Added the file for knn landmarks (no CGAL include yet). New algorithm for landmark selection: now 10 times faster!

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/witness@580 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 9de270bd67ac33fd1079de7692dd8974441db606

4 files changed, 172 insertions, 7 deletions

diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt
index 14d23551..fa594de7 100644
--- a/src/Witness_complex/example/CMakeLists.txt
+++ b/src/Witness_complex/example/CMakeLists.txt
@@ -14,9 +14,9 @@ project(GUDHIWitnessComplex)
    add_executable ( simple_witness_complex simple_witness_complex.cpp )
    add_test(simple_witness_complex ${CMAKE_CURRENT_BINARY_DIR}/simple_witness_complex)
 
-   #add_executable( witness_complex_from_file witness_complex_from_file.cpp )
+   add_executable( witness_complex_from_file witness_complex_from_file.cpp )
    #target_link_libraries(witness_complex_from_file ${EIGEN3_LIBRARIES} ${CGAL_LIBRARY})
-   #add_test( witness_complex_from_bunny &{CMAKE_CURRENT_BINARY_DIR}/witness_complex_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 100)   
+   add_test( witness_complex_from_bunny &{CMAKE_CURRENT_BINARY_DIR}/witness_complex_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 100)   
    
    add_executable( witness_complex_from_off witness_complex_from_off.cpp )
    
@@ -35,7 +35,7 @@ if(GMP_FOUND AND CGAL_FOUND)
    INCLUDE_DIRECTORIES(${EIGEN3_INCLUDE_DIRS})
    INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
    INCLUDE_DIRECTORIES(${CGAL_INCLUDE_DIRS})
-   add_executable (witness_complex_from_file witness_complex_from_file.cpp )
-   target_link_libraries(witness_complex_from_file ${GMP_LIBRARIES} ${EIGEN3_LIBRARIES} ${CGAL_LIBRARY})
-   add_test(witness_complex_from_file ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 100)
+   add_executable (witness_complex_knn_landmarks witness_complex_knn_landmarks.cpp )
+   target_link_libraries(witness_complex_knn_landmarks ${EIGEN3_LIBRARIES} ${CGAL_LIBRARY})
+   add_test(witness_complex_knn_landmarks ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_knn_landmarks ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 100)
 endif()
diff --git a/src/Witness_complex/example/witness_complex_from_file.cpp b/src/Witness_complex/example/witness_complex_from_file.cpp
index cf09899b..b842574b 100644
--- a/src/Witness_complex/example/witness_complex_from_file.cpp
+++ b/src/Witness_complex/example/witness_complex_from_file.cpp
@@ -109,9 +109,11 @@ int main (int argc, char * const argv[])
   witnessComplex.setNbL(nbL);
   //  witnessComplex.witness_complex_from_points(point_vector);
   std::vector<std::vector< int > > WL;
+  std::set<int> L;
   start = clock();
   //witnessComplex.landmark_choice_by_furthest_points(point_vector, point_vector.size(), WL);
-  witnessComplex.landmark_choice_by_random_points(point_vector, point_vector.size(), WL);
+  witnessComplex.landmark_choice_by_random_points(point_vector, point_vector.size(), L);
+  witnessComplex.nearest_landmarks(point_vector,L,WL);
   end = clock();
   std::cout << "Landmark choice took "
             << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
diff --git a/src/Witness_complex/example/witness_complex_from_off.cpp b/src/Witness_complex/example/witness_complex_from_off.cpp
index 04d4e601..948f09a8 100644
--- a/src/Witness_complex/example/witness_complex_from_off.cpp
+++ b/src/Witness_complex/example/witness_complex_from_off.cpp
@@ -148,9 +148,11 @@ int main (int argc, char * const argv[])
   witnessComplex.setNbL(nbL);
   //  witnessComplex.witness_complex_from_points(point_vector);
   std::vector<std::vector< int > > WL;
+  std::set<int> L;
   start = clock();
   //witnessComplex.landmark_choice_by_furthest_points(point_vector, point_vector.size(), WL);
-  witnessComplex.landmark_choice_by_random_points(point_vector, point_vector.size(), WL);
+  witnessComplex.landmark_choice_by_random_points(point_vector, point_vector.size(), L);
+  witnessComplex.nearest_landmarks(point_vector,L,WL);
   end = clock();
   std::cout << "Landmark choice took "
             << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
diff --git a/src/Witness_complex/example/witness_complex_knn_landmarks.cpp b/src/Witness_complex/example/witness_complex_knn_landmarks.cpp
new file mode 100644
index 00000000..2003f218
--- /dev/null
+++ b/src/Witness_complex/example/witness_complex_knn_landmarks.cpp
@@ -0,0 +1,161 @@
+/*    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):       Siargey Kachanovich
+ *
+ *    Copyright (C) 2015  INRIA Sophia Antipolis-Méditerranée (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 <iostream>
+#include <fstream>
+#include <ctime>
+
+#include <sys/types.h>
+#include <sys/stat.h>
+//#include <stdlib.h>
+
+//#include "gudhi/graph_simplicial_complex.h"
+#include "gudhi/Witness_complex.h"
+#include "gudhi/reader_utils.h"
+//#include <boost/filesystem.hpp>
+
+//#include <CGAL/Delaunay_triangulation.h>
+//#include <CGAL/Epick_d.h>
+#include <CGAL/K_neighbor_search.h>
+
+using namespace Gudhi;
+//using namespace boost::filesystem;
+
+typedef std::vector< Vertex_handle > typeVectorVertex;
+typedef std::vector< std::vector <double> > Point_Vector;
+//typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
+//typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
+
+
+/**
+ * \brief Customized version of read_points
+ * which takes into account a possible nbP first line
+ *
+ */
+inline void
+read_points_cust ( std::string file_name , std::vector< std::vector< double > > & points)
+{  
+  std::ifstream in_file (file_name.c_str(),std::ios::in);
+  if(!in_file.is_open())
+    {
+      std::cerr << "Unable to open file " << file_name << std::endl;
+      return;
+    }
+  std::string line;
+  double x;
+  while( getline ( in_file , line ) )
+    {
+      std::vector< double > point;
+      std::istringstream iss( line );
+      while(iss >> x) { point.push_back(x); }
+      if (point.size() != 1)
+        points.push_back(point);
+    }
+  in_file.close();
+}
+
+void write_wl( std::string file_name, std::vector< std::vector <int> > & WL)
+{
+  std::ofstream ofs (file_name, std::ofstream::out);
+  for (auto w : WL)
+    {
+      for (auto l: w)
+        ofs << l << " ";
+      ofs << "\n";
+    }
+  ofs.close();
+}
+
+int main (int argc, char * const argv[])
+{
+  if (argc != 3)
+    {
+      std::cerr << "Usage: " << argv[0]
+                << " path_to_point_file nbL \n";
+      return 0;
+    }
+  /*
+  boost::filesystem::path p;
+
+  for (; argc > 2; --argc, ++argv)
+    p /= argv[1];
+  */
+  std::string file_name   = argv[1];
+  int nbL       = atoi(argv[2]);
+  
+  clock_t start, end;
+  //Construct the Simplex Tree
+  Witness_complex<> witnessComplex;
+ 
+  std::cout << "Let the carnage begin!\n";
+  Point_Vector point_vector;
+  read_points_cust(file_name, point_vector);
+  //std::cout << "Successfully read the points\n";
+  witnessComplex.setNbL(nbL);
+  //  witnessComplex.witness_complex_from_points(point_vector);
+  std::vector<std::vector< int > > WL;
+  std::set<int> L;
+  int nbP = point_vector.size();
+  start = clock();
+  //witnessComplex.landmark_choice_by_furthest_points(point_vector, point_vector.size(), WL);
+  witnessComplex.landmark_choice_by_random_points(point_vector, nbP, L);
+  witnessComplex.nearest_landmarks(point_vector,L,WL);
+  end = clock();
+  std::cout << "Landmark choice took "
+            << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
+  // Write the WL matrix in a file
+  mkdir("output", S_IRWXU);
+  const size_t last_slash_idx = file_name.find_last_of("/");
+  if (std::string::npos != last_slash_idx)
+    {
+      file_name.erase(0, last_slash_idx + 1);
+    }
+  std::string out_file = "output/"+file_name+"_"+argv[2]+".wl";
+  //write_wl(out_file,WL);
+  start = clock();
+  witnessComplex.witness_complex(WL);
+  //
+  end = clock();
+  std::cout << "Howdy world! The process took "
+       << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
+  /*
+  char buffer[100];
+  int i = sprintf(buffer,"%s_%s_result.txt",argv[1],argv[2]);
+  if (i >= 0)
+    {
+      std::string out_file = (std::string)buffer;
+      std::ofstream ofs (out_file, std::ofstream::out);
+      witnessComplex.st_to_file(ofs);
+      ofs.close();
+    }
+  */
+
+  out_file = "output/"+file_name+"_"+argv[2]+".stree";
+  std::ofstream ofs (out_file, std::ofstream::out);
+  witnessComplex.st_to_file(ofs);
+  ofs.close();
+
+  out_file = "output/"+file_name+"_"+argv[2]+".badlinks";
+  std::ofstream ofs2(out_file, std::ofstream::out);
+  witnessComplex.write_bad_links(ofs2);
+  ofs2.close();
+}