Add an example with a Polyhedron_3

Heat_method_3/doc/Heat_method_3/Heat_method_3.txt

@@ -6,6 +6,10 @@ namespace CGAL {
 \cgalAutoToc
 \author Keenan Crane, Christina Vaz, Andreas Fabri
 
+\image html octopus.png
+
+\section sec_HM_introduction Introduction
+
 The <em>Heat Method</em> is an algorithm that solves the multiple-source
 shortest path problem by returning the geodesic distance for all vertices
 of a triangle mesh to the closest vertex in a given set of source vertices.
@@ -17,12 +21,12 @@ The method works well on triangle meshes with....     For triangle meshes
 that do not fulfill these requirements, applying edge flips to obtain an
 <em>Intrinsic Delaunay Triangulation</em> also gives good results.
 
-\cgalFigureBegin{landscape_meshes, landscape_meshes.png}
+\cgalFigureBegin{landscape_meshes, landscape.jpg}
   Isolines placed on a mesh with and without iDT remeshing.
 \cgalFigureEnd
 
-In the next section we give examples. Section \ref sec_HM_definitions presents
-the mathematical background. The last section is about the \ref sec_HM_history.
+In the next section we give some examples. Section \ref sec_HM_definitions presents
+the mathematical theory of the Heat method. The last section is about the \ref sec_HM_history.
 
 Note that this package requires the third party \ref thirdpartyEigen library.
 This implementation is based on \cgalCite{cgal:cww-ghnac-13} and \cgalCite{cgal:fsbs-acidt-06}
@@ -37,12 +41,20 @@ for the `Heat_method_3::Intrinsic_Delaunay_triangulation_3` class.
 
 \subsection HM_example_Free_function Using a Free Function
 
-The first example calls a free function that computes the distances to a single source vertex.
+The first example calls the free function `Heat_method_3::geodesic_distances_3()`
+which computes for all vertices of a triangle mesh the distances to a single source vertex.
+
 The distances are written into an internal property map of the surface mesh.
-For a `Polyhedron_3` you can use a `std::map` passed to the function `make_assoc_property_map()`, instead.
 
 \cgalExample{Heat_method_3/heat_method.cpp}
 
+For a `Polyhedron_3` you can either add a data field to the vertex type, or, as shown
+in the following exampole create a `boost::unordered_map` and pass it to the function
+`boost::make_assoc_property_map()` which generates a vertex distance property map.
+
+\cgalExample{Heat_method_3/heat_method_polyhedron.cpp}
+
+
 \subsection HM_example_Class Using the Heat Method Class
 
 The following example shows the heat method class. It can be used
@@ -55,11 +67,11 @@ the distances to these two sources.
 \cgalExample{Heat_method_3/heat_method_surface_mesh.cpp}
 
 
-\subsection HM_example_Intrinsic Using the Intrinsic Delaunay Triangulation
+\subsection HM_example_Intrinsic Using the Intrinsic Delaunay Triangulation Class
 
 The following example shows the heat method on a triangle mesh using
 the intrinsic Delaunay triangulation algorithm. This should be done when the
-triangles are very .....................
+triangles have small angles or  .....................
 
 \cgalExample{Heat_method_3/heat_method_surface_mesh_intrinsic.cpp}
 
@@ -67,8 +79,8 @@ triangles are very .....................
 
 \section sec_HM_definitions Theoretical Background
 
-Section \ref Subsection_HM_Definitions_Intro gives an overview of the theory needed by the heat method.
-Section \ref Subsection_HM_IDT_Definitions gives the background needed for the Intrinsic Delaunay Triangulation.
+Section \ref Subsection_HM_Definitions_Intro gives an overview of the theory needed by the Heat method.
+Section \ref Subsection_HM_IDT_Definitions gives the background needed for the Intrinsic Delaunay triangulation.
 
 \subsection Subsection_HM_Definitions_Intro The Heat Method Algorithm
 
@@ -177,14 +189,11 @@ The algorithm is as follows:
 
   The new \f$(\tilde K, \tilde L)\f$ are then used in the Heat Method distance computation.
 
+  We already in the beginning gave an example where the intrinsic Delaunay triangulation improves the results.
+  The mesh was obtained by giving elevation to a 2D triangulation, which lead to elongated triangles.
+
+  The situation is similar for any triangle mesh that has faces with very small angles as can be seen in the figures  below.
 
-  The following figures demonstrate the difference between the heat method with and without intrinsic Delaunay remeshing.
-  \cgalFigureBegin{landscape_mesh, landscape2withoutidt.png}
-    Isolines placed on a mesh without iDT remeshing
-  \cgalFigureEnd
-  \cgalFigureBegin{landscape_mesh_idt, landscape2withidt.png}
-    Isolines placed on a mesh with iDT remeshing
-  \cgalFigureEnd
   \cgalFigureBegin{circle_box, red_circle_box_without_idt_bottom.png}
     Isolines placed on a mesh without iDT remeshing
   \cgalFigureEnd

Heat_method_3/doc/Heat_method_3/dependencies

@@ -7,4 +7,4 @@ Stream_support
 Surface_mesh
 Solver_interface
 BGL
-Polyhedron_3
+Polyhedron

Heat_method_3/doc/Heat_method_3/examples.txt

@@ -1,5 +1,6 @@
 /*!
 \example Heat_method_3/heat_method.cpp
+\example Heat_method_3/heat_method_polyhedron.cpp
 \example Heat_method_3/heat_method_surface_mesh.cpp
 \example Heat_method_3/heat_method_surface_mesh_intrinsic.cpp
 */

Heat_method_3/examples/Heat_method_3/CMakeLists.txt

@@ -54,5 +54,6 @@ include_directories( BEFORE include )
 include( CGAL_CreateSingleSourceCGALProgram )
 
 create_single_source_cgal_program( "heat_method.cpp" )
+create_single_source_cgal_program( "heat_method_polyhedron.cpp" )
 create_single_source_cgal_program( "heat_method_surface_mesh.cpp" )
 create_single_source_cgal_program( "heat_method_surface_mesh_intrinsic.cpp" )

Heat_method_3/examples/Heat_method_3/heat_method.cpp

@@ -7,6 +7,8 @@
 #include <vector>
 #include <iostream>
 
+#include <boost/foreach.hpp>
+
 typedef CGAL::Simple_cartesian<double>                       Kernel;
 typedef Kernel::Point_3                                      Point_3;
 typedef CGAL::Surface_mesh<Point_3>                          Surface_mesh;
@@ -28,9 +30,10 @@ int main(int argc, char* argv[])
   
   CGAL::Heat_method_3::geodesic_distances_3(sm, heat_intensity,source) ;
 
-
+  std::cout << "Source vertex " << source << " at: " << sm.point(source) << std::endl;
   BOOST_FOREACH(vertex_descriptor vd , vertices(sm)){
-    std::cout << vd << "  is at distance " << get(heat_intensity, vd) << " from " << source << std::endl;
+    std::cout << vd << " ("<< sm.point(vd) << ")"
+              <<  " is at distance " << get(heat_intensity, vd) << std::endl;
   }
 
   return 0;

Heat_method_3/examples/Heat_method_3/heat_method_polyhedron.cpp

@@ -0,0 +1,40 @@
+#include <CGAL/Simple_cartesian.h>
+#include <CGAL/Polyhedron_3.h>
+#include <CGAL/Heat_method_3/Heat_method_3.h>
+
+#include <iostream>
+#include <fstream>
+#include <iostream>
+
+#include <boost/unordered_map.hpp>
+#include <boost/foreach.hpp>
+
+typedef CGAL::Simple_cartesian<double>                       Kernel;
+typedef Kernel::Point_3                                      Point_3;
+typedef CGAL::Polyhedron_3<Kernel>                           Surface_mesh;
+
+typedef boost::graph_traits<Surface_mesh>::vertex_descriptor vertex_descriptor;
+
+int main(int argc, char* argv[])
+{
+  //read in mesh
+  Surface_mesh sm;
+  const char* filename = (argc > 1) ? argv[1] : "./data/bunny.off";
+  std::ifstream in(filename);
+  in >> sm;
+
+  boost::unordered_map<vertex_descriptor, double> heat_intensity;
+
+  vertex_descriptor source = *(vertices(sm).first);
+  
+  CGAL::Heat_method_3::geodesic_distances_3(sm,
+                                            boost::make_assoc_property_map(heat_intensity),
+                                            source) ;
+
+  std::cout << "Source vertex at: " << source->point() << std::endl;
+  BOOST_FOREACH(vertex_descriptor vd , vertices(sm)){
+    std::cout << vd->point() << "  is at distance " << heat_intensity[vd] << std::endl;
+  }
+
+  return 0;
+}

Heat_method_3/examples/Heat_method_3/heat_method_surface_mesh.cpp

@@ -4,9 +4,10 @@
 
 #include <iostream>
 #include <fstream>
-#include <vector>
 #include <iostream>
 
+#include <boost/foreach.hpp>
+
 typedef CGAL::Simple_cartesian<double>                       Kernel;
 typedef Kernel::Point_3                                      Point_3;
 typedef CGAL::Surface_mesh<Point_3>                          Surface_mesh;
@@ -47,7 +48,6 @@ int main(int argc, char* argv[])
   }
   hm.add_source(far);
   hm.update();
-  
 
   BOOST_FOREACH(vertex_descriptor vd , vertices(sm)){
     std::cout << vd << "  is at distance " << get(heat_intensity, vd) << std::endl;

Heat_method_3/examples/Heat_method_3/heat_method_surface_mesh_intrinsic.cpp

@@ -5,9 +5,9 @@
 
 #include <iostream>
 #include <fstream>
-#include <vector>
 #include <iostream>
-#include <string>
+
+#include <boost/foreach.hpp>
 
 typedef CGAL::Simple_cartesian<double>                       Kernel;
 typedef Kernel::Point_3                                      Point_3;

Heat_method_3/include/CGAL/Heat_method_3/Heat_method_3.h

@@ -288,7 +288,7 @@ private:
   {
     //currently just working with a single vertex in source set, add the first one for now
     Index i;
-    Matrix K(num_vertices(tm), 1);
+    Matrix K(static_cast<int>(num_vertices(tm)), 1);
     if(sources.empty()) {
       i = 0;
       K.set_coef(i,0, 1, true);