Fix cpplint on examples.

Bug fix on persistence_from_simple_simplex_tree.
Add persistence examples tests.



git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@843 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 9b7b73abb4a5d6bb110376deb689247bfdae035c

1 files changed, 121 insertions, 118 deletions

diff --git a/src/Persistent_cohomology/example/persistence_from_file.cpp b/src/Persistent_cohomology/example/persistence_from_file.cpp
index e886aea7..8eb8d0f3 100644
--- a/src/Persistent_cohomology/example/persistence_from_file.cpp
+++ b/src/Persistent_cohomology/example/persistence_from_file.cpp
@@ -1,141 +1,144 @@
- /*    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):       Vincent Rouvreau
-  *
-  *    Copyright (C) 2014  INRIA Saclay (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/reader_utils.h"
-#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/distance_functions.h"
-#include "gudhi/Simplex_tree.h"
-#include "gudhi/Persistent_cohomology.h"
+/*    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):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2014  INRIA Saclay (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/reader_utils.h>
+#include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/distance_functions.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
 
 #include <boost/program_options.hpp>
 
+#include <string>
+
 using namespace Gudhi;
 using namespace Gudhi::persistent_cohomology;
 
-typedef int        Vertex_handle;
-typedef double     Filtration_value;
-
-void program_options( int argc, char *   argv[] 
-                    , std::string      & simplex_tree_file
-                    , std::string      & output_file
-                    , int              & p
-                    , Filtration_value & min_persistence );
-
-int main (int argc, char * argv[]) 
-{
-	std::string      simplex_tree_file;
-	std::string      output_file  ;
-	int              p         ;
-	Filtration_value min_persistence;
-
-	program_options(argc,argv,simplex_tree_file,output_file,p,min_persistence);
-
-	std::cout << "Simplex_tree from file=" << simplex_tree_file.c_str() << " - output_file=" << output_file.c_str() << std::endl;
-	std::cout << "     - p=" << p << " - min_persistence=" << min_persistence << std::endl;
-
-	// Construct the Rips complex in a Simplex Tree
-	Simplex_tree<> simplex_tree;
-
-	std::ifstream simplex_tree_stream(simplex_tree_file);
-	simplex_tree_stream >> simplex_tree;
-
-	std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices" << std::endl;
-	std::cout << "   - dimension " << simplex_tree.dimension() << "   - filtration " << simplex_tree.filtration() << std::endl;
-
-	/*
-	std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
-	for( auto f_simplex : simplex_tree.filtration_simplex_range() )
-	{ std::cout << "   " << "[" << simplex_tree.filtration(f_simplex) << "] ";
-	for( auto vertex : simplex_tree.simplex_vertex_range(f_simplex) )
-	{ std::cout << vertex << " "; }
-	std::cout << std::endl;
-	}*/
-
-	// Sort the simplices in the order of the filtration
-	simplex_tree.initialize_filtration();
-
-	// Compute the persistence diagram of the complex
-	Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh( simplex_tree );
-	pcoh.init_coefficients( p ); //initilizes the coefficient field for homology
-
-	pcoh.compute_persistent_cohomology( min_persistence );
-
-	// Output the diagram in output_file
-	if(output_file.empty()) {  pcoh.output_diagram(); }
-	else {
-		std::ofstream out(output_file);
-		pcoh.output_diagram(out);
-		out.close(); }
+typedef int Vertex_handle;
+typedef double Filtration_value;
+
+void program_options(int argc, char * argv[]
+                     , std::string & simplex_tree_file
+                     , std::string & output_file
+                     , int & p
+                     , Filtration_value & min_persistence);
+
+int main(int argc, char * argv[]) {
+  std::string simplex_tree_file;
+  std::string output_file;
+  int p;
+  Filtration_value min_persistence;
+
+  program_options(argc, argv, simplex_tree_file, output_file, p, min_persistence);
+
+  std::cout << "Simplex_tree from file=" << simplex_tree_file.c_str() << " - output_file=" << output_file.c_str()
+      << std::endl;
+  std::cout << "     - p=" << p << " - min_persistence=" << min_persistence << std::endl;
+
+  // Construct the Rips complex in a Simplex Tree
+  Simplex_tree<> simplex_tree;
+
+  std::ifstream simplex_tree_stream(simplex_tree_file);
+  simplex_tree_stream >> simplex_tree;
+
+  std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices" << std::endl;
+  std::cout << "   - dimension " << simplex_tree.dimension() << "   - filtration " << simplex_tree.filtration()
+      << std::endl;
+
+  /*
+  std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
+  for( auto f_simplex : simplex_tree.filtration_simplex_range() )
+  { std::cout << "   " << "[" << simplex_tree.filtration(f_simplex) << "] ";
+  for( auto vertex : simplex_tree.simplex_vertex_range(f_simplex) )
+  { std::cout << vertex << " "; }
+  std::cout << std::endl;
+  }*/
+
+  // Sort the simplices in the order of the filtration
+  simplex_tree.initialize_filtration();
+
+  // Compute the persistence diagram of the complex
+  Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh(simplex_tree);
+  // initializes the coefficient field for homology
+  pcoh.init_coefficients(p);
+
+  pcoh.compute_persistent_cohomology(min_persistence);
+
+  // Output the diagram in output_file
+  if (output_file.empty()) {
+    pcoh.output_diagram();
+  } else {
+    std::ofstream out(output_file);
+    pcoh.output_diagram(out);
+    out.close();
+  }
 
-	return 0;
+  return 0;
 }
 
-
-
-void program_options( int argc, char *   argv[] 
-                    , std::string      & simplex_tree_file
-                    , std::string      & output_file
-                    , int              & p
-                    , Filtration_value & min_persistence )
-{
+void program_options(int argc, char * argv[]
+                     , std::string & simplex_tree_file
+                     , std::string & output_file
+                     , int & p
+                     , Filtration_value & min_persistence) {
   namespace po = boost::program_options;
-  po::options_description     hidden("Hidden options");
+  po::options_description hidden("Hidden options");
   hidden.add_options()
-        ("input-file",  po::value<std::string>(&simplex_tree_file),
-          "Name of file containing a simplex set. Format is one simplex per line (cf. reader_utils.h - read_simplex):   Dim1 X11 X12 ... X1d Fil1  ");
-    
+      ("input-file", po::value<std::string>(&simplex_tree_file),
+       "Name of file containing a simplex set. Format is one simplex per line (cf. reader_utils.h - read_simplex): Dim1 X11 X12 ... X1d Fil1  ");
+
   po::options_description visible("Allowed options", 100);
   visible.add_options()
-        ("help,h",          "produce help message")
-        ("output-file,o", po::value<std::string>(&output_file)->default_value(std::string()),
-                   "Name of file in which the persistence diagram is written. Default print in std::cout")
-        ("field-charac,p", po::value<int>(&p)->default_value(11),                  
-                  "Characteristic p of the coefficient field Z/pZ for computing homology.")
-        ("min-persistence,m", po::value<Filtration_value>(&min_persistence), 
-                  "Minimal lifetime of homology feature to be recorded. Default is 0");
+      ("help,h", "produce help message")
+      ("output-file,o", po::value<std::string>(&output_file)->default_value(std::string()),
+       "Name of file in which the persistence diagram is written. Default print in std::cout")
+      ("field-charac,p", po::value<int>(&p)->default_value(11),
+       "Characteristic p of the coefficient field Z/pZ for computing homology.")
+      ("min-persistence,m", po::value<Filtration_value>(&min_persistence),
+       "Minimal lifetime of homology feature to be recorded. Default is 0");
 
   po::positional_options_description pos;
   pos.add("input-file", 1);
-  
-  po::options_description all; all.add(visible).add(hidden);
+
+  po::options_description all;
+  all.add(visible).add(hidden);
 
   po::variables_map vm;
   po::store(po::command_line_parser(argc, argv).
-                options(all).positional(pos).run(), vm);
+            options(all).positional(pos).run(), vm);
   po::notify(vm);
 
-  if (vm.count("help") || !vm.count("input-file"))
-  { 
-      std::cout << std::endl;
-      std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
-      std::cout << "of a Rips complex defined on a set of input points.\n \n";
-      std::cout << "The output diagram contains one bar per line, written with the convention: \n";
-      std::cout << "   p   dim b d \n";
-      std::cout << "where dim is the dimension of the homological feature,\n";
-      std::cout << "b and d are respectively the birth and death of the feature and \n";
-      std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
-
-      std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
-      std::cout << visible << std::endl; 
-      std::abort();
+  if (vm.count("help") || !vm.count("input-file")) {
+    std::cout << std::endl;
+    std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
+    std::cout << "of a Rips complex defined on a set of input points.\n \n";
+    std::cout << "The output diagram contains one bar per line, written with the convention: \n";
+    std::cout << "   p   dim b d \n";
+    std::cout << "where dim is the dimension of the homological feature,\n";
+    std::cout << "b and d are respectively the birth and death of the feature and \n";
+    std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
+
+    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
+    std::cout << visible << std::endl;
+    std::abort();
   }
 }