clang format all sources

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_representation_integration@2477 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 326d664483d6700f82be824f79a0bf5c082b4945

9 files changed, 395 insertions, 458 deletions

diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp
index 2d221d27..34fdb1f8 100644
--- a/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp
+++ b/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp
@@ -20,53 +20,45 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-
-
 #include <gudhi/Persistence_heat_maps.h>
 
-
-
 using namespace Gudhi;
 using namespace Gudhi::Persistence_representations;
 
 #include <iostream>
 
+int main(int argc, char** argv) {
+  std::cout << "This program computes average persistence landscape of persistence landscapes created based on "
+               "persistence diagrams provided as an input. Please call this program with the names of files with "
+               "persistence diagrams \n";
+  std::vector<const char*> filenames;
+
+  if (argc == 1) {
+    std::cout << "No input files given, the program will now terminate \n";
+    return 1;
+  }
+
+  for (int i = 1; i < argc; ++i) {
+    filenames.push_back(argv[i]);
+  }
+
+  std::cout << "Creating persistence landscapes...\n";
+  std::vector<Persistence_heat_maps<constant_scaling_function>*> maps;
+  for (size_t i = 0; i != filenames.size(); ++i) {
+    Persistence_heat_maps<constant_scaling_function>* l = new Persistence_heat_maps<constant_scaling_function>;
+    l->load_from_file(filenames[i]);
+    maps.push_back(l);
+  }
+
+  Persistence_heat_maps<constant_scaling_function> av;
+  av.compute_average(maps);
+
+  av.print_to_file("average.mps");
+
+  for (size_t i = 0; i != filenames.size(); ++i) {
+    delete maps[i];
+  }
 
-int main( int argc , char** argv )
-{
-	std::cout << "This program computes average persistence landscape of persistence landscapes created based on persistence diagrams provided as an input. Please call this program with the names of files with persistence diagrams \n";
-	std::vector< const char* > filenames;
-	
-	if ( argc == 1 )
-	{
-		std::cout << "No input files given, the program will now terminate \n";
-		return 1;
-	}
-	
-	for ( int i = 1 ; i < argc ; ++i )
-	{
-		filenames.push_back( argv[i] );
-	}
-	
-	std::cout << "Creating persistence landscapes...\n";
-	std::vector< Persistence_heat_maps<constant_scaling_function>* > maps;
-	for ( size_t i = 0 ; i != filenames.size() ; ++i )
-	{
-		Persistence_heat_maps<constant_scaling_function>* l = new Persistence_heat_maps<constant_scaling_function>;
-		l->load_from_file( filenames[i] );
-		maps.push_back( l );
-	}
-	
-	Persistence_heat_maps<constant_scaling_function> av;
-	av.compute_average( maps );
-	
-	av.print_to_file( "average.mps" );
-	
-	for ( size_t i = 0 ; i != filenames.size() ; ++i )
-	{
-		delete maps[i];
-	}
-	
-	std::cout << "Done \n";
-	return 0;
+  std::cout << "Done \n";
+  return 0;
 }
diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp
index 27a7836f..cfa209d1 100644
--- a/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp
+++ b/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp
@@ -20,89 +20,72 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-
 #include <gudhi/Persistence_heat_maps.h>
 
-
-
 using namespace Gudhi;
 using namespace Gudhi::Persistence_representations;
 
 #include <iostream>
 #include <sstream>
 
+int main(int argc, char** argv) {
+  std::cout << "This program compute distance of persistence heat maps stored in a file (the file needs to be created "
+               "beforehand). \n";
+  std::cout << "The first parameter of a program is an integer p. The program compute L^p distance of the two heat "
+               "maps. For L^infty distance choose p = -1. \n";
+  std::cout << "The remaining parameters of this programs are names of files with persistence heat maps.\n";
 
-int main( int argc , char** argv )
-{
-	std::cout << "This program compute distance of persistence heat maps stored in a file (the file needs to be created beforehand). \n";	
-	std::cout << "The first parameter of a program is an integer p. The program compute L^p distance of the two heat maps. For L^infty distance choose p = -1. \n";
-	std::cout << "The remaining parameters of this programs are names of files with persistence heat maps.\n";
-	
-	if ( argc < 3 )
-	{
-		std::cout << "Wrong number of parameters, the program will now terminate \n";
-		return 1;
-	}
-	
-	int pp = atoi( argv[1] );
-	double p = std::numeric_limits<double>::max();
-	if ( pp != -1 )
-	{
-		p = pp;
-	}
-	
+  if (argc < 3) {
+    std::cout << "Wrong number of parameters, the program will now terminate \n";
+    return 1;
+  }
 
-	std::vector< const char* > filenames;
-	for ( int i = 2 ; i < argc ; ++i )
-	{
-		filenames.push_back( argv[i] );
-	}
-	std::vector< Persistence_heat_maps<constant_scaling_function> > maps;
-	maps.reserve( filenames.size() );
-	for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no )
-	{
-		Persistence_heat_maps<constant_scaling_function> l;
-		l.load_from_file( filenames[file_no] );
-		maps.push_back( l );
-	}
-		
-	//and now we will compute the scalar product of landscapes.
-	
-	//first we prepare an array:
-	std::vector< std::vector< double > > distance( filenames.size() );
-	for ( size_t i = 0 ; i != filenames.size() ; ++i )
-	{
-		std::vector< double > v( filenames.size() , 0 );
-		distance[i] = v;
-	}
-	
-	//and now we can compute the distances:
-	for ( size_t i = 0 ; i != filenames.size() ; ++i )
-	{
-		for ( size_t j = i ; j != filenames.size() ; ++j )
-		{
-			distance[i][j] = distance[j][i] = maps[i].distance( maps[j] , p ) ;
-		}
-	}
-	
-	//and now output the result to the screen and a file:
-	std::ofstream out;
-	out.open( "distance" );
-	for ( size_t i = 0 ; i != distance.size() ; ++i )
-	{
-		for ( size_t j = 0 ; j != distance.size() ; ++j )
-		{
-			std::cout << distance[i][j] << " ";
-			out << distance[i][j] << " ";
-		}
-		std::cout << std::endl;
-		out << std::endl;
-	}
-	out.close();
-		
-	return 0;
-}
+  int pp = atoi(argv[1]);
+  double p = std::numeric_limits<double>::max();
+  if (pp != -1) {
+    p = pp;
+  }
 
+  std::vector<const char*> filenames;
+  for (int i = 2; i < argc; ++i) {
+    filenames.push_back(argv[i]);
+  }
+  std::vector<Persistence_heat_maps<constant_scaling_function> > maps;
+  maps.reserve(filenames.size());
+  for (size_t file_no = 0; file_no != filenames.size(); ++file_no) {
+    Persistence_heat_maps<constant_scaling_function> l;
+    l.load_from_file(filenames[file_no]);
+    maps.push_back(l);
+  }
 
+  // and now we will compute the scalar product of landscapes.
 
+  // first we prepare an array:
+  std::vector<std::vector<double> > distance(filenames.size());
+  for (size_t i = 0; i != filenames.size(); ++i) {
+    std::vector<double> v(filenames.size(), 0);
+    distance[i] = v;
+  }
 
+  // and now we can compute the distances:
+  for (size_t i = 0; i != filenames.size(); ++i) {
+    for (size_t j = i; j != filenames.size(); ++j) {
+      distance[i][j] = distance[j][i] = maps[i].distance(maps[j], p);
+    }
+  }
+
+  // and now output the result to the screen and a file:
+  std::ofstream out;
+  out.open("distance");
+  for (size_t i = 0; i != distance.size(); ++i) {
+    for (size_t j = 0; j != distance.size(); ++j) {
+      std::cout << distance[i][j] << " ";
+      out << distance[i][j] << " ";
+    }
+    std::cout << std::endl;
+    out << std::endl;
+  }
+  out.close();
+
+  return 0;
+}
diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp
index edbf16c1..22bb9e2e 100644
--- a/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp
+++ b/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp
@@ -20,70 +20,59 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-
 #include <gudhi/Persistence_heat_maps.h>
 
-
-
 using namespace Gudhi;
 using namespace Gudhi::Persistence_representations;
 
 #include <iostream>
 #include <sstream>
 
+int main(int argc, char** argv) {
+  std::cout << "This program compute scalar product of persistence landscapes stored in a file (the file needs to be "
+               "created beforehand). \n";
+  std::cout << "The parameters of this programs are names of files with persistence landscapes.\n";
+
+  std::vector<const char*> filenames;
+  for (int i = 1; i < argc; ++i) {
+    filenames.push_back(argv[i]);
+  }
+  std::vector<Persistence_heat_maps<constant_scaling_function> > maps;
+  maps.reserve(filenames.size());
+  for (size_t file_no = 0; file_no != filenames.size(); ++file_no) {
+    Persistence_heat_maps<constant_scaling_function> l;
+    l.load_from_file(filenames[file_no]);
+    maps.push_back(l);
+  }
+
+  // and now we will compute the scalar product of landscapes.
+
+  // first we prepare an array:
+  std::vector<std::vector<double> > scalar_product(filenames.size());
+  for (size_t i = 0; i != filenames.size(); ++i) {
+    std::vector<double> v(filenames.size(), 0);
+    scalar_product[i] = v;
+  }
+
+  // and now we can compute the scalar product:
+  for (size_t i = 0; i != maps.size(); ++i) {
+    for (size_t j = i; j != maps.size(); ++j) {
+      scalar_product[i][j] = scalar_product[j][i] = maps[i].compute_scalar_product(maps[j]);
+    }
+  }
 
-int main( int argc , char** argv )
-{
-	std::cout << "This program compute scalar product of persistence landscapes stored in a file (the file needs to be created beforehand). \n";	
-	std::cout << "The parameters of this programs are names of files with persistence landscapes.\n";
+  // and now output the result to the screen and a file:
+  std::ofstream out;
+  out.open("scalar_product");
+  for (size_t i = 0; i != scalar_product.size(); ++i) {
+    for (size_t j = 0; j != scalar_product.size(); ++j) {
+      std::cout << scalar_product[i][j] << " ";
+      out << scalar_product[i][j] << " ";
+    }
+    std::cout << std::endl;
+    out << std::endl;
+  }
+  out.close();
 
-	std::vector< const char* > filenames;
-	for ( int i = 1 ; i < argc ; ++i )
-	{
-		filenames.push_back( argv[i] );
-	}
-	std::vector< Persistence_heat_maps<constant_scaling_function> > maps;
-	maps.reserve( filenames.size() );
-	for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no )
-	{
-		Persistence_heat_maps<constant_scaling_function> l;
-		l.load_from_file( filenames[file_no] );
-		maps.push_back( l );
-	}
-		
-	//and now we will compute the scalar product of landscapes.
-	
-	//first we prepare an array:
-	std::vector< std::vector< double > > scalar_product( filenames.size() );
-	for ( size_t i = 0 ; i != filenames.size() ; ++i )
-	{
-		std::vector< double > v( filenames.size() , 0 );
-		scalar_product[i] = v;
-	}
-	
-	//and now we can compute the scalar product:
-	for ( size_t i = 0 ; i != maps.size() ; ++i )
-	{
-		for ( size_t j = i ; j != maps.size() ; ++j )
-		{
-			scalar_product[i][j] = scalar_product[j][i] = maps[i].compute_scalar_product( maps[j] ) ;
-		}
-	}
-	
-	//and now output the result to the screen and a file:
-	std::ofstream out;
-	out.open( "scalar_product" );
-	for ( size_t i = 0 ; i != scalar_product.size() ; ++i )
-	{
-		for ( size_t j = 0 ; j != scalar_product.size() ; ++j )
-		{
-			std::cout << scalar_product[i][j] << " ";
-			out << scalar_product[i][j] << " ";
-		}
-		std::cout << std::endl;
-		out << std::endl;
-	}
-	out.close();
-		
-	return 0;
+  return 0;
 }
diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp
index f755e9a6..942246a4 100644
--- a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp
+++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp
@@ -1,88 +1,82 @@
-	/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Pawel Dlotko
- *
- *    Copyright (C) 2015  INRIA (France)
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-
+/*    This file is part of the Gudhi Library. The Gudhi library
+*    (Geometric Understanding in Higher Dimensions) is a generic C++
+*    library for computational topology.
+*
+*    Author(s):       Pawel Dlotko
+*
+*    Copyright (C) 2015  INRIA (France)
+*
+*    This program is free software: you can redistribute it and/or modify
+*    it under the terms of the GNU General Public License as published by
+*    the Free Software Foundation, either version 3 of the License, or
+*    (at your option) any later version.
+*
+*    This program is distributed in the hope that it will be useful,
+*    but WITHOUT ANY WARRANTY; without even the implied warranty of
+*    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+*    GNU General Public License for more details.
+*
+*    You should have received a copy of the GNU General Public License
+*    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
 
 #include <gudhi/Persistence_heat_maps.h>
 
-
-
 using namespace Gudhi;
 using namespace Gudhi::Persistence_representations;
 
 #include <iostream>
 #include <sstream>
 
+int main(int argc, char** argv) {
+  std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are "
+               "weighted by the arc tangential of their persistence.\n";
+  std::cout << "The first parameter of a program is an integer, a size of a grid.\n";
+  std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed "
+               "based on the data, set them both to -1 \n";
+  std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number "
+               "of pixels \n";
+  std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the "
+               "persistence heat maps.";
+  std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the "
+               "procedure please provide the dimension of persistence you want to use.";
+  std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1."
+            << std::endl;
+  std::cout << "The remaining parameters are the names of files with persistence diagrams. \n";
+
+  if (argc < 5) {
+    std::cout << "Wrong parameter list, the program will now terminate \n";
+    return 1;
+  }
+
+  size_t size_of_grid = (size_t)atoi(argv[1]);
+  double min_ = atof(argv[2]);
+  double max_ = atof(argv[3]);
+  size_t stdiv = atof(argv[4]);
+
+  unsigned dimension = std::numeric_limits<unsigned>::max();
+  int dim = atoi(argv[5]);
+  if (dim >= 0) {
+    dimension = (unsigned)dim;
+  }
 
+  std::vector<const char*> filenames;
+  for (int i = 6; i < argc; ++i) {
+    filenames.push_back(argv[i]);
+  }
 
-int main( int argc , char** argv )
-{
-	std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are weighted by the arc tangential of their persistence.\n";
-	std::cout << "The first parameter of a program is an integer, a size of a grid.\n";
-	std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed based on the data, set them both to -1 \n";
-	std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number of pixels \n";
-	std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the persistence heat maps.";
-	std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the procedure please provide the dimension of persistence you want to use.";
-	std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." << std::endl;		
-	std::cout << "The remaining parameters are the names of files with persistence diagrams. \n";
+  std::cout << "Creating persistence heat maps...\n";
+  std::vector<std::vector<double> > filter = create_Gaussian_filter(stdiv, 1);
 
-	if ( argc < 5 )
-	{
-		std::cout << "Wrong parameter list, the program will now terminate \n";
-		return 1;
-	}
-	
-	size_t size_of_grid = (size_t)atoi( argv[1] );
-	double min_ = atof( argv[2] );
-	double max_ = atof( argv[3] );
-	size_t stdiv = atof( argv[4] );
-	
-	unsigned dimension = std::numeric_limits<unsigned>::max();
-	int dim = atoi( argv[5] );	 
-	if ( dim >= 0 )
-	{
-		dimension = (unsigned)dim;
-	}
-	
-	std::vector< const char* > filenames;
-	for ( int i = 6 ; i < argc ; ++i )
-	{
-		filenames.push_back( argv[i] );
-	}
+  for (size_t i = 0; i != filenames.size(); ++i) {
+    std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl;
+    Persistence_heat_maps<arc_tan_of_persistence_of_point> l(filenames[i], filter, false, size_of_grid, min_, max_,
+                                                             dimension);
 
-	
-	
-	std::cout << "Creating persistence heat maps...\n";	
-	std::vector< std::vector<double> > filter = create_Gaussian_filter(stdiv,1);
-	
-	for ( size_t i = 0 ; i != filenames.size() ; ++i )
-	{		
-		std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl;
-		Persistence_heat_maps<arc_tan_of_persistence_of_point> l( filenames[i] , filter, false , size_of_grid , min_ , max_ , dimension );		
-		
-		std::stringstream ss;
-		ss << filenames[i] << ".mps";
-		l.print_to_file( ss.str().c_str() );
-	}
-	std::cout << "Done \n";
-	return 0;
+    std::stringstream ss;
+    ss << filenames[i] << ".mps";
+    l.print_to_file(ss.str().c_str());
+  }
+  std::cout << "Done \n";
+  return 0;
 }
diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp
index 732b3768..fce874bd 100644
--- a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp
+++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp
@@ -20,68 +20,63 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-
 #include <gudhi/Persistence_heat_maps.h>
 
-
-
 using namespace Gudhi;
 using namespace Gudhi::Persistence_representations;
 
 #include <iostream>
 #include <sstream>
 
+int main(int argc, char** argv) {
+  std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are "
+               "weighted by the distance of a center from the diagonal.\n";
+  std::cout << "The first parameter of a program is an integer, a size of a grid.\n";
+  std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed "
+               "based on the data, set them both to -1 \n";
+  std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number "
+               "of pixels \n";
+  std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the "
+               "persistence heat maps.";
+  std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the "
+               "procedure please provide the dimension of persistence you want to use.";
+  std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1."
+            << std::endl;
+  std::cout << "The remaining parameters are the names of files with persistence diagrams. \n";
+
+  if (argc < 5) {
+    std::cout << "Wrong parameter list, the program will now terminate \n";
+    return 1;
+  }
+
+  size_t size_of_grid = (size_t)atoi(argv[1]);
+  double min_ = atof(argv[2]);
+  double max_ = atof(argv[3]);
+  size_t stdiv = atof(argv[4]);
+
+  unsigned dimension = std::numeric_limits<unsigned>::max();
+  int dim = atoi(argv[5]);
+  if (dim >= 0) {
+    dimension = (unsigned)dim;
+  }
+
+  std::vector<const char*> filenames;
+  for (int i = 6; i != argc; ++i) {
+    filenames.push_back(argv[i]);
+  }
 
+  std::cout << "Creating persistence heat maps...\n";
+  std::vector<std::vector<double> > filter = create_Gaussian_filter(stdiv, 1);
 
-int main( int argc , char** argv )
-{
-	std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are weighted by the distance of a center from the diagonal.\n";
-	std::cout << "The first parameter of a program is an integer, a size of a grid.\n";
-	std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed based on the data, set them both to -1 \n";
-	std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number of pixels \n";
-	std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the persistence heat maps.";
-	std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the procedure please provide the dimension of persistence you want to use.";
-	std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." << std::endl;			
-	std::cout << "The remaining parameters are the names of files with persistence diagrams. \n";
-	
-	if ( argc < 5 )
-	{
-		std::cout << "Wrong parameter list, the program will now terminate \n";
-		return 1;
-	}
-	
-	size_t size_of_grid = (size_t)atoi( argv[1] );
-	double min_ = atof( argv[2] );
-	double max_ = atof( argv[3] );
-	size_t stdiv = atof( argv[4] );
-	
-	unsigned dimension = std::numeric_limits<unsigned>::max();
-	int dim = atoi( argv[5] );	 
-	if ( dim >= 0 )
-	{
-		dimension = (unsigned)dim;
-	}
-	
-	std::vector< const char* > filenames;
-	for ( int i = 6 ; i != argc ; ++i )
-	{
-		filenames.push_back( argv[i] );
-	}
+  for (size_t i = 0; i != filenames.size(); ++i) {
+    std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl;
+    Persistence_heat_maps<distance_from_diagonal_scaling> l(filenames[i], filter, false, size_of_grid, min_, max_,
+                                                            dimension);
 
-	
-	
-	std::cout << "Creating persistence heat maps...\n";	
-	std::vector< std::vector<double> > filter = create_Gaussian_filter(stdiv,1);
-	
-	for ( size_t i = 0 ; i != filenames.size() ; ++i )
-	{		
-		std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl;
-		Persistence_heat_maps<distance_from_diagonal_scaling> l( filenames[i] , filter , false ,  size_of_grid , min_ , max_ , dimension );
-		
-		std::stringstream ss;
-		ss << filenames[i] << ".mps";
-		l.print_to_file( ss.str().c_str() );
-	}
-	std::cout << "Done \n";
-	return 0;
+    std::stringstream ss;
+    ss << filenames[i] << ".mps";
+    l.print_to_file(ss.str().c_str());
+  }
+  std::cout << "Done \n";
+  return 0;
 }
diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp
index 58406d08..92375387 100644
--- a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp
+++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp
@@ -20,66 +20,63 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-
 #include <gudhi/Persistence_heat_maps.h>
 
-
-
 using namespace Gudhi;
 using namespace Gudhi::Persistence_representations;
 
 #include <iostream>
 #include <sstream>
 
+int main(int argc, char** argv) {
+  std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are "
+               "weighted by the square of distance of a center from the diagonal.\n";
+  std::cout << "The first parameter of a program is an integer, a size of a grid.\n";
+  std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed "
+               "based on the data, set them both to -1 \n";
+  std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number "
+               "of pixels \n";
+  std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the "
+               "persistence heat maps.";
+  std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the "
+               "procedure please provide the dimension of persistence you want to use.";
+  std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1."
+            << std::endl;
+  std::cout << "The remaining parameters are the names of files with persistence diagrams. \n";
+
+  if (argc < 5) {
+    std::cout << "Wrong parameter list, the program will now terminate \n";
+    return 1;
+  }
+
+  size_t size_of_grid = (size_t)atoi(argv[1]);
+  double min_ = atof(argv[2]);
+  double max_ = atof(argv[3]);
+  size_t stdiv = atof(argv[4]);
+
+  unsigned dimension = std::numeric_limits<unsigned>::max();
+  int dim = atoi(argv[5]);
+  if (dim >= 0) {
+    dimension = (unsigned)dim;
+  }
 
+  std::vector<const char*> filenames;
+  for (int i = 6; i < argc; ++i) {
+    filenames.push_back(argv[i]);
+  }
 
-int main( int argc , char** argv )
-{
-	std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are weighted by the square of distance of a center from the diagonal.\n";
-	std::cout << "The first parameter of a program is an integer, a size of a grid.\n";
-	std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed based on the data, set them both to -1 \n";
-	std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number of pixels \n";
-	std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the persistence heat maps.";
-	std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the procedure please provide the dimension of persistence you want to use.";
-	std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." << std::endl;				
-	std::cout << "The remaining parameters are the names of files with persistence diagrams. \n";
+  std::cout << "Creating persistence heat maps...\n";
+  std::vector<std::vector<double> > filter = create_Gaussian_filter(stdiv, 1);
 
-	if ( argc < 5 )
-	{
-		std::cout << "Wrong parameter list, the program will now terminate \n";
-		return 1;
-	}
-	
-	size_t size_of_grid = (size_t)atoi( argv[1] );
-	double min_ = atof( argv[2] );
-	double max_ = atof( argv[3] );
-	size_t stdiv = atof( argv[4] );
+  for (size_t i = 0; i != filenames.size(); ++i) {
+    std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl;
+    Persistence_heat_maps<squared_distance_from_diagonal_scaling> l(filenames[i], filter, false, size_of_grid, min_,
+                                                                    max_, dimension);
 
-	unsigned dimension = std::numeric_limits<unsigned>::max();
-	int dim = atoi( argv[5] );	 
-	if ( dim >= 0 )
-	{
-		dimension = (unsigned)dim;
-	}
-	
-	std::vector< const char* > filenames;
-	for ( int i = 6 ; i < argc ; ++i )
-	{
-		filenames.push_back( argv[i] );
-	}
-	
-	std::cout << "Creating persistence heat maps...\n";	
-	std::vector< std::vector<double> > filter = create_Gaussian_filter(stdiv,1);
-	
-	for ( size_t i = 0 ; i != filenames.size() ; ++i )
-	{		
-		std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl;
-		Persistence_heat_maps<squared_distance_from_diagonal_scaling> l( filenames[i] , filter, false , size_of_grid , min_ , max_ , dimension );		
-		
-		std::stringstream ss;
-		ss << filenames[i] << ".mps";
-		l.print_to_file( ss.str().c_str() );
-	}
-	std::cout << "Done \n";
-	return 0;
+    std::stringstream ss;
+    ss << filenames[i] << ".mps";
+    l.print_to_file(ss.str().c_str());
+  }
+  std::cout << "Done \n";
+  return 0;
 }
diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp
index 90b50b0b..3b0fd8ae 100644
--- a/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp
+++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp
@@ -20,65 +20,60 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-
-
 #include <gudhi/Persistence_heat_maps.h>
 
-
-
 using namespace Gudhi;
 using namespace Gudhi::Persistence_representations;
 
 #include <iostream>
 #include <sstream>
 
+int main(int argc, char** argv) {
+  std::cout << "This program creates persistence heat map of diagrams provided as an input.\n";
+  std::cout << "The first parameter of a program is an integer, a size of a grid.\n";
+  std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed "
+               "based on the data, set them both to -1 \n";
+  std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number "
+               "of pixels \n";
+
+  std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the "
+               "persistence heat maps.";
+  std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the "
+               "procedure please provide the dimension of persistence you want to use.";
+  std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1."
+            << std::endl;
+  std::cout << "The remaining parameters are the names of files with persistence diagrams. \n";
+  if (argc < 5) {
+    std::cout << "Wrong parameter list, the program will now terminate \n";
+    return 1;
+  }
+  size_t size_of_grid = (size_t)atoi(argv[1]);
+  double min_ = atof(argv[2]);
+  double max_ = atof(argv[3]);
+  size_t stdiv = atof(argv[4]);
+
+  unsigned dimension = std::numeric_limits<unsigned>::max();
+  int dim = atoi(argv[5]);
+  if (dim >= 0) {
+    dimension = (unsigned)dim;
+  }
+  std::vector<const char*> filenames;
+  for (int i = 6; i < argc; ++i) {
+    filenames.push_back(argv[i]);
+  }
+
+  std::cout << "Creating persistence heat maps...\n";
+  std::vector<std::vector<double> > filter = create_Gaussian_filter(stdiv, 1);
 
+  for (size_t i = 0; i != filenames.size(); ++i) {
+    std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl;
+    Persistence_heat_maps<constant_scaling_function> l(filenames[i], filter, false, size_of_grid, min_, max_,
+                                                       dimension);
 
-int main( int argc , char** argv )
-{
-	std::cout << "This program creates persistence heat map of diagrams provided as an input.\n";
-	std::cout << "The first parameter of a program is an integer, a size of a grid.\n";
-	std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed based on the data, set them both to -1 \n";
-	std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number of pixels \n";
-	
-	std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the persistence heat maps.";
-	std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the procedure please provide the dimension of persistence you want to use.";
-	std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." << std::endl;	
-	std::cout << "The remaining parameters are the names of files with persistence diagrams. \n";
-	if ( argc < 5 )
-	{
-		std::cout << "Wrong parameter list, the program will now terminate \n";
-		return 1;
-	}	
-	size_t size_of_grid = (size_t)atoi( argv[1] );
-	double min_ = atof( argv[2] );
-	double max_ = atof( argv[3] );
-	size_t stdiv = atof( argv[4] );
-	
-	unsigned dimension = std::numeric_limits<unsigned>::max();
-	int dim = atoi( argv[5] );	 
-	if ( dim >= 0 )
-	{
-		dimension = (unsigned)dim;
-	}
-	std::vector< const char* > filenames;
-	for ( int i = 6 ; i < argc ; ++i )
-	{
-		filenames.push_back( argv[i] );
-	}
-	
-	std::cout << "Creating persistence heat maps...\n";	
-	std::vector< std::vector<double> > filter = create_Gaussian_filter(stdiv,1);
-	
-	for ( size_t i = 0 ; i != filenames.size() ; ++i )
-	{		
-		std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl;
-		Persistence_heat_maps<constant_scaling_function> l( filenames[i] , filter, false , size_of_grid , min_ , max_ , dimension );		
-		
-		std::stringstream ss;
-		ss << filenames[i] << ".mps";
-		l.print_to_file( ss.str().c_str() );
-	}
-	std::cout << "Done \n";
-	return 0;
+    std::stringstream ss;
+    ss << filenames[i] << ".mps";
+    l.print_to_file(ss.str().c_str());
+  }
+  std::cout << "Done \n";
+  return 0;
 }
diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp
index 6a07bf19..6b464378 100644
--- a/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp
+++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp
@@ -22,63 +22,59 @@
 
 #include <gudhi/PSSK.h>
 
-
-
 using namespace Gudhi;
 using namespace Gudhi::Persistence_representations;
 
 #include <iostream>
 #include <sstream>
 
+int main(int argc, char** argv) {
+  std::cout << "This program creates PSSK of diagrams provided as an input.\n";
+  std::cout << "The first parameter of a program is an integer, a size of a grid.\n";
+  std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed "
+               "based on the data, set them both to -1 \n";
+  std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number "
+               "of pixels \n";
+  std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the "
+               "persistence heat maps.";
+  std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the "
+               "procedure please provide the dimension of persistence you want to use.";
+  std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1."
+            << std::endl;
+  std::cout << "The remaining parameters are the names of files with persistence diagrams. \n";
+
+  if (argc < 5) {
+    std::cout << "Wrong parameter list, the program will now terminate \n";
+    return 1;
+  }
+
+  size_t size_of_grid = (size_t)atoi(argv[1]);
+  double min_ = atof(argv[2]);
+  double max_ = atof(argv[3]);
+  size_t stdiv = atof(argv[4]);
+
+  unsigned dimension = std::numeric_limits<unsigned>::max();
+  int dim = atoi(argv[5]);
+  if (dim >= 0) {
+    dimension = (unsigned)dim;
+  }
+
+  std::vector<const char*> filenames;
+  for (int i = 6; i < argc; ++i) {
+    filenames.push_back(argv[i]);
+  }
 
+  std::cout << "Creating persistence heat maps...\n";
+  std::vector<std::vector<double> > filter = create_Gaussian_filter(stdiv, 1);
 
-int main( int argc , char** argv )
-{
-	std::cout << "This program creates PSSK of diagrams provided as an input.\n";
-	std::cout << "The first parameter of a program is an integer, a size of a grid.\n";
-	std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed based on the data, set them both to -1 \n";
-	std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number of pixels \n";
-	std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the persistence heat maps.";
-	std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the procedure please provide the dimension of persistence you want to use.";
-	std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." << std::endl;					
-	std::cout << "The remaining parameters are the names of files with persistence diagrams. \n";
+  for (size_t i = 0; i != filenames.size(); ++i) {
+    std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl;
+    PSSK l(filenames[i], filter, size_of_grid, min_, max_, dimension);
 
-	if ( argc < 5 )
-	{
-		std::cout << "Wrong parameter list, the program will now terminate \n";
-		return 1;
-	}
-	
-	size_t size_of_grid = (size_t)atoi( argv[1] );
-	double min_ = atof( argv[2] );
-	double max_ = atof( argv[3] );
-	size_t stdiv = atof( argv[4] );
-	
-	unsigned dimension = std::numeric_limits<unsigned>::max();
-	int dim = atoi( argv[5] );	 
-	if ( dim >= 0 )
-	{
-		dimension = (unsigned)dim;
-	}
-	
-	std::vector< const char* > filenames;
-	for ( int i = 6 ; i < argc ; ++i )
-	{
-		filenames.push_back( argv[i] );
-	}	
-	
-	std::cout << "Creating persistence heat maps...\n";	
-	std::vector< std::vector<double> > filter = create_Gaussian_filter(stdiv,1);	
-	
-	for ( size_t i = 0 ; i != filenames.size() ; ++i )
-	{		
-		std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl;
-		PSSK l( filenames[i] , filter , size_of_grid , min_ , max_ , dimension );		
-		
-		std::stringstream ss;
-		ss << filenames[i] << ".pssk";
-		l.print_to_file( ss.str().c_str() );
-	}
-	std::cout << "Done \n";
-	return 0;
+    std::stringstream ss;
+    ss << filenames[i] << ".pssk";
+    l.print_to_file(ss.str().c_str());
+  }
+  std::cout << "Done \n";
+  return 0;
 }
diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp
index 7aedfbb1..59f12a7d 100644
--- a/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp
+++ b/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp
@@ -20,23 +20,19 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-
 #include <gudhi/Persistence_heat_maps.h>
 
-
-
 using namespace Gudhi;
 using namespace Gudhi::Persistence_representations;
 
 #include <iostream>
 #include <sstream>
 
-
-int main( int argc , char** argv )
-{
-	std::cout << "This program plot persistence landscape stored in a file (the file needs to be created beforehand). Please call the code with the name of a landscape file \n";	
-	Persistence_heat_maps<constant_scaling_function> l;
-	l.load_from_file( argv[1] );		
-	l.plot( argv[1] );	
-	return 0;
+int main(int argc, char** argv) {
+  std::cout << "This program plot persistence landscape stored in a file (the file needs to be created beforehand). "
+               "Please call the code with the name of a landscape file \n";
+  Persistence_heat_maps<constant_scaling_function> l;
+  l.load_from_file(argv[1]);
+  l.plot(argv[1]);
+  return 0;
 }