Add alpha shapes functionnality

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@488 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: ef821bf7026520540b5869e16c08c290d3ed9477

3 files changed, 239 insertions, 0 deletions

diff --git a/src/Alpha_shapes/example/CMakeLists.txt b/src/Alpha_shapes/example/CMakeLists.txt
new file mode 100644
index 00000000..fb94ca05
--- /dev/null
+++ b/src/Alpha_shapes/example/CMakeLists.txt
@@ -0,0 +1,31 @@
+cmake_minimum_required(VERSION 2.6)
+project(GUDHIAlphaShapesExample)
+
+# need CGAL 4.6
+# cmake -DCGAL_DIR=~/workspace/CGAL-4.6-beta1 ../../..
+if(CGAL_FOUND)
+  if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
+    message(STATUS "CGAL version: ${CGAL_VERSION}.")
+
+    include( ${CGAL_USE_FILE} )
+ 
+    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 ( dtoffrw Delaunay_triangulation_off_rw.cpp )
+      target_link_libraries(dtoffrw  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+      add_test(dtoffrw_tore3D ${CMAKE_CURRENT_BINARY_DIR}/dtoffrw ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off 3)
+
+      #add_definitions(-DDEBUG_TRACES)
+      add_executable ( stfromdt Simplex_tree_from_delaunay_triangulation.cpp )
+      target_link_libraries(stfromdt  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+    else()
+      message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")
+    endif()
+  else()
+    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.")
+  endif ()
+endif()
diff --git a/src/Alpha_shapes/example/Delaunay_triangulation_off_rw.cpp b/src/Alpha_shapes/example/Delaunay_triangulation_off_rw.cpp
new file mode 100644
index 00000000..03f6440d
--- /dev/null
+++ b/src/Alpha_shapes/example/Delaunay_triangulation_off_rw.cpp
@@ -0,0 +1,105 @@
+/*    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 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/>.
+ */
+
+// to construct a Delaunay_triangulation from a OFF file
+#include "gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h"
+
+#include <CGAL/Delaunay_triangulation.h>
+#include <CGAL/Epick_d.h>
+#include <CGAL/point_generators_d.h>
+#include <CGAL/algorithm.h>
+#include <CGAL/assertions.h>
+
+#include <iostream>
+#include <iterator>
+#include <vector>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string>
+
+// Use dynamic_dimension_tag for the user to be able to set dimension
+typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > K;
+typedef CGAL::Delaunay_triangulation<K> T;
+// The triangulation uses the default instanciation of the 
+// TriangulationDataStructure template parameter
+
+void usage(char * const progName) {
+  std::cerr << "Usage: " << progName << " filename.off dimension" << std::endl;
+  exit(-1); // ----- >>
+}
+
+int main(int argc, char **argv) {
+  if (argc != 3) {
+    std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl;
+    usage(argv[0]);
+  }
+
+  int dimension = 0;
+  int returnedScanValue = sscanf(argv[2], "%d", &dimension);
+  if ((returnedScanValue == EOF) || (dimension <= 0)) {
+    std::cerr << "Error: " << argv[2] << " is not correct" << std::endl;
+    usage(argv[0]);
+  }
+
+  T dt(dimension);
+  std::string offFileName(argv[1]);
+  Gudhi::alphashapes::Delaunay_triangulation_off_reader<T> off_reader(offFileName, dt, true, true);
+  if (!off_reader.is_valid()) {
+    std::cerr << "Unable to read file " << offFileName << std::endl;
+    exit(-1); // ----- >>
+  }
+
+  std::cout << "number of vertices=" << dt.number_of_vertices() << std::endl;
+  std::cout << "number of full cells=" << dt.number_of_full_cells() << std::endl;
+  std::cout << "number of finite full cells=" << dt.number_of_finite_full_cells() << std::endl;
+
+  // Points list
+  /*for (T::Vertex_iterator vit = dt.vertices_begin(); vit != dt.vertices_end(); ++vit) {
+        for (auto Coord = vit->point().cartesian_begin(); Coord != vit->point().cartesian_end(); ++Coord) {
+          std::cout << *Coord << " ";
+        }
+        std::cout << std::endl;
+  }
+  std::cout << std::endl;*/
+ 
+  int i = 0, j = 0;
+  typedef T::Full_cell_iterator Full_cell_iterator;
+  typedef T::Facet Facet;
+
+  for (Full_cell_iterator cit = dt.full_cells_begin(); cit != dt.full_cells_end(); ++cit) {
+    if (!dt.is_infinite(cit)) {
+      j++;
+      continue;
+    }
+    Facet fct(cit, cit->index(dt.infinite_vertex()));
+    i++;
+  }
+  std::cout << "There are " << i << " facets on the convex hull." << std::endl;
+  std::cout << "There are " << j << " facets not on the convex hull." << std::endl;
+
+
+  std::string offOutputFile("out.off");
+  Gudhi::alphashapes::Delaunay_triangulation_off_writer<T> off_writer(offOutputFile, dt);
+
+  return 0;
+}
\ No newline at end of file
diff --git a/src/Alpha_shapes/example/Simplex_tree_from_delaunay_triangulation.cpp b/src/Alpha_shapes/example/Simplex_tree_from_delaunay_triangulation.cpp
new file mode 100644
index 00000000..3a17b519
--- /dev/null
+++ b/src/Alpha_shapes/example/Simplex_tree_from_delaunay_triangulation.cpp
@@ -0,0 +1,103 @@
+/*    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 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/>.
+ */
+
+// to construct a Delaunay_triangulation from a OFF file
+#include "gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h"
+#include "gudhi/Alpha_shapes.h"
+
+// to construct a simplex_tree from Delaunay_triangulation
+#include "gudhi/graph_simplicial_complex.h"
+#include "gudhi/Simplex_tree.h"
+
+#include <CGAL/Delaunay_triangulation.h>
+#include <CGAL/Epick_d.h>
+#include <CGAL/point_generators_d.h>
+#include <CGAL/algorithm.h>
+#include <CGAL/assertions.h>
+
+#include <iostream>
+#include <iterator>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string>
+
+// Use dynamic_dimension_tag for the user to be able to set dimension
+typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > K;
+typedef CGAL::Delaunay_triangulation<K> T;
+// The triangulation uses the default instanciation of the 
+// TriangulationDataStructure template parameter
+
+void usage(char * const progName) {
+  std::cerr << "Usage: " << progName << " filename.off dimension" << std::endl;
+  exit(-1); // ----- >>
+}
+
+int main(int argc, char **argv) {
+  if (argc != 3) {
+    std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl;
+    usage(argv[0]);
+  }
+
+  int dimension = 0;
+  int returnedScanValue = sscanf(argv[2], "%d", &dimension);
+  if ((returnedScanValue == EOF) || (dimension <= 0)) {
+    std::cerr << "Error: " << argv[2] << " is not correct" << std::endl;
+    usage(argv[0]);
+  }
+
+  // ----------------------------------------------------------------------------
+  //
+  // Init of an alpha-shape from a Delaunay triangulation
+  //
+  // ----------------------------------------------------------------------------
+  T dt(dimension);
+  std::string off_file_name(argv[1]);
+
+  Gudhi::alphashapes::Delaunay_triangulation_off_reader<T> off_reader(off_file_name, dt, false, false);
+  if (!off_reader.is_valid()) {
+    std::cerr << "Unable to read file " << off_file_name << std::endl;
+    exit(-1); // ----- >>
+  }
+
+  std::cout << "number of vertices=" << dt.number_of_vertices() << std::endl;
+  std::cout << "number of full cells=" << dt.number_of_full_cells() << std::endl;
+  std::cout << "number of finite full cells=" << dt.number_of_finite_full_cells() << std::endl;
+
+  Gudhi::alphashapes::Alpha_shapes alpha_shapes_from_dt(dt);
+  //std::cout << alpha_shapes_from_dt << std::endl;
+
+  // ----------------------------------------------------------------------------
+  //
+  // Init of an alpha-shape from a OFF file
+  //
+  // ----------------------------------------------------------------------------
+  Gudhi::alphashapes::Alpha_shapes alpha_shapes_from_file(off_file_name, dimension);
+  //std::cout << alpha_shapes_from_file << std::endl;
+  
+  std::cout << "alpha_shapes_from_file.dimension()=" << alpha_shapes_from_file.dimension() << std::endl;
+  std::cout << "alpha_shapes_from_file.filtration()=" << alpha_shapes_from_file.filtration() << std::endl;
+  std::cout << "alpha_shapes_from_file.num_simplices()=" << alpha_shapes_from_file.num_simplices() << std::endl;
+  std::cout << "alpha_shapes_from_file.num_vertices()=" << alpha_shapes_from_file.num_vertices() << std::endl;
+
+  return 0;
+}
\ No newline at end of file