Merged last trunk modifications

Make Witness compile and test


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_module@1755 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: e6eec55ac0a4cc66da3bb081a222cae5b998c1cf

2 files changed, 125 insertions, 88 deletions

diff --git a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
index 4d7bf622..7380547f 100644
--- a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
+++ b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2015  INRIA Saclay (France)
+ *    Copyright (C) 2015  INRIA
  *
  *    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
@@ -33,12 +33,20 @@
 #include <vector>
 
 #include <gudhi/Alpha_complex.h>
+// to construct a simplex_tree from Delaunay_triangulation
+#include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/Simplex_tree.h>
+#include <boost/mpl/list.hpp>
 
 // Use dynamic_dimension_tag for the user to be able to set dimension
 typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel_d;
+// Use static dimension_tag for the user not to be able to set dimension
+typedef CGAL::Epick_d< CGAL::Dimension_tag<2> > Kernel_s;
 // The triangulation uses the default instantiation of the TriangulationDataStructure template parameter
 
-BOOST_AUTO_TEST_CASE(ALPHA_DOC_OFF_file) {
+typedef boost::mpl::list<Kernel_d, Kernel_s> list_of_kernel_variants;
+
+BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_from_OFF_file, TestedKernel, list_of_kernel_variants) {
   // ----------------------------------------------------------------------------
   //
   // Init of an alpha-complex from a OFF file
@@ -49,60 +57,55 @@ BOOST_AUTO_TEST_CASE(ALPHA_DOC_OFF_file) {
   std::cout << "========== OFF FILE NAME = " << off_file_name << " - alpha²=" <<
       max_alpha_square_value << "==========" << std::endl;
 
-  Gudhi::alpha_complex::Alpha_complex<Kernel_d> alpha_complex_from_file(off_file_name, max_alpha_square_value);
+  Gudhi::alpha_complex::Alpha_complex<TestedKernel> alpha_complex_from_file(off_file_name);
 
-  const int DIMENSION = 2;
-  std::cout << "alpha_complex_from_file.dimension()=" << alpha_complex_from_file.dimension() << std::endl;
-  BOOST_CHECK(alpha_complex_from_file.dimension() == DIMENSION);
+  std::cout << "alpha_complex_from_points.number_of_vertices()=" << alpha_complex_from_file.number_of_vertices()
+      << std::endl;
+  BOOST_CHECK(alpha_complex_from_file.number_of_vertices() == 7);
 
-  const int NUMBER_OF_VERTICES = 7;
-  std::cout << "alpha_complex_from_file.num_vertices()=" << alpha_complex_from_file.num_vertices() << std::endl;
-  BOOST_CHECK(alpha_complex_from_file.num_vertices() == NUMBER_OF_VERTICES);
+  Gudhi::Simplex_tree<> simplex_tree_60;
+  BOOST_CHECK(alpha_complex_from_file.create_complex(simplex_tree_60, max_alpha_square_value));
 
-  const int NUMBER_OF_SIMPLICES = 25;
-  std::cout << "alpha_complex_from_file.num_simplices()=" << alpha_complex_from_file.num_simplices() << std::endl;
-  BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES);
+  std::cout << "simplex_tree_60.dimension()=" << simplex_tree_60.dimension() << std::endl;
+  BOOST_CHECK(simplex_tree_60.dimension() == 2);
 
-}
+  std::cout << "alpha_complex_from_points.number_of_vertices()=" << alpha_complex_from_file.number_of_vertices()
+      << std::endl;
+  BOOST_CHECK(alpha_complex_from_file.number_of_vertices() == 7);
 
-BOOST_AUTO_TEST_CASE(ALPHA_DOC_OFF_file_filtered) {
-  // ----------------------------------------------------------------------------
-  //
-  // Init of an alpha-complex from a OFF file
-  //
-  // ----------------------------------------------------------------------------
-  std::string off_file_name("alphacomplexdoc.off");
-  double max_alpha_square_value = 59.0;
+  std::cout << "simplex_tree_60.num_vertices()=" << simplex_tree_60.num_vertices() << std::endl;
+  BOOST_CHECK(simplex_tree_60.num_vertices() == 7);
+
+  std::cout << "simplex_tree_60.num_simplices()=" << simplex_tree_60.num_simplices() << std::endl;
+  BOOST_CHECK(simplex_tree_60.num_simplices() == 25);
+
+  max_alpha_square_value = 59.0;
   std::cout << "========== OFF FILE NAME = " << off_file_name << " - alpha²=" <<
       max_alpha_square_value << "==========" << std::endl;
 
-  // Use of the default dynamic kernel
-  Gudhi::alpha_complex::Alpha_complex<> alpha_complex_from_file(off_file_name, max_alpha_square_value);
-
-  const int DIMENSION = 2;
-  std::cout << "alpha_complex_from_file.dimension()=" << alpha_complex_from_file.dimension() << std::endl;
-  BOOST_CHECK(alpha_complex_from_file.dimension() == DIMENSION);
+  Gudhi::Simplex_tree<> simplex_tree_59;
+  BOOST_CHECK(alpha_complex_from_file.create_complex(simplex_tree_59, max_alpha_square_value));
+  
+  std::cout << "simplex_tree_59.dimension()=" << simplex_tree_59.dimension() << std::endl;
+  BOOST_CHECK(simplex_tree_59.dimension() == 2);
 
-  const int NUMBER_OF_VERTICES = 7;
-  std::cout << "alpha_complex_from_file.num_vertices()=" << alpha_complex_from_file.num_vertices() << std::endl;
-  BOOST_CHECK(alpha_complex_from_file.num_vertices() == NUMBER_OF_VERTICES);
+  std::cout << "simplex_tree_59.num_vertices()=" << simplex_tree_59.num_vertices() << std::endl;
+  BOOST_CHECK(simplex_tree_59.num_vertices() == 7);
 
-  const int NUMBER_OF_SIMPLICES = 23;
-  std::cout << "alpha_complex_from_file.num_simplices()=" << alpha_complex_from_file.num_simplices() << std::endl;
-  BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES);
+  std::cout << "simplex_tree_59.num_simplices()=" << simplex_tree_59.num_simplices() << std::endl;
+  BOOST_CHECK(simplex_tree_59.num_simplices() == 23);
 }
 
 bool are_almost_the_same(float a, float b) {
   return std::fabs(a - b) < std::numeric_limits<float>::epsilon();
 }
 
-// Use dynamic_dimension_tag for the user to be able to set dimension
-typedef CGAL::Epick_d< CGAL::Dimension_tag<4> > Kernel_s;
-typedef Kernel_s::Point_d Point;
-typedef std::vector<Point> Vector_of_points;
-
+// Use static dimension_tag for the user not to be able to set dimension
+typedef CGAL::Epick_d< CGAL::Dimension_tag<4> > Kernel_4;
+typedef Kernel_4::Point_d Point_4;
+typedef std::vector<Point_4> Vector_4_Points;
 
-bool is_point_in_list(Vector_of_points points_list, Point point) {
+bool is_point_in_list(Vector_4_Points points_list, Point_4 point) {
   for (auto& point_in_list : points_list) {
     if (point_in_list == point) {
       return true;  // point found
@@ -115,57 +118,64 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) {
   // ----------------------------------------------------------------------------
   // Init of a list of points
   // ----------------------------------------------------------------------------
-  Vector_of_points points;
+  Vector_4_Points points;
   std::vector<double> coords = { 0.0, 0.0, 0.0, 1.0 };
-  points.push_back(Point(coords.begin(), coords.end()));
+  points.push_back(Point_4(coords.begin(), coords.end()));
   coords = { 0.0, 0.0, 1.0, 0.0 };
-  points.push_back(Point(coords.begin(), coords.end()));
+  points.push_back(Point_4(coords.begin(), coords.end()));
   coords = { 0.0, 1.0, 0.0, 0.0 };
-  points.push_back(Point(coords.begin(), coords.end()));
+  points.push_back(Point_4(coords.begin(), coords.end()));
   coords = { 1.0, 0.0, 0.0, 0.0 };
-  points.push_back(Point(coords.begin(), coords.end()));
+  points.push_back(Point_4(coords.begin(), coords.end()));
 
   // ----------------------------------------------------------------------------
   // Init of an alpha complex from the list of points
   // ----------------------------------------------------------------------------
-  Gudhi::alpha_complex::Alpha_complex<Kernel_s> alpha_complex_from_points(points);
+  Gudhi::alpha_complex::Alpha_complex<Kernel_4> alpha_complex_from_points(points);
 
   std::cout << "========== Alpha_complex_from_points ==========" << std::endl;
 
+  Gudhi::Simplex_tree<> simplex_tree;
+  BOOST_CHECK(alpha_complex_from_points.create_complex(simplex_tree));
+  
+  std::cout << "alpha_complex_from_points.number_of_vertices()=" << alpha_complex_from_points.number_of_vertices()
+      << std::endl;
+  BOOST_CHECK(alpha_complex_from_points.number_of_vertices() == points.size());
+
   // Another way to check num_simplices
   std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl;
   int num_simplices = 0;
-  for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) {
+  for (auto f_simplex : simplex_tree.filtration_simplex_range()) {
     num_simplices++;
     std::cout << "   ( ";
-    for (auto vertex : alpha_complex_from_points.simplex_vertex_range(f_simplex)) {
+    for (auto vertex : simplex_tree.simplex_vertex_range(f_simplex)) {
       std::cout << vertex << " ";
     }
-    std::cout << ") -> " << "[" << alpha_complex_from_points.filtration(f_simplex) << "] ";
+    std::cout << ") -> " << "[" << simplex_tree.filtration(f_simplex) << "] ";
     std::cout << std::endl;
   }
   BOOST_CHECK(num_simplices == 15);
-  std::cout << "alpha_complex_from_points.num_simplices()=" << alpha_complex_from_points.num_simplices() << std::endl;
-  BOOST_CHECK(alpha_complex_from_points.num_simplices() == 15);
+  std::cout << "simplex_tree.num_simplices()=" << simplex_tree.num_simplices() << std::endl;
+  BOOST_CHECK(simplex_tree.num_simplices() == 15);
 
-  std::cout << "alpha_complex_from_points.dimension()=" << alpha_complex_from_points.dimension() << std::endl;
-  BOOST_CHECK(alpha_complex_from_points.dimension() == 4);
-  std::cout << "alpha_complex_from_points.num_vertices()=" << alpha_complex_from_points.num_vertices() << std::endl;
-  BOOST_CHECK(alpha_complex_from_points.num_vertices() == 4);
+  std::cout << "simplex_tree.dimension()=" << simplex_tree.dimension() << std::endl;
+  BOOST_CHECK(simplex_tree.dimension() == 4);
+  std::cout << "simplex_tree.num_vertices()=" << simplex_tree.num_vertices() << std::endl;
+  BOOST_CHECK(simplex_tree.num_vertices() == 4);
 
-  for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) {
-    switch (alpha_complex_from_points.dimension(f_simplex)) {
+  for (auto f_simplex : simplex_tree.filtration_simplex_range()) {
+    switch (simplex_tree.dimension(f_simplex)) {
       case 0:
-        BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 0.0));
+        BOOST_CHECK(are_almost_the_same(simplex_tree.filtration(f_simplex), 0.0));
         break;
       case 1:
-        BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 1.0/2.0));
+        BOOST_CHECK(are_almost_the_same(simplex_tree.filtration(f_simplex), 1.0/2.0));
         break;
       case 2:
-        BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 2.0/3.0));
+        BOOST_CHECK(are_almost_the_same(simplex_tree.filtration(f_simplex), 2.0/3.0));
         break;
       case 3:
-        BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 3.0/4.0));
+        BOOST_CHECK(are_almost_the_same(simplex_tree.filtration(f_simplex), 3.0/4.0));
         break;
       default:
         BOOST_CHECK(false);  // Shall not happen
@@ -173,22 +183,22 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) {
     }
   }
 
-  Point p0 = alpha_complex_from_points.get_point(0);
+  Point_4 p0 = alpha_complex_from_points.get_point(0);
   std::cout << "alpha_complex_from_points.get_point(0)=" << p0 << std::endl;
   BOOST_CHECK(4 == p0.dimension());
   BOOST_CHECK(is_point_in_list(points, p0));
 
-  Point p1 = alpha_complex_from_points.get_point(1);
+  Point_4 p1 = alpha_complex_from_points.get_point(1);
   std::cout << "alpha_complex_from_points.get_point(1)=" << p1 << std::endl;
   BOOST_CHECK(4 == p1.dimension());
   BOOST_CHECK(is_point_in_list(points, p1));
 
-  Point p2 = alpha_complex_from_points.get_point(2);
+  Point_4 p2 = alpha_complex_from_points.get_point(2);
   std::cout << "alpha_complex_from_points.get_point(2)=" << p2 << std::endl;
   BOOST_CHECK(4 == p2.dimension());
   BOOST_CHECK(is_point_in_list(points, p2));
 
-  Point p3 = alpha_complex_from_points.get_point(3);
+  Point_4 p3 = alpha_complex_from_points.get_point(3);
   std::cout << "alpha_complex_from_points.get_point(3)=" << p3 << std::endl;
   BOOST_CHECK(4 == p3.dimension());
   BOOST_CHECK(is_point_in_list(points, p3));
@@ -199,40 +209,40 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) {
   BOOST_CHECK_THROW (alpha_complex_from_points.get_point(1234), std::out_of_range);
   
   // Test after prune_above_filtration
-  bool modified = alpha_complex_from_points.prune_above_filtration(0.6);
+  bool modified = simplex_tree.prune_above_filtration(0.6);
   if (modified) {
-    alpha_complex_from_points.initialize_filtration();
+    simplex_tree.initialize_filtration();
   }
   BOOST_CHECK(modified);
   
   // Another way to check num_simplices
   std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl;
   num_simplices = 0;
-  for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) {
+  for (auto f_simplex : simplex_tree.filtration_simplex_range()) {
     num_simplices++;
     std::cout << "   ( ";
-    for (auto vertex : alpha_complex_from_points.simplex_vertex_range(f_simplex)) {
+    for (auto vertex : simplex_tree.simplex_vertex_range(f_simplex)) {
       std::cout << vertex << " ";
     }
-    std::cout << ") -> " << "[" << alpha_complex_from_points.filtration(f_simplex) << "] ";
+    std::cout << ") -> " << "[" << simplex_tree.filtration(f_simplex) << "] ";
     std::cout << std::endl;
   }
   BOOST_CHECK(num_simplices == 10);
-  std::cout << "alpha_complex_from_points.num_simplices()=" << alpha_complex_from_points.num_simplices() << std::endl;
-  BOOST_CHECK(alpha_complex_from_points.num_simplices() == 10);
+  std::cout << "simplex_tree.num_simplices()=" << simplex_tree.num_simplices() << std::endl;
+  BOOST_CHECK(simplex_tree.num_simplices() == 10);
 
-  std::cout << "alpha_complex_from_points.dimension()=" << alpha_complex_from_points.dimension() << std::endl;
-  BOOST_CHECK(alpha_complex_from_points.dimension() == 4);
-  std::cout << "alpha_complex_from_points.num_vertices()=" << alpha_complex_from_points.num_vertices() << std::endl;
-  BOOST_CHECK(alpha_complex_from_points.num_vertices() == 4);
+  std::cout << "simplex_tree.dimension()=" << simplex_tree.dimension() << std::endl;
+  BOOST_CHECK(simplex_tree.dimension() == 4);
+  std::cout << "simplex_tree.num_vertices()=" << simplex_tree.num_vertices() << std::endl;
+  BOOST_CHECK(simplex_tree.num_vertices() == 4);
 
-  for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) {
-    switch (alpha_complex_from_points.dimension(f_simplex)) {
+  for (auto f_simplex : simplex_tree.filtration_simplex_range()) {
+    switch (simplex_tree.dimension(f_simplex)) {
       case 0:
-        BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 0.0));
+        BOOST_CHECK(are_almost_the_same(simplex_tree.filtration(f_simplex), 0.0));
         break;
       case 1:
-        BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 1.0/2.0));
+        BOOST_CHECK(are_almost_the_same(simplex_tree.filtration(f_simplex), 1.0/2.0));
         break;
       default:
         BOOST_CHECK(false);  // Shall not happen
@@ -241,3 +251,36 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) {
   }
 
 }
+
+BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_from_empty_points, TestedKernel, list_of_kernel_variants) {
+  std::cout << "========== Alpha_complex_from_empty_points ==========" << std::endl;
+
+  // ----------------------------------------------------------------------------
+  // Init of an empty list of points
+  // ----------------------------------------------------------------------------
+  std::vector<typename TestedKernel::Point_d> points;
+
+  // ----------------------------------------------------------------------------
+  // Init of an alpha complex from the list of points
+  // ----------------------------------------------------------------------------
+  Gudhi::alpha_complex::Alpha_complex<TestedKernel> alpha_complex_from_points(points);
+
+  // Test to the limit
+  BOOST_CHECK_THROW (alpha_complex_from_points.get_point(0), std::out_of_range);
+
+  Gudhi::Simplex_tree<> simplex_tree;
+  BOOST_CHECK(!alpha_complex_from_points.create_complex(simplex_tree));
+  
+  std::cout << "alpha_complex_from_points.number_of_vertices()=" << alpha_complex_from_points.number_of_vertices()
+      << std::endl;
+  BOOST_CHECK(alpha_complex_from_points.number_of_vertices() == points.size());
+
+  std::cout << "simplex_tree.num_simplices()=" << simplex_tree.num_simplices() << std::endl;
+  BOOST_CHECK(simplex_tree.num_simplices() == 0);
+
+  std::cout << "simplex_tree.dimension()=" << simplex_tree.dimension() << std::endl;
+  BOOST_CHECK(simplex_tree.dimension() == -1);
+  
+  std::cout << "simplex_tree.num_vertices()=" << simplex_tree.num_vertices() << std::endl;
+  BOOST_CHECK(simplex_tree.num_vertices() == 0);
+}
diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt
index b0723a41..efc0565f 100644
--- a/src/Alpha_complex/test/CMakeLists.txt
+++ b/src/Alpha_complex/test/CMakeLists.txt
@@ -10,8 +10,6 @@ if (GPROF_PATH)
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
 endif()
 
-# need CGAL 4.7
-# cmake -DCGAL_DIR=~/workspace/CGAL-4.7-Ic-41 ../../..
 if(CGAL_FOUND)
   if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
     if (EIGEN3_FOUND)
@@ -28,11 +26,7 @@ if(CGAL_FOUND)
       # XML format for Jenkins xUnit plugin 
       --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/AlphaComplexUT.xml --log_level=test_suite --report_level=no)
 
-    else()
-      message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha complex unitary tests.")
-    endif()
-  else()
-    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha complex unitary tests. Version 4.7.0 is required.")
-  endif ()
-endif()
+    endif(EIGEN3_FOUND)
+  endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+endif(CGAL_FOUND)