Merge last trunk modifications and fix new rips interface

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/gudhi_stat@2299 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 1e836cba1a372f609e94b66b6db512817a3d875e

5 files changed, 209 insertions, 136 deletions

diff --git a/src/Witness_complex/test/CMakeLists.txt b/src/Witness_complex/test/CMakeLists.txt
index bb55b0f1..e73f9c3a 100644
--- a/src/Witness_complex/test/CMakeLists.txt
+++ b/src/Witness_complex/test/CMakeLists.txt
@@ -10,21 +10,29 @@ if (GPROF_PATH)
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
 endif()
 
-add_executable ( simple_witness_complexUT simple_witness_complex.cpp )
-target_link_libraries(simple_witness_complexUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+add_executable ( Witness_complex_test_simple_witness_complex test_simple_witness_complex.cpp )
+target_link_libraries(Witness_complex_test_simple_witness_complex ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(Witness_complex_test_simple_witness_complex ${TBB_LIBRARIES})
+endif(TBB_FOUND)
 
 # Unitary tests definition and xml result file generation
-add_test(NAME simple_witness_complexUT
-  COMMAND ${CMAKE_CURRENT_BINARY_DIR}/simple_witness_complexUT 
+add_test(NAME simple_witness_complex
+  COMMAND ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_test_simple_witness_complex 
     # XML format for Jenkins xUnit plugin 
-    --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/simple_witness_complexUT.xml --log_level=test_suite --report_level=no)
+    --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Witness_complex_test_simple_witness_complexUT.xml --log_level=test_suite --report_level=no)
 
-add_executable ( witness_complex_pointsUT witness_complex_points.cpp )
-target_link_libraries(witness_complex_pointsUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
-
-# Unitary tests definition and xml result file generation
-add_test(NAME witness_complex_pointsUT
-  COMMAND ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_pointsUT 
-    # XML format for Jenkins xUnit plugin 
-    --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/witness_complex_pointsUT.xml --log_level=test_suite --report_level=no)
+# CGAL and Eigen3 are required for Euclidean version of Witness
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
+  add_executable ( Witness_complex_test_euclidean_simple_witness_complex test_euclidean_simple_witness_complex.cpp )
+  target_link_libraries(Witness_complex_test_euclidean_simple_witness_complex ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  if (TBB_FOUND)
+    target_link_libraries(Witness_complex_test_euclidean_simple_witness_complex ${TBB_LIBRARIES})
+  endif(TBB_FOUND)
 
+  # Unitary tests definition and xml result file generation
+  add_test(NAME euclidean_simple_witness_complex
+    COMMAND ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_test_euclidean_simple_witness_complex
+      # XML format for Jenkins xUnit plugin
+      --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Witness_complex_test_euclidean_simple_witness_complexUT.xml --log_level=test_suite --report_level=no)
+endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
diff --git a/src/Witness_complex/test/simple_witness_complex.cpp b/src/Witness_complex/test/simple_witness_complex.cpp
deleted file mode 100644
index 03df78ee..00000000
--- a/src/Witness_complex/test/simple_witness_complex.cpp
+++ /dev/null
@@ -1,59 +0,0 @@
-/*    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) 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
- *    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_TEST_DYN_LINK
-#define BOOST_TEST_MODULE "simple_witness_complex"
-#include <boost/test/unit_test.hpp>
-#include <boost/mpl/list.hpp>
-
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Witness_complex.h>
-
-#include <iostream>
-#include <ctime>
-#include <vector>
-
-typedef Gudhi::Simplex_tree<> Simplex_tree;
-typedef std::vector< Vertex_handle > typeVectorVertex;
-typedef Gudhi::witness_complex::Witness_complex<Simplex_tree> WitnessComplex;
-
-BOOST_AUTO_TEST_CASE(simple_witness_complex) {
-  Simplex_tree complex;
-  std::vector< typeVectorVertex > knn;
-
-  knn.push_back({1, 0, 5, 2, 6, 3, 4});
-  knn.push_back({2, 6, 4, 5, 0, 1, 3});
-  knn.push_back({3, 4, 2, 1, 5, 6, 0});
-  knn.push_back({4, 2, 1, 3, 5, 6, 0});
-  knn.push_back({5, 1, 6, 0, 2, 3, 4});
-  knn.push_back({6, 0, 5, 2, 1, 3, 4});
-  knn.push_back({0, 5, 6, 1, 2, 3, 4});
-  knn.push_back({2, 6, 4, 5, 3, 1, 0});
-  knn.push_back({1, 2, 5, 4, 3, 6, 0});
-  knn.push_back({3, 4, 0, 6, 5, 1, 2});
-  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, 7, 7, complex);
-
-  BOOST_CHECK(witnessComplex.is_witness_complex(knn, false));
-}
diff --git a/src/Witness_complex/test/test_euclidean_simple_witness_complex.cpp b/src/Witness_complex/test/test_euclidean_simple_witness_complex.cpp
new file mode 100644
index 00000000..62fd1157
--- /dev/null
+++ b/src/Witness_complex/test/test_euclidean_simple_witness_complex.cpp
@@ -0,0 +1,135 @@
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "euclidean_simple_witness_complex"
+#include <boost/test/unit_test.hpp>
+#include <boost/mpl/list.hpp>
+
+#include <CGAL/Epick_d.h>
+
+#include <gudhi/Simplex_tree.h>
+
+#include <gudhi/Witness_complex.h>
+#include <gudhi/Euclidean_witness_complex.h>
+#include <gudhi/Strong_witness_complex.h>
+#include <gudhi/Euclidean_strong_witness_complex.h>
+
+#include <gudhi/Kd_tree_search.h>
+
+#include <iostream>
+#include <ctime>
+#include <vector>
+
+typedef Gudhi::Simplex_tree<> Simplex_tree;
+typedef typename Simplex_tree::Vertex_handle Vertex_handle;
+typedef std::vector< Vertex_handle > typeVectorVertex;
+typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> Kernel;
+typedef typename Kernel::FT FT;
+typedef typename Kernel::Point_d Point_d;
+typedef Gudhi::witness_complex::Euclidean_witness_complex<Kernel> EuclideanWitnessComplex;
+typedef Gudhi::witness_complex::Euclidean_strong_witness_complex<Kernel> EuclideanStrongWitnessComplex;
+
+typedef std::vector<Point_d> Point_range;
+typedef Gudhi::spatial_searching::Kd_tree_search<Kernel, Point_range> Kd_tree;
+typedef Kd_tree::INS_range Nearest_landmark_range;
+typedef std::vector<Nearest_landmark_range> Nearest_landmark_table;
+typedef Gudhi::witness_complex::Witness_complex<Nearest_landmark_table> WitnessComplex;
+typedef Gudhi::witness_complex::Strong_witness_complex<Nearest_landmark_table> StrongWitnessComplex;
+
+
+/* All landmarks and witnesses are taken on the grid in the following manner.
+   LWLWL
+   WW.WW
+   L...L
+   WW.WW
+   LWLWL
+
+   Witness complex consists of 8 vertices, 12 edges and 4 triangles
+ */
+
+BOOST_AUTO_TEST_CASE(simple_witness_complex) {
+  Simplex_tree complex, relaxed_complex, strong_relaxed_complex, strong_relaxed_complex2;
+  Simplex_tree complex_ne, relaxed_complex_ne, strong_relaxed_complex_ne, strong_relaxed_complex2_ne;
+
+  Point_range witnesses, landmarks;
+
+  landmarks.push_back(Point_d(std::vector<FT>{-2,-2}));
+  landmarks.push_back(Point_d(std::vector<FT>{-2, 0}));
+  landmarks.push_back(Point_d(std::vector<FT>{-2, 2}));
+  landmarks.push_back(Point_d(std::vector<FT>{ 0,-2}));
+  landmarks.push_back(Point_d(std::vector<FT>{ 0, 2}));
+  landmarks.push_back(Point_d(std::vector<FT>{ 2,-2}));
+  landmarks.push_back(Point_d(std::vector<FT>{ 2, 0}));
+  landmarks.push_back(Point_d(std::vector<FT>{ 2, 2}));
+  witnesses.push_back(Point_d(std::vector<FT>{-2,-1}));
+  witnesses.push_back(Point_d(std::vector<FT>{-2, 1}));
+  witnesses.push_back(Point_d(std::vector<FT>{-1,-2}));
+  witnesses.push_back(Point_d(std::vector<FT>{-1,-1}));
+  witnesses.push_back(Point_d(std::vector<FT>{-1, 1}));
+  witnesses.push_back(Point_d(std::vector<FT>{-1, 2}));
+  witnesses.push_back(Point_d(std::vector<FT>{ 1,-2}));
+  witnesses.push_back(Point_d(std::vector<FT>{ 1,-1}));
+  witnesses.push_back(Point_d(std::vector<FT>{ 1, 1}));
+  witnesses.push_back(Point_d(std::vector<FT>{ 1, 2}));
+  witnesses.push_back(Point_d(std::vector<FT>{ 2,-1}));
+  witnesses.push_back(Point_d(std::vector<FT>{ 2, 1}));
+
+  Kd_tree landmark_tree(landmarks);
+  Nearest_landmark_table nearest_landmark_table;
+  for (auto w: witnesses)
+    nearest_landmark_table.push_back(landmark_tree.query_incremental_nearest_neighbors(w));
+
+  // Weak witness complex: Euclidean version
+  EuclideanWitnessComplex eucl_witness_complex(landmarks,
+                                               witnesses);
+  eucl_witness_complex.create_complex(complex, 0);
+
+  std::cout << "complex.num_simplices() = " << complex.num_simplices() << std::endl;
+  BOOST_CHECK(complex.num_simplices() == 24);
+
+  eucl_witness_complex.create_complex(relaxed_complex, 8.01);
+
+  std::cout << "relaxed_complex.num_simplices() = " << relaxed_complex.num_simplices() << std::endl;
+  BOOST_CHECK(relaxed_complex.num_simplices() == 239);
+  // The corner simplex {0,2,5,7} and its cofaces are missing.
+
+  // Weak witness complex: non-Euclidean version
+  WitnessComplex witness_complex(nearest_landmark_table);
+  witness_complex.create_complex(complex_ne, 0);
+
+  std::cout << "complex.num_simplices() = " << complex_ne.num_simplices() << std::endl;
+  BOOST_CHECK(complex_ne.num_simplices() == 24);
+
+  witness_complex.create_complex(relaxed_complex_ne, 8.01);
+
+  std::cout << "relaxed_complex.num_simplices() = " << relaxed_complex_ne.num_simplices() << std::endl;
+  BOOST_CHECK(relaxed_complex_ne.num_simplices() == 239);
+
+
+  // Strong complex : Euclidean version
+  EuclideanStrongWitnessComplex eucl_strong_witness_complex(landmarks,
+                                                            witnesses);
+
+  eucl_strong_witness_complex.create_complex(strong_relaxed_complex, 9.1);
+  eucl_strong_witness_complex.create_complex(strong_relaxed_complex2, 9.1, 2);
+
+  std::cout << "strong_relaxed_complex.num_simplices() = " << strong_relaxed_complex.num_simplices() << std::endl;
+  BOOST_CHECK(strong_relaxed_complex.num_simplices() == 239);
+
+  std::cout << "strong_relaxed_complex2.num_simplices() = " << strong_relaxed_complex2.num_simplices() << std::endl;
+  BOOST_CHECK(strong_relaxed_complex2.num_simplices() == 92);
+
+
+  // Strong complex : non-Euclidean version
+  StrongWitnessComplex strong_witness_complex(nearest_landmark_table);
+
+  strong_witness_complex.create_complex(strong_relaxed_complex_ne, 9.1);
+  strong_witness_complex.create_complex(strong_relaxed_complex2_ne, 9.1, 2);
+
+  std::cout << "strong_relaxed_complex.num_simplices() = " << strong_relaxed_complex_ne.num_simplices() << std::endl;
+  BOOST_CHECK(strong_relaxed_complex_ne.num_simplices() == 239);
+
+  std::cout << "strong_relaxed_complex2.num_simplices() = " << strong_relaxed_complex2_ne.num_simplices() << std::endl;
+  BOOST_CHECK(strong_relaxed_complex2_ne.num_simplices() == 92);
+
+
+  // 8 vertices, 28 edges, 56 triangles
+}
diff --git a/src/Witness_complex/test/test_simple_witness_complex.cpp b/src/Witness_complex/test/test_simple_witness_complex.cpp
new file mode 100644
index 00000000..9e3509d3
--- /dev/null
+++ b/src/Witness_complex/test/test_simple_witness_complex.cpp
@@ -0,0 +1,53 @@
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "simple_witness_complex"
+#include <boost/test/unit_test.hpp>
+#include <boost/mpl/list.hpp>
+
+#include <gudhi/Simplex_tree.h>
+
+#include <gudhi/Witness_complex.h>
+
+#include <iostream>
+#include <vector>
+#include <utility>
+
+
+BOOST_AUTO_TEST_CASE(simple_witness_complex) {
+  using Nearest_landmark_range = std::vector<std::pair<std::size_t, double>>;
+  using Nearest_landmark_table = std::vector<Nearest_landmark_range>;
+  using Witness_complex = Gudhi::witness_complex::Witness_complex<Nearest_landmark_table>;
+  using Simplex_tree = Gudhi::Simplex_tree<>;
+
+  Simplex_tree stree;
+  Nearest_landmark_table nlt;
+
+  // Example contains 5 witnesses and 5 landmarks
+  Nearest_landmark_range w0 = {std::make_pair(0, 0), std::make_pair(1, 1), std::make_pair(2, 2),
+                               std::make_pair(3, 3), std::make_pair(4, 4)}; nlt.push_back(w0);
+  Nearest_landmark_range w1 = {std::make_pair(1, 0), std::make_pair(2, 1), std::make_pair(3, 2),
+                               std::make_pair(4, 3), std::make_pair(0, 4)}; nlt.push_back(w1);
+  Nearest_landmark_range w2 = {std::make_pair(2, 0), std::make_pair(3, 1), std::make_pair(4, 2),
+                               std::make_pair(0, 3), std::make_pair(1, 4)}; nlt.push_back(w2);
+  Nearest_landmark_range w3 = {std::make_pair(3, 0), std::make_pair(4, 1), std::make_pair(0, 2),
+                               std::make_pair(1, 3), std::make_pair(2, 4)}; nlt.push_back(w3);
+  Nearest_landmark_range w4 = {std::make_pair(4, 0), std::make_pair(0, 1), std::make_pair(1, 2),
+                               std::make_pair(2, 3), std::make_pair(3, 4)}; nlt.push_back(w4);
+
+  Witness_complex witness_complex(nlt);
+  BOOST_CHECK(witness_complex.create_complex(stree, 4.1));
+
+  std::cout << "Number of simplices: " << stree.num_simplices() << std::endl;
+  BOOST_CHECK(stree.num_simplices() == 31);
+
+  // Check when complex not empty
+  BOOST_CHECK(!witness_complex.create_complex(stree, 4.1));
+
+  // Check when max_alpha_square negative
+  Simplex_tree stree2;
+  BOOST_CHECK(!witness_complex.create_complex(stree2, -0.02));
+
+  witness_complex.create_complex(stree2, 4.1, 2);
+  std::cout << "Number of simplices: " << stree2.num_simplices() << std::endl;
+  BOOST_CHECK(stree2.num_simplices() == 25);
+
+}
diff --git a/src/Witness_complex/test/witness_complex_points.cpp b/src/Witness_complex/test/witness_complex_points.cpp
deleted file mode 100644
index bd3df604..00000000
--- a/src/Witness_complex/test/witness_complex_points.cpp
+++ /dev/null
@@ -1,64 +0,0 @@
-/*    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) 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
- *    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_TEST_DYN_LINK
-#define BOOST_TEST_MODULE "witness_complex_points"
-#include <boost/test/unit_test.hpp>
-#include <boost/mpl/list.hpp>
-
-#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 <iostream>
-#include <vector>
-
-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;
-
-BOOST_AUTO_TEST_CASE(witness_complex_points) {
-  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 = false;
-  // First test: random choice
-  Simplex_tree complex1;
-  Gudhi::witness_complex::landmark_choice_by_random_point(points, 100, knn);
-  assert(!knn.empty());
-  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, 100, 3, complex2);
-  BOOST_CHECK(witnessComplex2.is_witness_complex(knn, b_print_output));
-}