Merge trunk + alpha complex fixes

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@753 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: a0a1f71420736a0a702e6dbc76bc010b36bf5e13

3 files changed, 35 insertions, 224 deletions

diff --git a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
index c15f07e1..b2597eff 100644
--- a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
+++ b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
@@ -40,144 +40,68 @@
 typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel_d;
 // The triangulation uses the default instantiation of the TriangulationDataStructure template parameter
 
-BOOST_AUTO_TEST_CASE(S4_100_OFF_file) {
+BOOST_AUTO_TEST_CASE(ALPHA_DOC_OFF_file) {
   // ----------------------------------------------------------------------------
   //
   // Init of an alpha-complex from a OFF file
   //
   // ----------------------------------------------------------------------------
-  std::string off_file_name("S4_100.off");
-  double max_alpha_square_value = 1e10;
-  std::cout << "========== OFF FILE NAME = " << off_file_name << " - alpha²=" <<
-      max_alpha_square_value << "==========" << std::endl;
-
-  Gudhi::alphacomplex::Alpha_complex<Kernel_d> alpha_complex_from_file(off_file_name, max_alpha_square_value);
-
-  const int DIMENSION = 4;
-  std::cout << "alpha_complex_from_file.dimension()=" << alpha_complex_from_file.dimension() << std::endl;
-  BOOST_CHECK(alpha_complex_from_file.dimension() == DIMENSION);
-
-  const int NUMBER_OF_VERTICES = 100;
-  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);
-
-  const int NUMBER_OF_SIMPLICES = 6879;
-  std::cout << "alpha_complex_from_file.num_simplices()=" << alpha_complex_from_file.num_simplices() << std::endl;
-  // TODO(VR) : BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES);
-
-  // + TODO(VR) : in wait of num_simplices fix in Simplex_tree [
-  int num_simplices = 0;
-  for (auto f_simplex : alpha_complex_from_file.filtration_simplex_range()) {
-    num_simplices++;
-  }
-  std::cout << "num_simplices=" << num_simplices << std::endl;
-  BOOST_CHECK(num_simplices == NUMBER_OF_SIMPLICES);
-  // - TODO(VR) : in wait of num_simplices fix in Simplex_tree ]
-}
-
-BOOST_AUTO_TEST_CASE(S4_100_OFF_file_filtered) {
-  // ----------------------------------------------------------------------------
-  //
-  // Init of an alpha-complex from a OFF file
-  //
-  // ----------------------------------------------------------------------------
-  std::string off_file_name("S4_100.off");
-  double max_alpha_square_value = 0.999;
+  std::string off_file_name("../../../data/points/alphacomplexdoc.off");
+  double max_alpha_square_value = 60.0;
   std::cout << "========== OFF FILE NAME = " << off_file_name << " - alpha²=" <<
       max_alpha_square_value << "==========" << std::endl;
 
   Gudhi::alphacomplex::Alpha_complex<Kernel_d> alpha_complex_from_file(off_file_name, max_alpha_square_value);
 
-  const int DIMENSION = 4;
+  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);
 
-  const int NUMBER_OF_VERTICES = 100;
+  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);
 
-  const int NUMBER_OF_SIMPLICES = 5966;  // Versus 6879, because of filtered alpha value
+  const int NUMBER_OF_SIMPLICES = 25;
   std::cout << "alpha_complex_from_file.num_simplices()=" << alpha_complex_from_file.num_simplices() << std::endl;
-  // TODO(VR) : BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES);
+  BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES);
 
-  // + TODO(VR) : in wait of num_simplices fix in Simplex_tree [
-  int num_simplices = 0;
-  for (auto f_simplex : alpha_complex_from_file.filtration_simplex_range()) {
-    num_simplices++;
-  }
-  std::cout << "num_simplices=" << num_simplices << std::endl;
-  BOOST_CHECK(num_simplices == NUMBER_OF_SIMPLICES);
-  // - TODO(VR) : in wait of num_simplices fix in Simplex_tree ]
 }
 
-BOOST_AUTO_TEST_CASE(S8_10_OFF_file) {
+BOOST_AUTO_TEST_CASE(ALPHA_DOC_OFF_file_filtered) {
   // ----------------------------------------------------------------------------
   //
   // Init of an alpha-complex from a OFF file
   //
   // ----------------------------------------------------------------------------
-  std::string off_file_name("S8_10.off");
-  double max_alpha_square_value = 1e10;
+  std::string off_file_name("../../../data/points/alphacomplexdoc.off");
+  double max_alpha_square_value = 59.0;
   std::cout << "========== OFF FILE NAME = " << off_file_name << " - alpha²=" <<
       max_alpha_square_value << "==========" << std::endl;
 
   Gudhi::alphacomplex::Alpha_complex<Kernel_d> alpha_complex_from_file(off_file_name, max_alpha_square_value);
 
-  const int DIMENSION = 8;
+  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);
 
-  const int NUMBER_OF_VERTICES = 10;
+  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);
 
-  const int NUMBER_OF_SIMPLICES = 1007;
+  const int NUMBER_OF_SIMPLICES = 25;
   std::cout << "alpha_complex_from_file.num_simplices()=" << alpha_complex_from_file.num_simplices() << std::endl;
-  // TODO(VR) : BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES);
+  BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES);
 
-  // + TODO(VR) : in wait of num_simplices fix in Simplex_tree [
-  int num_simplices = 0;
+  int num_filtered_simplices = 0;
   for (auto f_simplex : alpha_complex_from_file.filtration_simplex_range()) {
-    num_simplices++;
+    if (alpha_complex_from_file.filtration(f_simplex) <= alpha_complex_from_file.filtration()) {
+      num_filtered_simplices++;
+    }
   }
-  std::cout << "num_simplices=" << num_simplices << std::endl;
-  BOOST_CHECK(num_simplices == NUMBER_OF_SIMPLICES);
-  // - TODO(VR) : in wait of num_simplices fix in Simplex_tree ]
-}
-
-BOOST_AUTO_TEST_CASE(S8_10_OFF_file_filtered) {
-  // ----------------------------------------------------------------------------
-  //
-  // Init of an alpha-complex from a OFF file
-  //
-  // ----------------------------------------------------------------------------
-  std::string off_file_name("S8_10.off");
-  double max_alpha_square_value = 1.0;
-  std::cout << "========== OFF FILE NAME = " << off_file_name << " - alpha²=" <<
-      max_alpha_square_value << "==========" << std::endl;
-
-  Gudhi::alphacomplex::Alpha_complex<Kernel_d> alpha_complex_from_file(off_file_name, max_alpha_square_value);
-
-  const int DIMENSION = 8;
-  std::cout << "alpha_complex_from_file.dimension()=" << alpha_complex_from_file.dimension() << std::endl;
-  BOOST_CHECK(alpha_complex_from_file.dimension() == DIMENSION);
-
-  const int NUMBER_OF_VERTICES = 10;
-  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);
-
-  const int NUMBER_OF_SIMPLICES = 1004;  // Versus 1007, because of filtered alpha value
-  std::cout << "alpha_complex_from_file.num_simplices()=" << alpha_complex_from_file.num_simplices() << std::endl;
-  // TODO(VR) : BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES);
+  const int NUMBER_OF_FILTERED_SIMPLICES = 23;
+  std::cout << "num_filtered_simplices=" << num_filtered_simplices << std::endl;
+  BOOST_CHECK(num_filtered_simplices == NUMBER_OF_FILTERED_SIMPLICES);
 
-  // + TODO(VR) : in wait of num_simplices fix in Simplex_tree [
-  int num_simplices = 0;
-  for (auto f_simplex : alpha_complex_from_file.filtration_simplex_range()) {
-    num_simplices++;
-  }
-  std::cout << "num_simplices=" << num_simplices << std::endl;
-  BOOST_CHECK(num_simplices == NUMBER_OF_SIMPLICES);
-  // - TODO(VR) : in wait of num_simplices fix in Simplex_tree ]
 }
 
 bool are_almost_the_same(float a, float b) {
@@ -222,10 +146,11 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) {
 
   std::cout << "========== Alpha_complex_from_points ==========" << std::endl;
 
+  // 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;  // TODO(VR) : in wait of num_simplices fix in Simplex_tree
+  int num_simplices = 0;
   for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) {
-    num_simplices++;  // TODO(VR) : in wait of num_simplices fix in Simplex_tree
+    num_simplices++;
     std::cout << "   ( ";
     for (auto vertex : alpha_complex_from_points.simplex_vertex_range(f_simplex)) {
       std::cout << vertex << " ";
@@ -233,13 +158,12 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) {
     std::cout << ") -> " << "[" << alpha_complex_from_points.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 << "alpha_complex_from_points.dimension()=" << alpha_complex_from_points.dimension() << std::endl;
   BOOST_CHECK(alpha_complex_from_points.dimension() == 4);
-  // TODO(VR) : std::cout << "alpha_complex_from_points.num_simplices()=" << alpha_complex_from_points.num_simplices()
-  // << std::endl;
-  // TODO(VR) : BOOST_CHECK(alpha_complex_from_points.num_simplices() == 15);
-  BOOST_CHECK(num_simplices == 15);  // TODO(VR) : in wait of num_simplices fix in Simplex_tree
   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);
 
@@ -263,6 +187,11 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) {
     }
   }
 
+  Point 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);
   std::cout << "alpha_complex_from_points.get_point(1)=" << p1 << std::endl;
   BOOST_CHECK(4 == p1.dimension());
@@ -278,12 +207,8 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) {
   BOOST_CHECK(4 == p3.dimension());
   BOOST_CHECK(is_point_in_list(points, p3));
 
-  Point p4 = alpha_complex_from_points.get_point(4);
-  std::cout << "alpha_complex_from_points.get_point(4)=" << p4 << std::endl;
-  BOOST_CHECK(4 == p4.dimension());
-  BOOST_CHECK(is_point_in_list(points, p4));
-
-  BOOST_CHECK_THROW (alpha_complex_from_points.get_point(5), std::out_of_range);
-  BOOST_CHECK_THROW (alpha_complex_from_points.get_point(0), std::out_of_range);
+  // Test to the limit
+  BOOST_CHECK_THROW (alpha_complex_from_points.get_point(4), std::out_of_range);
+  BOOST_CHECK_THROW (alpha_complex_from_points.get_point(-1), std::out_of_range);
   BOOST_CHECK_THROW (alpha_complex_from_points.get_point(1234), std::out_of_range);
 }
diff --git a/src/Alpha_complex/test/S4_100.off b/src/Alpha_complex/test/S4_100.off
deleted file mode 100644
index cd017e12..00000000
--- a/src/Alpha_complex/test/S4_100.off
+++ /dev/null
@@ -1,102 +0,0 @@
-nOFF
-4 100 0 0
-0.562921 -0.735261 -0.256472 0.277007
--0.803733 -0.0527915 -0.315125 0.501918
--0.24946 -0.354982 -0.410773 -0.801887
-0.916381 -0.0512295 0.371049 0.141223
-0.182222 0.940836 -0.171362 -0.228599
--0.787145 -0.129213 0.568102 -0.202402
-0.0187866 -0.22093 -0.832882 -0.507095
--0.4702 -0.533814 0.353776 0.607286
--0.159798 -0.504771 0.263586 0.806346
-0.295546 0.162541 0.452931 0.825279
-0.242043 -0.107437 -0.913612 -0.308521
-0.875759 -0.113035 -0.469189 -0.0114505
-0.547877 -0.762247 -0.256972 -0.229729
--0.172302 0.521057 0.412013 -0.727363
--0.724729 -0.0574074 -0.0290602 0.686023
-0.700434 -0.102636 0.687285 0.162779
--0.681386 0.0946893 0.610047 0.393178
--0.847553 -0.357132 0.383743 0.0827718
-0.72297 -0.161631 -0.608517 0.284424
-0.757394 0.141549 0.196065 -0.606528
-0.78094 0.00901997 0.434536 0.448586
-0.14166 -0.619339 0.614589 -0.467582
-0.473105 -0.537832 -0.0103746 0.697711
--0.208004 0.536218 0.818027 0.00605288
-0.743694 -0.628926 0.188072 0.126488
--0.462228 -0.278147 0.35514 -0.76345
--0.17361 0.249211 0.758567 -0.57648
-0.416958 -0.254924 -0.576373 -0.654946
--0.590751 -0.286089 -0.424896 0.623402
--0.639538 -0.739693 -0.203745 0.0482932
-0.0731787 0.132121 0.864022 0.480266
--0.149644 -0.164724 -0.249746 -0.94239
--0.348592 0.0120379 -0.928656 -0.126239
-0.395328 -0.54513 0.149976 -0.723917
--0.974164 0.14707 0.157191 0.068302
--0.166425 0.119943 -0.627304 -0.751269
-0.031947 -0.358518 -0.708301 -0.607251
-0.93781 -0.155368 -0.30951 0.0240237
-0.276094 -0.753155 -0.597088 -0.00387459
--0.642876 -0.200551 -0.263517 -0.690687
-0.178711 0.604987 -0.262989 0.729993
--0.520347 0.497922 -0.676144 0.155374
--0.703999 0.500219 -0.484381 0.139789
--0.131013 0.835735 0.506779 0.166004
--0.536116 -0.566557 0.229226 0.582279
--0.334105 0.158252 0.926091 0.0754059
--0.0362677 0.296076 0.897108 0.325915
--0.57486 0.798575 0.15324 -0.0912754
-0.498602 0.0186805 0.72824 0.469801
--0.960329 0.0473356 0.261005 -0.0860505
-0.899134 -0.381392 -0.214508 0.00921711
-0.570576 0.567224 0.393019 -0.445237
--0.761763 -0.614589 -0.0546476 -0.197513
-0.188584 0.289531 0.174031 0.922129
--0.458506 -0.583876 0.639297 -0.2004
-0.785343 -0.21571 0.0794082 -0.574804
-0.0819036 0.65961 -0.247426 0.704973
-0.573125 0.49706 0.373026 0.534145
--0.513286 -0.626226 0.208535 -0.548536
-0.460558 0.468686 0.507832 -0.55707
-0.716158 -0.488201 0.388209 -0.313164
-0.881074 0.152441 0.380128 -0.236589
-0.885793 0.0386389 0.161009 -0.433537
--0.365162 0.298384 0.292846 0.831784
-0.364934 0.632269 -0.197205 -0.654346
--0.31469 -0.429991 0.665304 -0.522923
--0.734198 0.462914 -0.135691 -0.477756
--0.422885 0.674444 -0.364143 -0.483419
-0.829218 -0.154622 -0.381147 0.378439
-0.887881 0.310479 -0.109528 0.321363
--0.354398 -0.693974 0.456019 -0.429941
--0.492045 -0.160008 0.044387 0.854587
-0.0595532 0.158421 0.412577 -0.895062
--0.211441 0.491794 -0.153521 0.83058
--0.33558 -0.504711 0.353831 -0.71236
--0.735211 -0.197714 0.525626 0.379593
-0.465818 -0.424245 0.769469 -0.104627
--0.641071 -0.286339 -0.704442 -0.103923
--0.00446569 0.0249849 -0.194417 -0.980591
--0.610081 -0.252448 0.176698 -0.729966
--0.0859217 -0.154471 0.715027 0.676382
-0.091315 0.0723382 -0.855023 -0.505337
-0.165362 0.200983 -0.428242 -0.865373
--0.587465 0.303019 -0.152442 0.734729
-0.454946 -0.319828 0.437063 -0.706902
--0.384368 0.277509 0.879225 -0.0470385
-0.523335 -0.330233 -0.208592 0.757335
-0.895086 0.0448492 0.268089 -0.353466
--0.0272491 -0.567336 -0.72254 -0.39411
--0.0745014 -0.121818 -0.882466 0.448179
-0.382304 -0.240135 0.851109 -0.267941
--0.418057 -0.852847 -0.3128 0.00606452
--0.554046 0.304237 0.272381 -0.725453
-0.155115 -0.0894732 -0.245017 -0.952838
-0.114459 -0.130722 0.953669 0.245614
-0.0913002 -0.462466 0.244433 0.847374
--0.198849 0.0785111 0.131441 -0.967997
--0.303154 -0.686484 0.639333 0.167604
-0.521455 0.256835 -0.0584503 -0.811606
--0.109787 0.870544 0.161523 0.451676
diff --git a/src/Alpha_complex/test/S8_10.off b/src/Alpha_complex/test/S8_10.off
deleted file mode 100644
index 4e147c44..00000000
--- a/src/Alpha_complex/test/S8_10.off
+++ /dev/null
@@ -1,12 +0,0 @@
-nOFF
-8 10 0 0
-0.440036 -0.574754 -0.200485 0.216537 -0.501251 -0.0329236 -0.196529 0.313023
--0.129367 -0.184089 -0.213021 -0.415848 0.783529 -0.0438025 0.317256 0.120749
-0.132429 0.683748 -0.124536 -0.166133 -0.540695 -0.0887576 0.390234 -0.139031
-0.0137399 -0.161581 -0.609142 -0.370872 -0.320669 -0.364053 0.24127 0.41416
--0.115313 -0.36425 0.190208 0.581871 0.204605 0.112527 0.313562 0.571337
-0.168272 -0.0746917 -0.635156 -0.214488 0.629498 -0.0812499 -0.337255 -0.00823068
-0.369896 -0.514626 -0.173493 -0.1551 -0.127105 0.384377 0.303936 -0.536566
--0.49013 -0.0388242 -0.0196532 0.463953 0.515962 -0.0756047 0.506276 0.119908
--0.434258 0.060347 0.388793 0.250579 -0.653127 -0.275207 0.295714 0.0637842
-0.596172 -0.133284 -0.501793 0.234541 0.428452 0.0800735 0.110912 -0.343109