Merge of alpha complex feature from trunk

Add Eigen3 in installation
Add alpha complex in introduction
All examples directory moved to example (was example/common, example/Alpha_complex)


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Doxygen_for_GUDHI_1.3.0@1110 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0b88a4f2b102e2189f4b916b8358ffb2458a72f0

3 files changed, 300 insertions, 0 deletions

diff --git a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
new file mode 100644
index 00000000..80b39924
--- /dev/null
+++ b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
@@ -0,0 +1,243 @@
+/*    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) 2015  INRIA Saclay (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 "alpha_complex"
+#include <boost/test/unit_test.hpp>
+
+#include <CGAL/Delaunay_triangulation.h>
+#include <CGAL/Epick_d.h>
+
+#include <cmath>  // float comparison
+#include <limits>
+#include <string>
+#include <vector>
+
+#include <gudhi/Alpha_complex.h>
+
+// Use dynamic_dimension_tag for the user to be able to set dimension
+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(ALPHA_DOC_OFF_file) {
+  // ----------------------------------------------------------------------------
+  //
+  // Init of an alpha-complex from a OFF file
+  //
+  // ----------------------------------------------------------------------------
+  std::string off_file_name("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 = 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 = 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 = 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);
+
+}
+
+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 << "========== OFF FILE NAME = " << off_file_name << " - alpha²=" <<
+      max_alpha_square_value << "==========" << std::endl;
+
+  // Use of the default dynamic kernel
+  Gudhi::alphacomplex::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);
+
+  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 = 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);
+}
+
+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;
+
+
+bool is_point_in_list(Vector_of_points points_list, Point point) {
+  for (auto& point_in_list : points_list) {
+    if (point_in_list == point) {
+      return true;  // point found
+    }
+  }
+  return false;  // point not found
+}
+
+BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) {
+  // ----------------------------------------------------------------------------
+  // Init of a list of points
+  // ----------------------------------------------------------------------------
+  Vector_of_points points;
+  std::vector<double> coords = { 0.0, 0.0, 0.0, 1.0 };
+  points.push_back(Point(coords.begin(), coords.end()));
+  coords = { 0.0, 0.0, 1.0, 0.0 };
+  points.push_back(Point(coords.begin(), coords.end()));
+  coords = { 0.0, 1.0, 0.0, 0.0 };
+  points.push_back(Point(coords.begin(), coords.end()));
+  coords = { 1.0, 0.0, 0.0, 0.0 };
+  points.push_back(Point(coords.begin(), coords.end()));
+
+  // ----------------------------------------------------------------------------
+  // Init of an alpha complex from the list of points
+  // ----------------------------------------------------------------------------
+  Gudhi::alphacomplex::Alpha_complex<Kernel_s> alpha_complex_from_points(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;
+  for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) {
+    num_simplices++;
+    std::cout << "   ( ";
+    for (auto vertex : alpha_complex_from_points.simplex_vertex_range(f_simplex)) {
+      std::cout << vertex << " ";
+    }
+    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);
+  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);
+
+  for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) {
+    switch (alpha_complex_from_points.dimension(f_simplex)) {
+      case 0:
+        BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.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));
+        break;
+      case 2:
+        BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.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));
+        break;
+      default:
+        BOOST_CHECK(false);  // Shall not happen
+        break;
+    }
+  }
+
+  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());
+  BOOST_CHECK(is_point_in_list(points, p1));
+
+  Point 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);
+  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));
+
+  // 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);
+  
+  // Test after prune_above_filtration
+  bool modified = alpha_complex_from_points.prune_above_filtration(0.6);
+  if (modified) {
+    alpha_complex_from_points.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()) {
+    num_simplices++;
+    std::cout << "   ( ";
+    for (auto vertex : alpha_complex_from_points.simplex_vertex_range(f_simplex)) {
+      std::cout << vertex << " ";
+    }
+    std::cout << ") -> " << "[" << alpha_complex_from_points.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 << "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);
+
+  for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) {
+    switch (alpha_complex_from_points.dimension(f_simplex)) {
+      case 0:
+        BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.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));
+        break;
+      default:
+        BOOST_CHECK(false);  // Shall not happen
+        break;
+    }
+  }
+
+}
diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt
new file mode 100644
index 00000000..e24588d7
--- /dev/null
+++ b/src/Alpha_complex/test/CMakeLists.txt
@@ -0,0 +1,45 @@
+cmake_minimum_required(VERSION 2.6)
+project(GUDHIAlphaComplexTest)
+
+if (GCOVR_PATH)
+  # for gcovr to make coverage reports - Corbera Jenkins plugin
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
+endif()
+if (GPROF_PATH)
+  # for gprof to make coverage reports - Jenkins
+  set(CMAKE_CXX_FLAGS "${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)
+    message(STATUS "CGAL version: ${CGAL_VERSION}.")
+
+    find_package(Eigen3 3.1.0)
+    if (EIGEN3_FOUND)
+      message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
+      include( ${EIGEN3_USE_FILE} )
+      include_directories (BEFORE "../../include")
+
+      add_executable ( AlphaComplexUT Alpha_complex_unit_test.cpp )
+      target_link_libraries(AlphaComplexUT  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+      if (TBB_FOUND)
+        target_link_libraries(AlphaComplexUT ${TBB_RELEASE_LIBRARY})
+      endif()
+
+      # Do not forget to copy test files in current binary dir
+      file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+
+      add_test(AlphaComplexUT ${CMAKE_CURRENT_BINARY_DIR}/AlphaComplexUT
+      # XML format for Jenkins xUnit plugin 
+      --log_format=XML --log_sink=${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 feature.")
+    endif()
+  else()
+    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha complex feature. Version 4.6.0 is required.")
+  endif ()
+endif()
+
diff --git a/src/Alpha_complex/test/README b/src/Alpha_complex/test/README
new file mode 100644
index 00000000..45b87d91
--- /dev/null
+++ b/src/Alpha_complex/test/README
@@ -0,0 +1,12 @@
+To compile:
+***********
+
+cmake .
+make
+
+To launch with details:
+***********************
+
+./AlphaComplexUnitTest --report_level=detailed --log_level=all 
+
+   ==> echo $? returns 0 in case of success (non-zero otherwise)