Merge branch bottleneckDistance on a up-to-date branch

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1492 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: bccdeaf8456b7b88ad2da71205dbb4c5d08a53ee

2 files changed, 90 insertions, 0 deletions

diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt
new file mode 100644
index 00000000..adf298aa
--- /dev/null
+++ b/src/Bottleneck_distance/example/CMakeLists.txt
@@ -0,0 +1,12 @@
+cmake_minimum_required(VERSION 2.6)
+project(Bottleneck_distance_examples)
+
+# need CGAL 4.6
+# cmake -DCGAL_DIR=~/workspace/CGAL-4.6-beta1 ../../..
+if(CGAL_FOUND)
+  if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
+    if (EIGEN3_FOUND)
+      add_executable (bottleneck_example bottleneck_example.cpp)
+    endif()
+  endif ()
+endif()
diff --git a/src/Bottleneck_distance/example/bottleneck_example.cpp b/src/Bottleneck_distance/example/bottleneck_example.cpp
new file mode 100644
index 00000000..472c5c84
--- /dev/null
+++ b/src/Bottleneck_distance/example/bottleneck_example.cpp
@@ -0,0 +1,78 @@
+/*    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):       Francois Godi, small modifications by Pawel Dlotko
+ *
+ *    Copyright (C) 2015  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/>.
+ */
+
+#define CGAL_HAS_THREADS
+
+#include <gudhi/Graph_matching.h>
+#include <iostream>
+#include <fstream>
+#include <sstream>
+#include <string>
+
+using namespace std;
+
+//PD: I am using this type of procedures a lot in Gudhi stat. We should make one for all at some point.
+std::vector< std::pair<double, double> > read_diagram_from_file( const char* filename )
+{
+    ifstream in;
+    in.open( filename );
+    std::vector< std::pair<double, double> > result;
+    if ( !in.is_open() )
+    {
+        std::cerr << "File : " << filename << " do not exist. The program will now terminate \n";
+        throw "File do not exist \n";
+    }
+
+    std::string line;
+    while (!in.eof())
+    {
+        getline(in,line);
+        if ( line.length() != 0 )
+        {
+            std::stringstream lineSS;
+            lineSS << line;
+            double beginn, endd;
+            lineSS >> beginn;
+            lineSS >> endd;
+            result.push_back( std::make_pair( beginn , endd ) );
+        }
+    }
+    in.close();
+    return result;
+}//read_diagram_from_file
+
+int main( int argc , char** argv )
+{
+  if ( argc < 3 )
+  {
+      std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck distance (set by default to zero). The program will now terminate \n";
+  }
+  std::vector< std::pair< double , double > > diag1 = read_diagram_from_file( argv[1] );
+  std::vector< std::pair< double , double > > diag2 = read_diagram_from_file( argv[2] );
+  double tolerance = 0;
+  if ( argc == 4 )
+  {
+      tolerance = atof( argv[3] );
+  }
+  double b = Gudhi::Bottleneck_distance::compute(diag1, diag2, tolerance);
+  std::cout << "The distance between the diagrams is : " << b << ". The tolerace is : " << tolerance << std::endl;
+}