * This procedure loads a landscape from file. It erase all the data that was previously stored in this landscape.
@@ -285,7 +287,7 @@ class Persistence_landscape {
    *distance, we need to take its absolute value. This is the purpose of this procedure.
   **/
   Persistence_landscape abs();
-  
+
   Persistence_landscape* new_abs();
 
   /**
@@ -453,7 +455,8 @@ class Persistence_landscape {
   size_t number_of_functions_for_vectorization;
   size_t number_of_functions_for_projections_to_reals;
 
-  void construct_persistence_landscape_from_barcode(const std::vector<std::pair<double, double> >& p , size_t number_of_levels = std::numeric_limits<size_t>::max());
+  void construct_persistence_landscape_from_barcode(const std::vector<std::pair<double, double> >& p,
+                                                    size_t number_of_levels = std::numeric_limits<size_t>::max());
   Persistence_landscape multiply_lanscape_by_real_number_not_overwrite(double x) const;
   void multiply_lanscape_by_real_number_overwrite(double x);
   friend double compute_maximal_distance_non_symmetric(const Persistence_landscape& pl1,
@@ -473,7 +476,7 @@ Persistence_landscape::Persistence_landscape(const char* filename, size_t dimens
   } else {
     barcode = read_persistence_intervals_in_one_dimension_from_file(filename);
   }
-  this->construct_persistence_landscape_from_barcode(barcode,number_of_levels);
+  this->construct_persistence_landscape_from_barcode(barcode, number_of_levels);
   this->set_up_numbers_of_functions_for_vectorization_and_projections_to_reals();
 }
 
@@ -506,14 +509,14 @@ bool Persistence_landscape::operator==(const Persistence_landscape& rhs) const {
   return true;
 }
 
-Persistence_landscape::Persistence_landscape(const std::vector<std::pair<double, double> >& p,size_t number_of_levels) {
-  this->construct_persistence_landscape_from_barcode(p,number_of_levels);
+Persistence_landscape::Persistence_landscape(const std::vector<std::pair<double, double> >& p,
+                                             size_t number_of_levels) {
+  this->construct_persistence_landscape_from_barcode(p, number_of_levels);
   this->set_up_numbers_of_functions_for_vectorization_and_projections_to_reals();
 }
 
 void Persistence_landscape::construct_persistence_landscape_from_barcode(
-    const std::vector<std::pair<double, double> >& p, size_t number_of_levels) 
-    {
+    const std::vector<std::pair<double, double> >& p, size_t number_of_levels) {
   bool dbg = false;
   if (dbg) {
     std::cerr << "Persistence_landscape::Persistence_landscape( const std::vector< std::pair< double , double > >& p )"
@@ -648,12 +651,11 @@ void Persistence_landscape::construct_persistence_landscape_from_barcode(
 
     lambda_n.erase(std::unique(lambda_n.begin(), lambda_n.end()), lambda_n.end());
     this->land.push_back(lambda_n);
-    
+
     ++number_of_levels_in_the_landscape;
-    if ( number_of_levels == number_of_levels_in_the_landscape )
-    {
-		break;
-	}
+    if (number_of_levels == number_of_levels_in_the_landscape) {
+      break;
+    }
   }
 }
 
@@ -857,58 +859,47 @@ Persistence_landscape Persistence_landscape::abs() {
   return result;
 }
 
+Persistence_landscape* Persistence_landscape::new_abs() {
+  Persistence_landscape* result = new Persistence_landscape(*this);
+  for (size_t level = 0; level != this->land.size(); ++level) {
+    if (AbsDbg) {
+      std::cout << "level: " << level << std::endl;
+    }
+    std::vector<std::pair<double, double> > lambda_n;
+    lambda_n.push_back(std::make_pair(-std::numeric_limits<int>::max(), 0));
+    for (size_t i = 1; i != this->land[level].size(); ++i) {
+      if (AbsDbg) {
+        std::cout << "this->land[" << level << "][" << i << "] : " << this->land[level][i].first << " "
+                  << this->land[level][i].second << std::endl;
+      }
+      // if a line segment between this->land[level][i-1] and this->land[level][i] crosses the x-axis, then we have to
+      // add one landscape point t o result
+      if ((this->land[level][i - 1].second) * (this->land[level][i].second) < 0) {
+        double zero =
+            find_zero_of_a_line_segment_between_those_two_points(this->land[level][i - 1], this->land[level][i]);
 
-Persistence_landscape* Persistence_landscape::new_abs() 
-{
-	Persistence_landscape* result = new Persistence_landscape(*this);	 
-	for (size_t level = 0; level != this->land.size(); ++level) 
-	{
-		if (AbsDbg) 
-		{
-			std::cout << "level: " << level << std::endl;
-		}
-		std::vector<std::pair<double, double> > lambda_n;
-		lambda_n.push_back(std::make_pair(-std::numeric_limits<int>::max(), 0));
-		for (size_t i = 1; i != this->land[level].size(); ++i) 
-		{
-			if (AbsDbg) 
-			{
-				std::cout << "this->land[" << level << "][" << i << "] : " << this->land[level][i].first << " "
-					  << this->land[level][i].second << std::endl;
-			}
-			// if a line segment between this->land[level][i-1] and this->land[level][i] crosses the x-axis, then we have to
-			// add one landscape point t o result
-			if ((this->land[level][i - 1].second) * (this->land[level][i].second) < 0) {
-			double zero =
-				find_zero_of_a_line_segment_between_those_two_points(this->land[level][i - 1], this->land[level][i]);
-
-			lambda_n.push_back(std::make_pair(zero, 0));
-			lambda_n.push_back(std::make_pair(this->land[level][i].first, fabs(this->land[level][i].second)));
-			if (AbsDbg) 
-			{
-				std::cout << "Adding pair : (" << zero << ",0)" << std::endl;
-				std::cout << "In the same step adding pair : (" << this->land[level][i].first << ","
-						<< fabs(this->land[level][i].second) << ") " << std::endl;
-				std::cin.ignore();
-			}
-			} 
-			else 
-			{
-				lambda_n.push_back(std::make_pair(this->land[level][i].first, fabs(this->land[level][i].second)));
-				if (AbsDbg) 
-				{
-					std::cout << "Adding pair : (" << this->land[level][i].first << "," << fabs(this->land[level][i].second)
-							<< ") " << std::endl;
-					std::cin.ignore();
-				}
-			}
-	   }
-	result->land.push_back(lambda_n);
-	}	
-	return result;
+        lambda_n.push_back(std::make_pair(zero, 0));
+        lambda_n.push_back(std::make_pair(this->land[level][i].first, fabs(this->land[level][i].second)));
+        if (AbsDbg) {
+          std::cout << "Adding pair : (" << zero << ",0)" << std::endl;
+          std::cout << "In the same step adding pair : (" << this->land[level][i].first << ","
+                    << fabs(this->land[level][i].second) << ") " << std::endl;
+          std::cin.ignore();
+        }
+      } else {
+        lambda_n.push_back(std::make_pair(this->land[level][i].first, fabs(this->land[level][i].second)));
+        if (AbsDbg) {
+          std::cout << "Adding pair : (" << this->land[level][i].first << "," << fabs(this->land[level][i].second)
+                    << ") " << std::endl;
+          std::cin.ignore();
+        }
+      }
+    }
+    result->land.push_back(lambda_n);
+  }
+  return result;
 }
 
-
 Persistence_landscape Persistence_landscape::multiply_lanscape_by_real_number_not_overwrite(double x) const {
   std::vector<std::vector<std::pair<double, double> > > result(this->land.size());
   for (size_t dim = 0; dim != this->land.size(); ++dim) {
@@ -954,7 +945,7 @@ void Persistence_landscape::load_landscape_from_file(const char* filename) {
   std::vector<std::pair<double, double> > landscapeAtThisLevel;
 
   bool isThisAFirsLine = true;
-  while (!in.eof()) {
+  while (in.good()) {
     getline(in, line);
     if (!(line.length() == 0 || line[0] == '#')) {
       std::stringstream lineSS;
diff --git a/src/Persistence_representations/include/gudhi/Persistence_vectors.h b/src/Persistence_representations/include/gudhi/Persistence_vectors.h
index 0fb49eee..aed48b73 100644
--- a/src/Persistence_representations/include/gudhi/Persistence_vectors.h
+++ b/src/Persistence_representations/include/gudhi/Persistence_vectors.h
@@ -617,9 +617,7 @@ void Vector_distances_in_diagram<F>::load_from_file(const char* filename) {
   }
 
   double number;
-  while (true) {
-    in >> number;
-    if (in.eof()) break;
+  while (in >> number) {
     this->sorted_vector_of_distances.push_back(number);
   }
   in.close();
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 770da15b..450c223c 100644
--- a/src/Persistence_representations/include/gudhi/read_persistence_from_file.h
+++ b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h
@@ -50,81 +50,73 @@ 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::string line;
-  std::vector<std::pair<double, double> > barcode_initial = read_persistence_intervals_in_dimension(filename,(int)dimension);
+  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();
+  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();
   }
-  
-  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. 
-		}		
+
+  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();
+
+  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;  
+
+  return final_barcode;
 }  // read_persistence_intervals_in_one_dimension_from_file
 
 }  // namespace Persistence_representations