From 7e40efa04f1cc528f49da82df1502af85feb78d1 Mon Sep 17 00:00:00 2001
From: skachano <skachano@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 13 Jan 2016 19:08:03 +0000
Subject: Added a test, moved the old test from example

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/witness@964 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 5744fdd3d30735cebdbd7442f023585a70bf0fca
---
 .../test/simple_witness_complex.cpp                | 55 +++++++++++++++++++
 .../test/witness_complex_points.cpp                | 64 ++++++++++++++++++++++
 2 files changed, 119 insertions(+)
 create mode 100644 src/Witness_complex/test/simple_witness_complex.cpp
 create mode 100644 src/Witness_complex/test/witness_complex_points.cpp

(limited to 'src/Witness_complex/test')

diff --git a/src/Witness_complex/test/simple_witness_complex.cpp b/src/Witness_complex/test/simple_witness_complex.cpp
new file mode 100644
index 00000000..c7d85a4d
--- /dev/null
+++ b/src/Witness_complex/test/simple_witness_complex.cpp
@@ -0,0 +1,55 @@
+/*    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 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 <ctime>
+//#include "gudhi/graph_simplicial_complex.h"
+#include "gudhi/Simplex_tree.h"
+#include "gudhi/Witness_complex.h"
+
+using namespace Gudhi;
+
+typedef std::vector< Vertex_handle > typeVectorVertex;
+typedef Witness_complex<Simplex_tree<>> WitnessComplex;
+//typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
+//typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
+
+int main (int argc, char * const argv[])
+{
+  Simplex_tree<> complex;
+  std::vector< typeVectorVertex > knn;
+  typeVectorVertex witness0  = {1,0,5,2,6,3,4}; knn.push_back(witness0 );
+  typeVectorVertex witness1  = {2,6,4,5,0,1,3}; knn.push_back(witness1 );
+  typeVectorVertex witness2  = {3,4,2,1,5,6,0}; knn.push_back(witness2 );
+  typeVectorVertex witness3  = {4,2,1,3,5,6,0}; knn.push_back(witness3 );
+  typeVectorVertex witness4  = {5,1,6,0,2,3,4}; knn.push_back(witness4 );
+  typeVectorVertex witness5  = {6,0,5,2,1,3,4}; knn.push_back(witness5 );
+  typeVectorVertex witness6  = {0,5,6,1,2,3,4}; knn.push_back(witness6 );
+  typeVectorVertex witness7  = {2,6,4,5,3,1,0}; knn.push_back(witness7 );
+  typeVectorVertex witness8  = {1,2,5,4,3,6,0}; knn.push_back(witness8 );
+  typeVectorVertex witness9  = {3,4,0,6,5,1,2}; knn.push_back(witness9 );
+  typeVectorVertex witness10 = {5,0,1,3,6,2,4}; knn.push_back(witness10);
+  typeVectorVertex witness11 = {5,6,1,0,2,3,4}; knn.push_back(witness11);
+  typeVectorVertex witness12 = {1,6,0,5,2,3,4}; knn.push_back(witness12);
+  WitnessComplex witnessComplex(knn, complex, 7, 7);
+  assert(witnessComplex.is_witness_complex(knn, true));
+}
diff --git a/src/Witness_complex/test/witness_complex_points.cpp b/src/Witness_complex/test/witness_complex_points.cpp
new file mode 100644
index 00000000..f9680874
--- /dev/null
+++ b/src/Witness_complex/test/witness_complex_points.cpp
@@ -0,0 +1,64 @@
+/*    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 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 <ctime>
+//#include "gudhi/graph_simplicial_complex.h"
+#include "gudhi/Simplex_tree.h"
+#include "gudhi/Witness_complex.h"
+#include "gudhi/Landmark_choice_by_random_point.h"
+#include "gudhi/Landmark_choice_by_furthest_point.h"
+
+
+using namespace Gudhi;
+
+typedef std::vector< Vertex_handle > typeVectorVertex;
+typedef Witness_complex<Simplex_tree<>> WitnessComplex;
+typedef std::vector<double> Point;
+//typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
+//typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
+
+int main (int argc, char * const argv[])
+{
+  std::vector< typeVectorVertex > knn;
+  std::vector< Point > points;
+  // Add grid points as witnesses
+  for (double i = 0; i < 10; i += 1.0)
+    for (double j = 0; j < 10; j += 1.0)
+      for (double k = 0; k < 10; k += 1.0)
+        points.push_back(Point({i,j,k}));
+
+  bool b_print_output = true;
+  // First test: random choice
+  Simplex_tree<> complex1;
+  Landmark_choice_by_random_point lcrp(points, 100, knn);
+  assert(!knn.empty());
+  WitnessComplex witnessComplex1(knn, complex1, 100, 3);
+  assert(witnessComplex1.is_witness_complex(knn, b_print_output));
+
+  // Second test: furthest choice
+  knn.clear();
+  Simplex_tree<> complex2;
+  Landmark_choice_by_furthest_point lcfp(points, 100, knn);
+  WitnessComplex witnessComplex2(knn, complex2, 100, 3);
+  assert(witnessComplex2.is_witness_complex(knn, b_print_output));
+}
-- 
cgit v1.2.3


From e9f91fe2787f41dd7791c055592ade552ce8df8a Mon Sep 17 00:00:00 2001
From: skachano <skachano@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 13 Jan 2016 19:08:48 +0000
Subject: Oh, forgot the CMakeList in test folder

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/witness@965 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: d4a5301e5a48a27050bec9a43c35980a98d8837b
---
 src/Witness_complex/test/CMakeLists.txt | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 src/Witness_complex/test/CMakeLists.txt

(limited to 'src/Witness_complex/test')

diff --git a/src/Witness_complex/test/CMakeLists.txt b/src/Witness_complex/test/CMakeLists.txt
new file mode 100644
index 00000000..a13fd94a
--- /dev/null
+++ b/src/Witness_complex/test/CMakeLists.txt
@@ -0,0 +1,16 @@
+cmake_minimum_required(VERSION 2.6)
+project(GUDHITestWitnessComplex)
+
+#if(NOT MSVC)
+#  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
+#  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} --coverage")	
+#  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} --coverage")
+#endif()
+
+add_executable ( simple_witness_complex simple_witness_complex.cpp )
+add_test(test ${CMAKE_CURRENT_BINARY_DIR}/simple_witness_complex)
+
+add_executable ( witness_complex_points witness_complex_points.cpp )
+add_test(test ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_points)
+
+#cpplint_add_tests("${CMAKE_SOURCE_DIR}/src/Simplex_tree/include/gudhi")
-- 
cgit v1.2.3


From 309699bf1dfd0582e671c730aee6bdf0f5031a1a Mon Sep 17 00:00:00 2001
From: skachano <skachano@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 14 Jan 2016 10:37:35 +0000
Subject: Fixed the bug in Landmark_selection_by_furthest_point

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/witness@966 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: cbda37a8c267348800fe04e82c58c4021744292e
---
 .../include/gudhi/Landmark_choice_by_furthest_point.h    | 16 ++++++----------
 src/Witness_complex/test/witness_complex_points.cpp      |  2 +-
 2 files changed, 7 insertions(+), 11 deletions(-)

(limited to 'src/Witness_complex/test')

diff --git a/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h b/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h
index ebee96ad..6ac59ae9 100644
--- a/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h
+++ b/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h
@@ -60,7 +60,7 @@ public:
       double curr_max_dist = 0;                                 // used for defining the furhest point from L
       const double infty = std::numeric_limits<double>::infinity(); // infinity (see next entry)
       std::vector< double > dist_to_L(nb_points,infty);         // vector of current distances to L from points
-      int dim = points.begin()->size();
+      //int dim = points.begin()->size();
       
       int rand_int = rand() % nb_points;
       int curr_max_w = rand_int; //For testing purposes a pseudo-random number is used here
@@ -69,8 +69,6 @@ public:
         {
           //curr_max_w at this point is the next landmark
           chosen_landmarks.push_back(curr_max_w);
-          for (auto& v: knn)
-            v.push_back(current_number_of_landmarks);
           unsigned i = 0;
           for (auto& p: points)
             {
@@ -79,13 +77,6 @@ public:
               knn[i].push_back(current_number_of_landmarks);
               if (curr_dist < dist_to_L[i])
                 dist_to_L[i] = curr_dist;
-              int j = current_number_of_landmarks;
-              while (j > 0 && wit_land_dist[i][j-1] > wit_land_dist[i][j])
-                {
-                  std::swap(knn[i][j], knn[i][j-1]);
-                  std::swap(wit_land_dist[i][j-1], wit_land_dist[i][j-1]);
-                  --j;
-                }
               ++i;
             }
           curr_max_dist = 0;
@@ -96,6 +87,11 @@ public:
                 curr_max_w = i;
               }
         }
+      for (unsigned i = 0; i < points.size(); ++i)
+        std::sort(knn[i].begin(),
+                  knn[i].end(),
+                  [&wit_land_dist, i](int a, int b)
+                  { return wit_land_dist[i][a] < wit_land_dist[i][b]; });
     }
 
 };
diff --git a/src/Witness_complex/test/witness_complex_points.cpp b/src/Witness_complex/test/witness_complex_points.cpp
index f9680874..a86bf493 100644
--- a/src/Witness_complex/test/witness_complex_points.cpp
+++ b/src/Witness_complex/test/witness_complex_points.cpp
@@ -47,7 +47,7 @@ int main (int argc, char * const argv[])
       for (double k = 0; k < 10; k += 1.0)
         points.push_back(Point({i,j,k}));
 
-  bool b_print_output = true;
+  bool b_print_output = false;
   // First test: random choice
   Simplex_tree<> complex1;
   Landmark_choice_by_random_point lcrp(points, 100, knn);
-- 
cgit v1.2.3


From f44d72644fc31bc863d0c81d0ae80630ebc506e5 Mon Sep 17 00:00:00 2001
From: skachano <skachano@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 14 Jan 2016 16:17:51 +0000
Subject: Added example stuff

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/witness@968 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: a769b41f7d2d784a2740c149da08dac8124e3df9
---
 src/Witness_complex/example/CMakeLists.txt         |  11 +-
 src/Witness_complex/example/generators.h           | 134 +++++++++++++++++++++
 .../example/witness_complex_sphere.cpp             | 126 +++++++++++++++++++
 .../include/gudhi/Witness_complex.h                |   2 +-
 .../test/simple_witness_complex.cpp                |   5 +-
 .../test/witness_complex_points.cpp                |   9 +-
 6 files changed, 271 insertions(+), 16 deletions(-)
 create mode 100644 src/Witness_complex/example/generators.h
 create mode 100644 src/Witness_complex/example/witness_complex_sphere.cpp

(limited to 'src/Witness_complex/test')

diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt
index 4473078a..b5770ba6 100644
--- a/src/Witness_complex/example/CMakeLists.txt
+++ b/src/Witness_complex/example/CMakeLists.txt
@@ -4,9 +4,6 @@ project(GUDHIWitnessComplex)
 # A simple example
    add_executable( witness_complex_from_file witness_complex_from_file.cpp )
    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_bench witness_complex_bench.cpp )
-   add_test( witness_complex_bench_from_bunny &{CMAKE_CURRENT_BINARY_DIR}/witness_complex_bench ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 100)   
 
 if(CGAL_FOUND)
   if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
@@ -21,12 +18,12 @@ if(CGAL_FOUND)
       message(STATUS "Eigen3 use file: ${EIGEN3_USE_FILE}.")
       include_directories (BEFORE "../../include")
 
-      add_executable ( witness_complex_bench2 witness_complex_bench2.cpp )
-      target_link_libraries(witness_complex_bench2 ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+      add_executable ( witness_complex_sphere witness_complex_sphere.cpp )
+      target_link_libraries(witness_complex_sphere ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
     else()
-      message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")      
+      message(WARNING "Eigen3 not found. Version 3.1.0 is required for witness_complex_sphere example.")      
     endif()
   else()
-    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.")
+    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile witness_complex_sphere example. Version 4.6.0 is required.")
   endif ()
 endif()
diff --git a/src/Witness_complex/example/generators.h b/src/Witness_complex/example/generators.h
new file mode 100644
index 00000000..0d42cda2
--- /dev/null
+++ b/src/Witness_complex/example/generators.h
@@ -0,0 +1,134 @@
+#ifndef GENERATORS_H
+#define GENERATORS_H
+
+#include <fstream>
+
+#include <CGAL/Epick_d.h>
+#include <CGAL/point_generators_d.h>
+
+typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
+typedef K::FT FT;
+typedef K::Point_d Point_d;
+typedef std::vector<Point_d> Point_Vector;
+typedef CGAL::Random_points_in_cube_d<Point_d> Random_cube_iterator;
+typedef CGAL::Random_points_in_ball_d<Point_d> Random_point_iterator;
+
+/**
+ * \brief Rock age method of reading off file
+ *
+ */
+inline void
+off_reader_cust ( std::string file_name , std::vector<Point_d> & 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;
+  // Line OFF. No need in it
+  if (!getline(in_file, line))
+    {
+      std::cerr << "No line OFF\n";
+      return;
+    }
+  // Line with 3 numbers. No need
+  if (!getline(in_file, line))
+    {
+      std::cerr << "No line with 3 numbers\n";
+      return;
+    }
+  // Reading points
+  while( getline ( in_file , line ) )
+    {
+      std::vector< double > point;
+      std::istringstream iss( line );
+      while(iss >> x) { point.push_back(x); }
+      points.push_back(Point_d(point));
+    }
+  in_file.close();
+}
+
+/**
+ * \brief Customized version of read_points
+ * which takes into account a possible nbP first line
+ *
+ */
+inline void
+read_points_cust ( std::string file_name , Point_Vector & 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); }
+      Point_d p(point.begin(), point.end());
+      if (point.size() != 1)
+        points.push_back(p);
+    }
+  in_file.close();
+}
+
+/** \brief Generate points on a grid in a cube of side 2
+ * having {+-1}^D as vertices and insert them in W.
+ * The grid has "width" points on each side. 
+ * If torus is true then it is supposed that the cube represents
+ * a flat torus, hence the opposite borders are associated.
+ * The points on border in this case are not placed twice.
+ */
+void generate_points_grid(Point_Vector& W, int width, int D, bool torus)
+{
+  int nb_points = 1;
+  for (int i = 0; i < D; ++i)
+    nb_points *= width;
+  for (int i = 0; i < nb_points; ++i)
+    {
+      std::vector<double> point;
+      int cell_i = i;
+      for (int l = 0; l < D; ++l)
+        {
+          if (torus)
+            point.push_back(-1+(2.0/(width-1))*(cell_i%width));
+          else
+            point.push_back(-1+(2.0/width)*(cell_i%width));
+          //attention: the bottom and the right are covered too!
+          cell_i /= width;
+        }
+      W.push_back(point);
+    }
+}
+
+/** \brief Generate nbP points uniformly in a cube of side 2
+ * having {+-1}^dim as its vertices and insert them in W.
+ */
+void generate_points_random_box(Point_Vector& W, int nbP, int dim)
+{
+  Random_cube_iterator rp(dim, 1.0);
+  for (int i = 0; i < nbP; i++)
+    {
+      W.push_back(*rp++);
+    }
+}
+
+/** \brief Generate nbP points uniformly on a (dim-1)-sphere
+ *  and insert them in W.
+ */
+void generate_points_sphere(Point_Vector& W, int nbP, int dim)
+{
+  CGAL::Random_points_on_sphere_d<Point_d> rp(dim,1);
+  for (int i = 0; i < nbP; i++)
+    W.push_back(*rp++);
+}
+
+
+#endif
diff --git a/src/Witness_complex/example/witness_complex_sphere.cpp b/src/Witness_complex/example/witness_complex_sphere.cpp
new file mode 100644
index 00000000..1fa0fc42
--- /dev/null
+++ b/src/Witness_complex/example/witness_complex_sphere.cpp
@@ -0,0 +1,126 @@
+/*    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/>.
+ */
+#define BOOST_PARAMETER_MAX_ARITY 12
+
+
+#include <iostream>
+#include <fstream>
+#include <ctime>
+#include <utility> 
+
+#include <sys/types.h>
+#include <sys/stat.h>
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Witness_complex.h>
+#include <gudhi/Landmark_choice_by_random_point.h>
+#include <gudhi/reader_utils.h>
+
+#include "generators.h"
+
+using namespace Gudhi;
+
+typedef std::vector< Vertex_handle > typeVectorVertex;
+//typedef std::vector< std::vector <double> > Point_Vector;
+
+typedef Witness_complex< Simplex_tree<> > WitnessComplex;
+
+/**
+ * \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();
+}
+
+/** Write a gnuplot readable file.
+ *  Data range is a random access range of pairs (arg, value)
+ */
+template < typename Data_range >
+void write_data( Data_range & data, std::string filename )
+{
+  std::ofstream ofs(filename, std::ofstream::out);
+  for (auto entry: data)
+    ofs << entry.first << ", " << entry.second << "\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;
+    }
+
+  std::string file_name   = argv[1];
+  int nbL       = atoi(argv[2]);
+  clock_t start, end;
+
+  // Construct the Simplex Tree
+  Simplex_tree<> simplex_tree;
+
+  std::vector< std::pair<int, double> > l_time;      
+  
+  // Read the point file
+  for (int nbP = 500; nbP < 10000; nbP += 500)
+    {
+      Point_Vector point_vector;
+      generate_points_sphere(point_vector, nbP, 4);
+      std::cout << "Successfully generated " << point_vector.size() << " points.\n";
+      std::cout << "Ambient dimension is " << point_vector[0].size() << ".\n";
+            
+      // Choose landmarks
+      start = clock();
+      std::vector<std::vector< int > > knn;
+      Landmark_choice_by_random_point(point_vector, nbL, knn);
+      
+      // Compute witness complex
+      WitnessComplex(knn, simplex_tree, nbL, point_vector[0].size());
+      end = clock();
+      double time = (double)(end-start)/CLOCKS_PER_SEC;
+      std::cout << "Witness complex for " << nbL << " landmarks took "
+       << time << " s. \n";
+      l_time.push_back(std::make_pair(nbP,time));
+    }
+  write_data(l_time, "w_time.dat");
+}
diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h
index 791d0e45..915e445c 100644
--- a/src/Witness_complex/include/gudhi/Witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Witness_complex.h
@@ -27,7 +27,7 @@
 #include <boost/iterator/transform_iterator.hpp>
 #include <algorithm>
 #include <utility>
-#include "gudhi/distance_functions.h"
+#include <gudhi/distance_functions.h>
 #include <vector>
 #include <list>
 #include <set>
diff --git a/src/Witness_complex/test/simple_witness_complex.cpp b/src/Witness_complex/test/simple_witness_complex.cpp
index c7d85a4d..ea38b5c0 100644
--- a/src/Witness_complex/test/simple_witness_complex.cpp
+++ b/src/Witness_complex/test/simple_witness_complex.cpp
@@ -22,9 +22,8 @@
 
 #include <iostream>
 #include <ctime>
-//#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Simplex_tree.h"
-#include "gudhi/Witness_complex.h"
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Witness_complex.h>
 
 using namespace Gudhi;
 
diff --git a/src/Witness_complex/test/witness_complex_points.cpp b/src/Witness_complex/test/witness_complex_points.cpp
index a86bf493..0a50101d 100644
--- a/src/Witness_complex/test/witness_complex_points.cpp
+++ b/src/Witness_complex/test/witness_complex_points.cpp
@@ -22,11 +22,10 @@
 
 #include <iostream>
 #include <ctime>
-//#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Simplex_tree.h"
-#include "gudhi/Witness_complex.h"
-#include "gudhi/Landmark_choice_by_random_point.h"
-#include "gudhi/Landmark_choice_by_furthest_point.h"
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Witness_complex.h>
+#include <gudhi/Landmark_choice_by_random_point.h>
+#include <gudhi/Landmark_choice_by_furthest_point.h>
 
 
 using namespace Gudhi;
-- 
cgit v1.2.3


From 500d18704bc26166983ea005278bd187e2d3020c Mon Sep 17 00:00:00 2001
From: skachano <skachano@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 15 Jan 2016 08:53:03 +0000
Subject: Fixed namespaces

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/witness@970 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: f71d4840583611d3829d8c4f1049e5d2b01ce71d
---
 src/Witness_complex/example/witness_complex_from_file.cpp        | 1 +
 src/Witness_complex/example/witness_complex_sphere.cpp           | 1 +
 .../include/gudhi/Landmark_choice_by_furthest_point.h            | 8 ++++++++
 .../include/gudhi/Landmark_choice_by_random_point.h              | 8 ++++++++
 src/Witness_complex/include/gudhi/Witness_complex.h              | 9 +++++----
 src/Witness_complex/test/simple_witness_complex.cpp              | 5 ++---
 src/Witness_complex/test/witness_complex_points.cpp              | 1 +
 7 files changed, 26 insertions(+), 7 deletions(-)

(limited to 'src/Witness_complex/test')

diff --git a/src/Witness_complex/example/witness_complex_from_file.cpp b/src/Witness_complex/example/witness_complex_from_file.cpp
index 6add4e0a..72caf30b 100644
--- a/src/Witness_complex/example/witness_complex_from_file.cpp
+++ b/src/Witness_complex/example/witness_complex_from_file.cpp
@@ -33,6 +33,7 @@
 #include "gudhi/reader_utils.h"
 
 using namespace Gudhi;
+using namespace Gudhi::witness_complex;
 
 typedef std::vector< Vertex_handle > typeVectorVertex;
 typedef std::vector< std::vector <double> > Point_Vector;
diff --git a/src/Witness_complex/example/witness_complex_sphere.cpp b/src/Witness_complex/example/witness_complex_sphere.cpp
index 1fa0fc42..d73445b9 100644
--- a/src/Witness_complex/example/witness_complex_sphere.cpp
+++ b/src/Witness_complex/example/witness_complex_sphere.cpp
@@ -38,6 +38,7 @@
 #include "generators.h"
 
 using namespace Gudhi;
+using namespace Gudhi::witness_complex;
 
 typedef std::vector< Vertex_handle > typeVectorVertex;
 //typedef std::vector< std::vector <double> > Point_Vector;
diff --git a/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h b/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h
index 6ac59ae9..050286f2 100644
--- a/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h
+++ b/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h
@@ -23,6 +23,10 @@
 #ifndef GUDHI_LANDMARK_CHOICE_BY_FURTHEST_POINT_H_
 #define GUDHI_LANDMARK_CHOICE_BY_FURTHEST_POINT_H_
 
+namespace Gudhi {
+
+namespace witness_complex {
+
 /**
  *  \class Landmark_choice_by_furthest_point
  *  \brief The class `Landmark_choice_by_furthest_point` allows to construct the matrix
@@ -96,4 +100,8 @@ public:
 
 };
 
+}
+
+}
+
 #endif
diff --git a/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h b/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
index fa822591..038deff6 100644
--- a/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
+++ b/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
@@ -23,6 +23,10 @@
 #ifndef GUDHI_LANDMARK_CHOICE_BY_RANDOM_POINT_H_
 #define GUDHI_LANDMARK_CHOICE_BY_RANDOM_POINT_H_
 
+namespace Gudhi {
+
+namespace witness_complex {
+
 /** 
  *  \class Landmark_choice_by_random_point
  *  \brief The class `Landmark_choice_by_random_point` allows to construct the matrix
@@ -81,4 +85,8 @@ public:
 
 };
 
+}
+  
+}
+  
 #endif
diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h
index 915e445c..8938e59d 100644
--- a/src/Witness_complex/include/gudhi/Witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Witness_complex.h
@@ -44,7 +44,8 @@
 
 namespace Gudhi {
 
-
+  namespace witness_complex {
+  
   /** 
       \class Witness_complex
       \brief Constructs the witness complex for the given set of witnesses and landmarks.
@@ -256,13 +257,13 @@ namespace Gudhi {
               return false;
             }
         }
-      return true; // Arrive here if the not_witnessed check failed all the time
+      return true;
     }
 
     
-}; //class Witness_complex
-
+  }; //class Witness_complex
 
+  }  //namespace witness_complex
   
 } // namespace Guhdi
 
diff --git a/src/Witness_complex/test/simple_witness_complex.cpp b/src/Witness_complex/test/simple_witness_complex.cpp
index ea38b5c0..86f5bcd1 100644
--- a/src/Witness_complex/test/simple_witness_complex.cpp
+++ b/src/Witness_complex/test/simple_witness_complex.cpp
@@ -26,11 +26,10 @@
 #include <gudhi/Witness_complex.h>
 
 using namespace Gudhi;
+using namespace Gudhi::witness_complex;
 
 typedef std::vector< Vertex_handle > typeVectorVertex;
 typedef Witness_complex<Simplex_tree<>> WitnessComplex;
-//typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
-//typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
 
 int main (int argc, char * const argv[])
 {
@@ -50,5 +49,5 @@ int main (int argc, char * const argv[])
   typeVectorVertex witness11 = {5,6,1,0,2,3,4}; knn.push_back(witness11);
   typeVectorVertex witness12 = {1,6,0,5,2,3,4}; knn.push_back(witness12);
   WitnessComplex witnessComplex(knn, complex, 7, 7);
-  assert(witnessComplex.is_witness_complex(knn, true));
+  assert(witnessComplex.is_witness_complex(knn, false));
 }
diff --git a/src/Witness_complex/test/witness_complex_points.cpp b/src/Witness_complex/test/witness_complex_points.cpp
index 0a50101d..e9fac9b8 100644
--- a/src/Witness_complex/test/witness_complex_points.cpp
+++ b/src/Witness_complex/test/witness_complex_points.cpp
@@ -29,6 +29,7 @@
 
 
 using namespace Gudhi;
+using namespace Gudhi::witness_complex;
 
 typedef std::vector< Vertex_handle > typeVectorVertex;
 typedef Witness_complex<Simplex_tree<>> WitnessComplex;
-- 
cgit v1.2.3


From d13a8867ca368b1f56be3ba151d2042728fb4754 Mon Sep 17 00:00:00 2001
From: skachano <skachano@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 20 Jan 2016 10:43:59 +0000
Subject: Almost all Vincent's remarks

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/witness@982 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 32564e3521e0807e26bd2c07d682751a3d47e6da
---
 .../example/witness_complex_sphere.cpp             | 34 ++--------------------
 .../test/simple_witness_complex.cpp                |  4 +--
 .../test/witness_complex_points.cpp                |  4 +--
 3 files changed, 7 insertions(+), 35 deletions(-)

(limited to 'src/Witness_complex/test')

diff --git a/src/Witness_complex/example/witness_complex_sphere.cpp b/src/Witness_complex/example/witness_complex_sphere.cpp
index d73445b9..9dc458d4 100644
--- a/src/Witness_complex/example/witness_complex_sphere.cpp
+++ b/src/Witness_complex/example/witness_complex_sphere.cpp
@@ -41,36 +41,9 @@ using namespace Gudhi;
 using namespace Gudhi::witness_complex;
 
 typedef std::vector< Vertex_handle > typeVectorVertex;
-//typedef std::vector< std::vector <double> > Point_Vector;
 
 typedef Witness_complex< Simplex_tree<> > WitnessComplex;
 
-/**
- * \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();
-}
 
 /** Write a gnuplot readable file.
  *  Data range is a random access range of pairs (arg, value)
@@ -86,15 +59,14 @@ void write_data( Data_range & data, std::string filename )
 
 int main (int argc, char * const argv[])
 {
-  if (argc != 3)
+  if (argc != 2)
     {
       std::cerr << "Usage: " << argv[0]
-                << " path_to_point_file nbL \n";
+                << " nbL \n";
       return 0;
     }
 
-  std::string file_name   = argv[1];
-  int nbL       = atoi(argv[2]);
+  int nbL       = atoi(argv[1]);
   clock_t start, end;
 
   // Construct the Simplex Tree
diff --git a/src/Witness_complex/test/simple_witness_complex.cpp b/src/Witness_complex/test/simple_witness_complex.cpp
index 86f5bcd1..7735ca6f 100644
--- a/src/Witness_complex/test/simple_witness_complex.cpp
+++ b/src/Witness_complex/test/simple_witness_complex.cpp
@@ -2,9 +2,9 @@
  *    (Geometric Understanding in Higher Dimensions) is a generic C++
  *    library for computational topology.
  *
- *    Author(s):       Vincent Rouvreau
+ *    Author(s):       Siargey Kachanovich
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+ *    Copyright (C) 2016  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
diff --git a/src/Witness_complex/test/witness_complex_points.cpp b/src/Witness_complex/test/witness_complex_points.cpp
index e9fac9b8..3850bd82 100644
--- a/src/Witness_complex/test/witness_complex_points.cpp
+++ b/src/Witness_complex/test/witness_complex_points.cpp
@@ -2,9 +2,9 @@
  *    (Geometric Understanding in Higher Dimensions) is a generic C++
  *    library for computational topology.
  *
- *    Author(s):       Vincent Rouvreau
+ *    Author(s):       Siargey Kachanovich
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+ *    Copyright (C) 2016  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
-- 
cgit v1.2.3


From 945a98537205d4f3e3f7c3c652f373af89723731 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 21 Jan 2016 21:41:33 +0000
Subject: Warning fix - if not BOOST_CHECK, variable b_print_output seen as not
 used.

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/VR_witness@986 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 171f360b478c98edd9e177808e2c0b8410bfbd37
---
 src/Witness_complex/test/witness_complex_points.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'src/Witness_complex/test')

diff --git a/src/Witness_complex/test/witness_complex_points.cpp b/src/Witness_complex/test/witness_complex_points.cpp
index 78f01e08..300b2ac5 100644
--- a/src/Witness_complex/test/witness_complex_points.cpp
+++ b/src/Witness_complex/test/witness_complex_points.cpp
@@ -55,12 +55,12 @@ BOOST_AUTO_TEST_CASE(witness_complex_points) {
   Landmark_choice_by_random_point lcrp(points, 100, knn);
   assert(!knn.empty());
   WitnessComplex witnessComplex1(knn, complex1, 100, 3);
-  assert(witnessComplex1.is_witness_complex(knn, b_print_output));
+  BOOST_CHECK(witnessComplex1.is_witness_complex(knn, b_print_output));
 
   // Second test: furthest choice
   knn.clear();
   Simplex_tree complex2;
   Landmark_choice_by_furthest_point lcfp(points, 100, knn);
   WitnessComplex witnessComplex2(knn, complex2, 100, 3);
-  assert(witnessComplex2.is_witness_complex(knn, b_print_output));
+  BOOST_CHECK(witnessComplex2.is_witness_complex(knn, b_print_output));
 }
-- 
cgit v1.2.3


From 7e667b71d937f83b82240afbf90b8cde7225eb8a Mon Sep 17 00:00:00 2001
From: skachano <skachano@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 2 Feb 2016 14:49:56 +0000
Subject: landmark choice functions are now static

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/witness@994 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: f83d337feab944e2c823b8e127f1a8d612d0a1bd
---
 .../example/witness_complex_from_file.cpp          |  2 +-
 .../example/witness_complex_sphere.cpp             |  2 +-
 .../gudhi/Landmark_choice_by_furthest_point.h      | 22 +++++----------------
 .../gudhi/Landmark_choice_by_random_point.h        | 23 ++++++----------------
 .../test/witness_complex_points.cpp                |  6 ++----
 5 files changed, 15 insertions(+), 40 deletions(-)

(limited to 'src/Witness_complex/test')

diff --git a/src/Witness_complex/example/witness_complex_from_file.cpp b/src/Witness_complex/example/witness_complex_from_file.cpp
index d94502b1..77109512 100644
--- a/src/Witness_complex/example/witness_complex_from_file.cpp
+++ b/src/Witness_complex/example/witness_complex_from_file.cpp
@@ -102,7 +102,7 @@ int main(int argc, char * const argv[]) {
   // Choose landmarks
   start = clock();
   std::vector<std::vector< int > > knn;
-  Landmark_choice_by_random_point(point_vector, nbL, knn);
+  Gudhi::witness_complex::landmark_choice_by_random_point(point_vector, nbL, knn);
   end = clock();
   std::cout << "Landmark choice for " << nbL << " landmarks took "
       << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
diff --git a/src/Witness_complex/example/witness_complex_sphere.cpp b/src/Witness_complex/example/witness_complex_sphere.cpp
index 36f63437..1ff35bff 100644
--- a/src/Witness_complex/example/witness_complex_sphere.cpp
+++ b/src/Witness_complex/example/witness_complex_sphere.cpp
@@ -82,7 +82,7 @@ int main(int argc, char * const argv[]) {
     // Choose landmarks
     start = clock();
     std::vector<std::vector< int > > knn;
-    Landmark_choice_by_random_point(point_vector, nbL, knn);
+    Gudhi::witness_complex::landmark_choice_by_random_point(point_vector, nbL, knn);
 
     // Compute witness complex
     WitnessComplex(knn, simplex_tree, nbL, point_vector[0].size());
diff --git a/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h b/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h
index bb7e87f5..47cd888d 100644
--- a/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h
+++ b/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h
@@ -31,20 +31,9 @@ namespace Gudhi {
 
 namespace witness_complex {
 
-/**
- *  \class Landmark_choice_by_furthest_point
- *  \brief The class `Landmark_choice_by_furthest_point` allows to construct the matrix
- *  of closest landmarks per witness by iteratively choosing the furthest witness
- *  from the set of already chosen landmarks as the new landmark. 
- *  \ingroup witness_complex
- */
-
-class Landmark_choice_by_furthest_point {
- private:
-  typedef std::vector<int> typeVectorVertex;
+ typedef std::vector<int> typeVectorVertex;
 
- public:
-    /** 
+  /** 
    *  \brief Landmark choice strategy by iteratively adding the furthest witness from the
    *  current landmark set as the new landmark. 
    *  \details It chooses nbL landmarks from a random access range `points` and
@@ -53,9 +42,9 @@ class Landmark_choice_by_furthest_point {
 
   template <typename KNearestNeighbours,
   typename Point_random_access_range>
-  Landmark_choice_by_furthest_point(Point_random_access_range const &points,
-                                    int nbL,
-                                    KNearestNeighbours &knn) {
+  void landmark_choice_by_furthest_point(Point_random_access_range const &points,
+                                         int nbL,
+                                         KNearestNeighbours &knn) {
     int nb_points = points.end() - points.begin();
     assert(nb_points >= nbL);
     // distance matrix witness x landmarks
@@ -98,7 +87,6 @@ class Landmark_choice_by_furthest_point {
                 [&wit_land_dist, i](int a, int b) {
                   return wit_land_dist[i][a] < wit_land_dist[i][b]; });
   }
-};
 
 }  // namespace witness_complex
 
diff --git a/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h b/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
index 4747dd73..dc364007 100644
--- a/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
+++ b/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
@@ -32,26 +32,16 @@ namespace Gudhi {
 
 namespace witness_complex {
 
-/** 
- *  \class Landmark_choice_by_random_point
- *  \brief The class `Landmark_choice_by_random_point` allows to construct the matrix
- *  of closest landmarks per witness by iteratively choosing a random non-chosen witness
- *  as a new landmark. 
- *  \ingroup witness_complex
- */
-
-class Landmark_choice_by_random_point {
- public:
   /** \brief Landmark choice strategy by taking random vertices for landmarks.
    *  \details It chooses nbL distinct landmarks from a random access range `points`
    *  and outputs a matrix {witness}*{closest landmarks} in knn.
    */
 
   template <typename KNearestNeighbours,
-  typename Point_random_access_range>
-  Landmark_choice_by_random_point(Point_random_access_range const &points,
-                                  int nbL,
-                                  KNearestNeighbours &knn) {
+            typename Point_random_access_range>
+  void landmark_choice_by_random_point(Point_random_access_range const &points,
+                                       int nbL,
+                                       KNearestNeighbours &knn) {
     int nbP = points.end() - points.begin();
     assert(nbP >= nbL);
     std::set<int> landmarks;
@@ -71,8 +61,8 @@ class Landmark_choice_by_random_point {
     knn = KNearestNeighbours(nbP);
     for (int points_i = 0; points_i < nbP; points_i++) {
       std::priority_queue<dist_i, std::vector<dist_i>, comp> l_heap([&](dist_i j1, dist_i j2) {
-        return j1.first > j2.first;
-      });
+          return j1.first > j2.first;
+        });
       std::set<int>::iterator landmarks_it;
       int landmarks_i = 0;
       for (landmarks_it = landmarks.begin(), landmarks_i = 0; landmarks_it != landmarks.end();
@@ -87,7 +77,6 @@ class Landmark_choice_by_random_point {
       }
     }
   }
-};
 
 }  // namespace witness_complex
 
diff --git a/src/Witness_complex/test/witness_complex_points.cpp b/src/Witness_complex/test/witness_complex_points.cpp
index 300b2ac5..cb1639e1 100644
--- a/src/Witness_complex/test/witness_complex_points.cpp
+++ b/src/Witness_complex/test/witness_complex_points.cpp
@@ -37,8 +37,6 @@ typedef std::vector<double> Point;
 typedef std::vector< Vertex_handle > typeVectorVertex;
 typedef Gudhi::Simplex_tree<> Simplex_tree;
 typedef Gudhi::witness_complex::Witness_complex<Simplex_tree> WitnessComplex;
-typedef Gudhi::witness_complex::Landmark_choice_by_random_point Landmark_choice_by_random_point;
-typedef Gudhi::witness_complex::Landmark_choice_by_furthest_point Landmark_choice_by_furthest_point;
 
 BOOST_AUTO_TEST_CASE(witness_complex_points) {
   std::vector< typeVectorVertex > knn;
@@ -52,7 +50,7 @@ BOOST_AUTO_TEST_CASE(witness_complex_points) {
   bool b_print_output = false;
   // First test: random choice
   Simplex_tree complex1;
-  Landmark_choice_by_random_point lcrp(points, 100, knn);
+  Gudhi::witness_complex::landmark_choice_by_random_point(points, 100, knn);
   assert(!knn.empty());
   WitnessComplex witnessComplex1(knn, complex1, 100, 3);
   BOOST_CHECK(witnessComplex1.is_witness_complex(knn, b_print_output));
@@ -60,7 +58,7 @@ BOOST_AUTO_TEST_CASE(witness_complex_points) {
   // Second test: furthest choice
   knn.clear();
   Simplex_tree complex2;
-  Landmark_choice_by_furthest_point lcfp(points, 100, knn);
+  Gudhi::witness_complex::landmark_choice_by_furthest_point(points, 100, knn);
   WitnessComplex witnessComplex2(knn, complex2, 100, 3);
   BOOST_CHECK(witnessComplex2.is_witness_complex(knn, b_print_output));
 }
-- 
cgit v1.2.3


From b7796215d4eac6b4c43ad70998c3737a6527eebb Mon Sep 17 00:00:00 2001
From: skachano <skachano@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 11 Feb 2016 16:05:15 +0000
Subject: Commited Marc's remarks

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/witness@1017 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: d87eb82f60f4f943f59622f33521bcdce7873091
---
 src/Witness_complex/concept/Simplicial_complex.h       | 11 ++---------
 .../example/witness_complex_from_file.cpp              | 13 +------------
 src/Witness_complex/example/witness_complex_sphere.cpp | 10 +++++-----
 .../include/gudhi/Landmark_choice_by_random_point.h    |  6 ++++++
 src/Witness_complex/include/gudhi/Witness_complex.h    | 18 ++++++------------
 src/Witness_complex/test/simple_witness_complex.cpp    |  2 +-
 src/Witness_complex/test/witness_complex_points.cpp    |  4 ++--
 7 files changed, 23 insertions(+), 41 deletions(-)

(limited to 'src/Witness_complex/test')

diff --git a/src/Witness_complex/concept/Simplicial_complex.h b/src/Witness_complex/concept/Simplicial_complex.h
index d7f3496d..9e9f2ff8 100644
--- a/src/Witness_complex/concept/Simplicial_complex.h
+++ b/src/Witness_complex/concept/Simplicial_complex.h
@@ -40,16 +40,11 @@ struct Simplicial_complex {
   /** Returns a Simplex_hanlde that is different from all simplex handles 
    * of the simplices. */
   Simplex_handle null_simplex();
-  /** \brief Returns the number of simplices in the complex.
-   *
-   * Does not count the empty simplex. */
-  size_t num_simplices();
 
   /** \brief Iterator over the simplices of the complex,
    * in an arbitrary order.
    *
    * 'value_type' must be 'Simplex_handle'.*/
-  typedef unspecified Complex_simplex_iterator;
   typedef unspecified Complex_simplex_range;
 
   /**
@@ -71,19 +66,17 @@ struct Simplicial_complex {
    */
   typedef unspecified Insertion_result_type;
 
-  /** \brief Input range of vertices.
-   * 'value_type' must be 'Vertex_handle'. */
-  typedef unspecified Input_vertex_range;
-
   /** \brief Inserts a simplex with vertices from a given range
    *  'vertex_range' in the simplicial complex.
    *  */
+  template< typedef Input_vertex_range >
   Insertion_result_type insert_simplex(Input_vertex_range const & vertex_range);
 
   /** \brief Finds a simplex with vertices given by a range
    *
    * If a simplex exists, its Simplex_handle is returned.
    * Otherwise null_simplex() is returned. */
+  template< typedef Input_vertex_range >
   Simplex_handle find(Input_vertex_range const & vertex_range);
 };
 
diff --git a/src/Witness_complex/example/witness_complex_from_file.cpp b/src/Witness_complex/example/witness_complex_from_file.cpp
index 77109512..98d1fe9c 100644
--- a/src/Witness_complex/example/witness_complex_from_file.cpp
+++ b/src/Witness_complex/example/witness_complex_from_file.cpp
@@ -68,17 +68,6 @@ read_points_cust(std::string file_name, std::vector< std::vector< double > > & p
   in_file.close();
 }
 
-/** Write a gnuplot readable file.
- *  Data range is a random access range of pairs (arg, value)
- */
-template < typename Data_range >
-void write_data(Data_range & data, std::string filename) {
-  std::ofstream ofs(filename, std::ofstream::out);
-  for (auto entry : data)
-    ofs << entry.first << ", " << entry.second << "\n";
-  ofs.close();
-}
-
 int main(int argc, char * const argv[]) {
   if (argc != 3) {
     std::cerr << "Usage: " << argv[0]
@@ -109,7 +98,7 @@ int main(int argc, char * const argv[]) {
 
   // Compute witness complex
   start = clock();
-  WitnessComplex(knn, simplex_tree, nbL, point_vector[0].size());
+  WitnessComplex(knn, nbL, point_vector[0].size(), simplex_tree);
   end = clock();
   std::cout << "Witness complex took "
       << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
diff --git a/src/Witness_complex/example/witness_complex_sphere.cpp b/src/Witness_complex/example/witness_complex_sphere.cpp
index f9d0b5a2..fae80d67 100644
--- a/src/Witness_complex/example/witness_complex_sphere.cpp
+++ b/src/Witness_complex/example/witness_complex_sphere.cpp
@@ -60,11 +60,11 @@ void write_data(Data_range & data, std::string filename) {
 int main(int argc, char * const argv[]) {
   if (argc != 2) {
     std::cerr << "Usage: " << argv[0]
-        << " nbL \n";
+        << " number_of_landmarks \n";
     return 0;
   }
 
-  int nbL = atoi(argv[1]);
+  int number_of_landmarks = atoi(argv[1]);
   clock_t start, end;
 
   // Construct the Simplex Tree
@@ -82,13 +82,13 @@ int main(int argc, char * const argv[]) {
     // Choose landmarks
     start = clock();
     std::vector<std::vector< int > > knn;
-    Gudhi::witness_complex::landmark_choice_by_random_point(point_vector, nbL, knn);
+    Gudhi::witness_complex::landmark_choice_by_random_point(point_vector, number_of_landmarks, knn);
 
     // Compute witness complex
-    WitnessComplex(knn, simplex_tree, nbL, point_vector[0].size());
+    WitnessComplex(knn, number_of_landmarks, point_vector[0].size(), simplex_tree);
     end = clock();
     double time = static_cast<double>(end - start) / CLOCKS_PER_SEC;
-    std::cout << "Witness complex for " << nbL << " landmarks took "
+    std::cout << "Witness complex for " << number_of_landmarks << " landmarks took "
         << time << " s. \n";
     std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n";
     l_time.push_back(std::make_pair(nbP, time));
diff --git a/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h b/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
index dc364007..617c0258 100644
--- a/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
+++ b/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
@@ -35,6 +35,12 @@ namespace witness_complex {
   /** \brief Landmark choice strategy by taking random vertices for landmarks.
    *  \details It chooses nbL distinct landmarks from a random access range `points`
    *  and outputs a matrix {witness}*{closest landmarks} in knn.
+   *
+   *  The type KNearestNeighbors can be seen as 
+   *  Witness_range<Closest_landmark_range<Vertex_handle>>, where
+   *  Witness_range and Closest_landmark_range are random access ranges and
+   *  Vertex_handle is the label type of a vertex in a simplicial complex.
+   *  Closest_landmark_range needs to have push_back operation.
    */
 
   template <typename KNearestNeighbours,
diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h
index 34cbc882..3e14a623 100644
--- a/src/Witness_complex/include/gudhi/Witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Witness_complex.h
@@ -71,7 +71,6 @@ class Witness_complex {
   typedef std::vector< double > Point_t;
   typedef std::vector< Point_t > Point_Vector;
 
-  // typedef typename Simplicial_complex::Filtration_value Filtration_value;
   typedef std::vector< Vertex_handle > typeVectorVertex;
   typedef std::pair< typeVectorVertex, Filtration_value> typeSimplex;
   typedef std::pair< Simplex_handle, bool > typePairSimplexBool;
@@ -109,9 +108,9 @@ class Witness_complex {
    */
   template< typename KNearestNeighbors >
   Witness_complex(KNearestNeighbors const & knn,
-                  Simplicial_complex & sc_,
                   int nbL_,
-                  int dim) : nbL(nbL_), sc(sc_) {
+                  int dim,
+                  Simplicial_complex & sc_) : nbL(nbL_), sc(sc_) {
     // Construction of the active witness list
     int nbW = knn.size();
     typeVectorVertex vv;
@@ -120,7 +119,7 @@ class Witness_complex {
      * it will diminuish in the course of iterations
      */
     ActiveWitnessList active_w;  // = new ActiveWitnessList();
-    for (int i = 0; i != nbL; ++i) {
+    for (Vertex_handle i = 0; i != nbL; ++i) {
       // initial fill of 0-dimensional simplices
       // by doing it we don't assume that landmarks are necessarily witnesses themselves anymore
       counter++;
@@ -131,9 +130,7 @@ class Witness_complex {
     int k = 1; /* current dimension in iterative construction */
     for (int i = 0; i != nbW; ++i)
       active_w.push_back(i);
-    // std::cout << "Successfully added edges" << std::endl;
     while (!active_w.empty() && k < dim) {
-      // std::cout << "Started the step k=" << k << std::endl;
       typename ActiveWitnessList::iterator it = active_w.begin();
       while (it != active_w.end()) {
         typeVectorVertex simplex_vector;
@@ -142,7 +139,7 @@ class Witness_complex {
         if (ok) {
           for (int i = 0; i != k + 1; ++i)
             simplex_vector.push_back(knn[*it][i]);
-          sc.insert_simplex(simplex_vector, 0.0);
+          sc.insert_simplex(simplex_vector);
           // TODO(SK) Error if not inserted : normally no need here though
           it++;
         } else {
@@ -162,9 +159,7 @@ class Witness_complex {
    */
   template <typename KNearestNeighbors>
   bool all_faces_in(KNearestNeighbors const &knn, int witness_id, int k) {
-    // std::cout << "All face in with the landmark " << inserted_vertex << std::endl;
     std::vector< Vertex_handle > facet;
-    // Vertex_handle curr_vh = curr_sh->first;
     // CHECK ALL THE FACETS
     for (int i = 0; i != k + 1; ++i) {
       facet = {};
@@ -175,7 +170,6 @@ class Witness_complex {
       }  // endfor
       if (sc.find(facet) == sc.null_simplex())
         return false;
-      // std::cout << "++++ finished loop safely\n";
     }  // endfor
     return true;
   }
@@ -206,12 +200,12 @@ class Witness_complex {
       bool is_witnessed = false;
       typeVectorVertex simplex;
       int nbV = 0;  // number of verticed in the simplex
-      for (int v : sc.simplex_vertex_range(sh))
+      for (Vertex_handle v : sc.simplex_vertex_range(sh))
         simplex.push_back(v);
       nbV = simplex.size();
       for (typeVectorVertex w : knn) {
         bool has_vertices = true;
-        for (int v : simplex)
+        for (Vertex_handle v : simplex)
           if (std::find(w.begin(), w.begin() + nbV, v) == w.begin() + nbV) {
             has_vertices = false;
             // break;
diff --git a/src/Witness_complex/test/simple_witness_complex.cpp b/src/Witness_complex/test/simple_witness_complex.cpp
index 7d44b90c..03df78ee 100644
--- a/src/Witness_complex/test/simple_witness_complex.cpp
+++ b/src/Witness_complex/test/simple_witness_complex.cpp
@@ -53,7 +53,7 @@ BOOST_AUTO_TEST_CASE(simple_witness_complex) {
   knn.push_back({5, 0, 1, 3, 6, 2, 4});
   knn.push_back({5, 6, 1, 0, 2, 3, 4});
   knn.push_back({1, 6, 0, 5, 2, 3, 4});
-  WitnessComplex witnessComplex(knn, complex, 7, 7);
+  WitnessComplex witnessComplex(knn, 7, 7, complex);
 
   BOOST_CHECK(witnessComplex.is_witness_complex(knn, false));
 }
diff --git a/src/Witness_complex/test/witness_complex_points.cpp b/src/Witness_complex/test/witness_complex_points.cpp
index cb1639e1..bd3df604 100644
--- a/src/Witness_complex/test/witness_complex_points.cpp
+++ b/src/Witness_complex/test/witness_complex_points.cpp
@@ -52,13 +52,13 @@ BOOST_AUTO_TEST_CASE(witness_complex_points) {
   Simplex_tree complex1;
   Gudhi::witness_complex::landmark_choice_by_random_point(points, 100, knn);
   assert(!knn.empty());
-  WitnessComplex witnessComplex1(knn, complex1, 100, 3);
+  WitnessComplex witnessComplex1(knn, 100, 3, complex1);
   BOOST_CHECK(witnessComplex1.is_witness_complex(knn, b_print_output));
 
   // Second test: furthest choice
   knn.clear();
   Simplex_tree complex2;
   Gudhi::witness_complex::landmark_choice_by_furthest_point(points, 100, knn);
-  WitnessComplex witnessComplex2(knn, complex2, 100, 3);
+  WitnessComplex witnessComplex2(knn, 100, 3, complex2);
   BOOST_CHECK(witnessComplex2.is_witness_complex(knn, b_print_output));
 }
-- 
cgit v1.2.3


From 607fc8aa10122089aa2b3debf36e48250e2dfb5b Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 8 Apr 2016 13:34:12 +0000
Subject: Modification on CMakeLists.txt for code coverage were not propagated
 on these 2 test files

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@1109 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 8dc143d808040f903ac9c5e0b967fcf3fc4c9ba4
---
 src/Bitmap_cubical_complex/test/CMakeLists.txt | 4 ----
 src/Witness_complex/test/CMakeLists.txt        | 4 ----
 2 files changed, 8 deletions(-)

(limited to 'src/Witness_complex/test')

diff --git a/src/Bitmap_cubical_complex/test/CMakeLists.txt b/src/Bitmap_cubical_complex/test/CMakeLists.txt
index 97c374e6..b6fc8a3b 100644
--- a/src/Bitmap_cubical_complex/test/CMakeLists.txt
+++ b/src/Bitmap_cubical_complex/test/CMakeLists.txt
@@ -4,14 +4,10 @@ project(GUDHIBitmapCCUT)
 if (GCOVR_PATH)
   # for gcovr to make coverage reports - Corbera Jenkins plugin
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage")	
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage")
 endif()
 if (GPROF_PATH)
   # for gprof to make coverage reports - Jenkins
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg")
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg")
 endif()
 
 add_executable ( BitmapCCUT Bitmap_test.cpp )
diff --git a/src/Witness_complex/test/CMakeLists.txt b/src/Witness_complex/test/CMakeLists.txt
index 9422c152..37bef2d0 100644
--- a/src/Witness_complex/test/CMakeLists.txt
+++ b/src/Witness_complex/test/CMakeLists.txt
@@ -4,14 +4,10 @@ project(GUDHIWitnessComplexUT)
 if (GCOVR_PATH)
   # for gcovr to make coverage reports - Corbera Jenkins plugin
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage")	
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage")
 endif()
 if (GPROF_PATH)
   # for gprof to make coverage reports - Jenkins
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg")
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg")
 endif()
 
 add_executable ( simple_witness_complexUT simple_witness_complex.cpp )
-- 
cgit v1.2.3