Update reference manual

Point_set_3/doc/Point_set_3/PackageDescription.txt

@@ -6,7 +6,7 @@
 
 \cgalPkgSummaryBegin
 \cgalPkgAuthors{Simon Giraudot}
-\cgalPkgDesc{This component provides the user with a flexible 3D point set data structure. The user can easily define any additional property needed (such a normal vectors, colors, labels, etc.). All data structures needed to apply \cgal algorithms on point sets are provided.}
+\cgalPkgDesc{This component provides the user with a flexible 3D point set data structure. The user can easily define any additional property needed such a normal vectors, colors or labels. All data structures needed to apply \cgal algorithms on point sets are provided.}
 \cgalPkgManuals{Chapter_Point_Set_3, PkgPointSet3}
 \cgalPkgSummaryEnd
 
@@ -33,8 +33,8 @@
 user to call point set processing algorithms without having to handle
 manually property maps and iterators.
 
-The overloads all follow the same templates based on the original
+The overloads all follow the same pattern based on the original point
-point set processing functions:
+set processing functions:
 
 - Iterators and property maps of the original function are replaced
 with a single parameter `CGAL::Point_set_3<Point,Vector>`

Point_set_3/doc/Point_set_3/examples.txt

@@ -4,4 +4,5 @@
 \example Point_set_3/point_set_algo.cpp
 \example Point_set_3/point_set_read_xyz.cpp
 \example Point_set_3/point_set_read_ply.cpp
+\example Point_set_3/point_set_advanced.cpp
 */

Point_set_3/include/CGAL/Point_set_3.h

@@ -62,22 +62,11 @@ public:
   typedef Point Point_type;
   typedef Vector Vector_type;
   typedef Point_set_3<Point, Vector> Point_set;
-  /// \endcond
 
-  /*!
-    \brief This represents a point with associated properties.
-    \cgalModels `Index`
-    \cgalModels `LessThanComparable`
-    \cgalModels `Hashable`
-  */
   class Index;
 
-
-  /// \cond SKIP_IN_MANUAL
   typedef typename Properties::Property_container<Index> Base;
-  /// \endcond
 
-  /// \cond SKIP_IN_MANUAL
   template <class Type>
   struct Property_map
     : public Properties::Property_map<Index, Type>
@@ -87,9 +76,17 @@ public:
 
   template <typename Property>
   class Push_property_map;
+  /// \endcond
   
+  /*!
+    \brief This represents a point with associated properties.
+    \cgalModels `Index`
+    \cgalModels `LessThanComparable`
+    \cgalModels `Hashable`
+  */
   class Index
   {
+    /// \cond SKIP_IN_MANUAL
     friend class Point_set_3;
     friend class Properties::Property_container<Index>;
     template <class> friend class Properties::Property_array;
@@ -99,9 +96,9 @@ public:
     std::size_t value;
     
     // Only Point_set_3 and other friend classes are allowed to
-    // instanciate an Index with a specific value
+    // instantiate an Index with a specific value
     Index (const std::size_t& value) : value (value) { }
-
+    /// \endcond
   public:
     Index (const Index& index) : value (index) { }
     Index () : value ((std::size_t)(-1)) { }
@@ -116,8 +113,6 @@ public:
     Index operator-- (int) { Index tmp(*this); -- value; return tmp; }
   };
   
-  /// \endcond
-  
 
 #ifdef DOXYGEN_RUNNING
   typedef unspecified_type iterator; ///< Iterator type of the point set \cgalModels RandomAccessIterator
@@ -761,12 +756,44 @@ public:
   /// @}
 
   
+  /*!
+  
+    \ingroup PkgPointSet3
+
+    \brief Reads the point set from an input stream that can be either:
+
+    - XYZ
+    - OFF
+    - PLY
+
+    The format is detected from the stream. If the stream contains
+    normal vectors, the normal map is added to the point set. For PLY
+    input, all point properties found in the header are added.
+    \relates Point_set_3
+  */
+  template <typename P>
+  friend std::istream& operator>>(std::istream& is, Point_set_3<P>& ps)
+  {
+    // Check format identifier on first line
+    // std::string line;
+    // if (!getline(stream, line))
+    //   return is;
+    // stream.seekg(0);
+    // if (line == "OFF" || line == "NOFF")
+    //   CGAL::read_off_point_set (is, ps);
+    // else if (line == "ply")
+    //   CGAL::read_ply_point_set (is, ps);
+    // else
+    //   CGAL::read_xyz_point_set (is, ps);
+    
+    return is;
+  }
   /*!
   
     \ingroup PkgPointSet3
 
     \brief Inserts the point set in an output stream in Ascii PLY
-    format. All properties are inserted in their instanciation order.
+    format. All properties are inserted in their instantiation order.
 
     \relates Point_set_3
   */
@@ -791,21 +818,21 @@ public:
           os << "property double nx" << std::endl
              << "property double ny" << std::endl
              << "property double nz" << std::endl;
-        else if (ps.m_base.template get<boost::int8_t>(prop[i]).first)
+        else if (ps.m_base.template get<boost::int8_t>(prop[i]).second)
           os << "property char " << prop[i] << std::endl;
-        else if (ps.m_base.template get<boost::uint8_t>(prop[i]).first)
+        else if (ps.m_base.template get<boost::uint8_t>(prop[i]).second)
           os << "property uchar " << prop[i] << std::endl;
-        else if (ps.m_base.template get<boost::int16_t>(prop[i]).first)
+        else if (ps.m_base.template get<boost::int16_t>(prop[i]).second)
           os << "property short " << prop[i] << std::endl;
-        else if (ps.m_base.template get<boost::uint16_t>(prop[i]).first)
+        else if (ps.m_base.template get<boost::uint16_t>(prop[i]).second)
           os << "property ushort " << prop[i] << std::endl;
-        else if (ps.m_base.template get<boost::int32_t>(prop[i]).first)
+        else if (ps.m_base.template get<boost::int32_t>(prop[i]).second)
           os << "property int " << prop[i] << std::endl;
-        else if (ps.m_base.template get<boost::uint32_t>(prop[i]).first)
+        else if (ps.m_base.template get<boost::uint32_t>(prop[i]).second)
           os << "property uint " << prop[i] << std::endl;
-        else if (ps.m_base.template get<float>(prop[i]).first)
+        else if (ps.m_base.template get<float>(prop[i]).second)
           os << "property float " << prop[i] << std::endl;
-        else if (ps.m_base.template get<double>(prop[i]).first)
+        else if (ps.m_base.template get<double>(prop[i]).second)
           os << "property double " << prop[i] << std::endl;
         else
           os << "property " << boost::core::demangle(ps.m_base.get_type(prop[i]).name())

Point_set_3/include/CGAL/Point_set_3/IO.h

@@ -39,7 +39,7 @@ template <typename Point, typename Vector>
 bool
 read_xyz_point_set(
   std::istream& stream, ///< input stream.
-  Point_set_3<Point, Vector>& point_set) ///< point set
+  CGAL::Point_set_3<Point, Vector>& point_set) ///< point set
 {
   point_set.add_normal_map();
 
@@ -50,7 +50,7 @@ read_xyz_point_set(
      point_set.normal_push_map());
 
   bool has_normals = false;
-  for (typename Point_set_3<Point, Vector>::const_iterator it = point_set.begin();
+  for (typename CGAL::Point_set_3<Point, Vector>::const_iterator it = point_set.begin();
        it != point_set.end(); ++ it)
     if (point_set.normal(*it) != CGAL::NULL_VECTOR)
       {
@@ -71,7 +71,7 @@ template <typename Point, typename Vector>
 bool
 read_off_point_set(
   std::istream& stream, ///< input stream.
-  Point_set_3<Point, Vector>& point_set) ///< point set
+  CGAL::Point_set_3<Point, Vector>& point_set) ///< point set
 {
   point_set.add_normal_map();
 
@@ -82,7 +82,7 @@ read_off_point_set(
      point_set.normal_push_map());
 
   bool has_normals = false;
-  for (typename Point_set_3<Point, Vector>::const_iterator it = point_set.begin();
+  for (typename CGAL::Point_set_3<Point, Vector>::const_iterator it = point_set.begin();
        it != point_set.end(); ++ it)
     if (point_set.normal(*it) != CGAL::NULL_VECTOR)
       {
@@ -105,7 +105,7 @@ template <typename Point, typename Vector>
 bool
 read_ply_point_set(
   std::istream& stream, ///< input stream.
-  Point_set_3<Point, Vector>& point_set) ///< point set
+  CGAL::Point_set_3<Point, Vector>& point_set) ///< point set
 {
   CGAL::Ply_interpreter_point_set_3<Point, Vector> interpreter (point_set);
 
@@ -121,7 +121,7 @@ template <typename Point, typename Vector>
 bool
 write_xyz_point_set(
   std::ostream& stream, ///< output stream.
-  const Point_set_3<Point, Vector>& point_set)  ///< point set
+  const CGAL::Point_set_3<Point, Vector>& point_set)  ///< point set
 {
   if (point_set.has_normal_map())
     return CGAL::write_xyz_points_and_normals
@@ -140,7 +140,7 @@ template <typename Point, typename Vector>
 bool
 write_off_point_set(
   std::ostream& stream, ///< output stream.
-  const Point_set_3<Point, Vector>& point_set)  ///< point set
+  const CGAL::Point_set_3<Point, Vector>& point_set)  ///< point set
 {
   if (point_set.has_normal_map())
     return CGAL::write_off_points_and_normals
@@ -159,7 +159,7 @@ template <typename Point, typename Vector>
 bool
 write_ply_point_set(
   std::ostream& stream, ///< output stream.
-  const Point_set_3<Point, Vector>& point_set)  ///< point set
+  const CGAL::Point_set_3<Point, Vector>& point_set)  ///< point set
 {
 
   stream << point_set;

Point_set_3/include/CGAL/Point_set_3/Point_set_processing_3.h

@@ -46,7 +46,7 @@ template <typename Concurrency_tag,
           typename Vector>
 double
 bilateral_smooth_point_set(
-  Point_set_3<Point, Vector>& point_set, ///< point set
+  CGAL::Point_set_3<Point, Vector>& point_set, ///< point set
   const unsigned int k,     ///< number of neighbors.
   double sharpness_angle)   ///< control sharpness(0-90)
 {
@@ -64,7 +64,7 @@ template <typename Concurrency_tag,
 	  typename Point, typename Vector>
 double
 compute_average_spacing(
-  const Point_set_3<Point, Vector>& point_set, ///< point set
+  const CGAL::Point_set_3<Point, Vector>& point_set, ///< point set
   unsigned int k) ///< number of neighbors.
 {
   return CGAL::compute_average_spacing<Concurrency_tag>
@@ -78,7 +78,7 @@ template <typename Concurrency_tag,
           typename Point, typename Vector>
 void
 edge_aware_upsample_point_set(
-  Point_set_3<Point, Vector>& point_set, ///< point set
+  CGAL::Point_set_3<Point, Vector>& point_set, ///< point set
   double sharpness_angle = 30,  ///< control sharpness(0-90)
   double edge_sensitivity = 1,  ///< edge sensitivity(0-5)
   double neighbor_radius = -1, ///< initial size of neighbors.
@@ -99,7 +99,7 @@ edge_aware_upsample_point_set(
  */
 template <typename Point, typename Vector>
 void grid_simplify_point_set(
-  Point_set_3<Point, Vector>& point_set, ///< point set
+  CGAL::Point_set_3<Point, Vector>& point_set, ///< point set
   double epsilon) ///< tolerance value when merging 3D points.
 {
   point_set.remove_from
@@ -115,7 +115,7 @@ void grid_simplify_point_set(
  */
 template <typename Point, typename Vector>
 void hierarchy_simplify_point_set(
-  Point_set_3<Point, Vector>& point_set, ///< point set
+  CGAL::Point_set_3<Point, Vector>& point_set, ///< point set
   const unsigned int size = 10, ///< maximum cluster size
   const double var_max = 0.333) ///< maximal surface variation
 {
@@ -135,7 +135,7 @@ template <typename Concurrency_tag,
 	  typename Point, typename Vector>
 void
 jet_estimate_normals(
-  Point_set_3<Point, Vector>& point_set, ///< point set
+  CGAL::Point_set_3<Point, Vector>& point_set, ///< point set
   unsigned int k, ///< number of neighbors.
   unsigned int degree_fitting = 2) ///< fitting degree
 {
@@ -155,7 +155,7 @@ template <typename Concurrency_tag,
 	  typename Point, typename Vector>
 void
 jet_smooth_point_set(
-  Point_set_3<Point, Vector>& point_set, ///< point set
+  CGAL::Point_set_3<Point, Vector>& point_set, ///< point set
   unsigned int k, ///< number of neighbors.
   unsigned int degree_fitting = 2, ///< fitting degree
   unsigned int degree_monge = 2)  ///< Monge degree
@@ -170,9 +170,9 @@ jet_smooth_point_set(
   \ingroup PkgPointSet3PointSetProcessing3
 */
 template <typename Point, typename Vector>
-typename Point_set_3<Point, Vector>::iterator
+typename CGAL::Point_set_3<Point, Vector>::iterator
 mst_orient_normals(
-  Point_set_3<Point, Vector>& point_set, ///< point set
+  CGAL::Point_set_3<Point, Vector>& point_set, ///< point set
   unsigned int k) ///< number of neighbors
 {
   return CGAL::mst_orient_normals
@@ -189,7 +189,7 @@ template <typename Concurrency_tag,
 	  typename Point, typename Vector>
 void
 pca_estimate_normals(
-  Point_set_3<Point, Vector>& point_set, ///< point set
+  CGAL::Point_set_3<Point, Vector>& point_set, ///< point set
   unsigned int k) ///< number of neighbors.
 {
   point_set.add_normal_map();
@@ -208,7 +208,7 @@ pca_estimate_normals(
  */
 template <typename Point, typename Vector>
 void random_simplify_point_set(
-  Point_set_3<Point, Vector>& point_set, ///< point set
+  CGAL::Point_set_3<Point, Vector>& point_set, ///< point set
   double removed_percentage) ///< percentage of points to remove
 {
   point_set.remove_from
@@ -225,7 +225,7 @@ void random_simplify_point_set(
  */
 template <typename Point, typename Vector>
 void remove_outliers(
-  Point_set_3<Point, Vector>& point_set, ///< point set
+  CGAL::Point_set_3<Point, Vector>& point_set, ///< point set
   unsigned int k, ///< number of neighbors.
   double threshold_percent) ///< percentage of points to remove
 {
@@ -242,7 +242,7 @@ void remove_outliers(
 template <typename Point, typename Vector>
 void
 vcm_estimate_normals(
-  Point_set_3<Point, Vector>& point_set, ///< point set
+  CGAL::Point_set_3<Point, Vector>& point_set, ///< point set
   double offset_radius, ///< offset radius.
   double convolution_radius) ///< convolution radius.
 {
@@ -262,7 +262,7 @@ vcm_estimate_normals(
 template <typename Point, typename Vector>
 void
 vcm_estimate_normals(
-  Point_set_3<Point, Vector>& point_set, ///< point set
+  CGAL::Point_set_3<Point, Vector>& point_set, ///< point set
   double offset_radius, ///< offset radius.
   unsigned int nb_neighbors_convolve) ///< number of neighbors used during the convolution.
 {
@@ -281,8 +281,8 @@ template <typename Concurrency_tag,
           typename Point, typename Vector>
 void
 wlop_simplify_and_regularize_point_set(
-  const Point_set_3<Point, Vector>& input_point_set, ///< input point set
+  const CGAL::Point_set_3<Point, Vector>& input_point_set, ///< input point set
-  Point_set_3<Point, Vector>& output_point_set, ///< output point set
+  CGAL::Point_set_3<Point, Vector>& output_point_set, ///< output point set
   const double select_percentage = 5,     ///< percentage of points to retain
   double neighbor_radius = -1,       ///< size of neighbors.
   const unsigned int max_iter_number = 35, ///< number of iterations.