Isosurfacing_3 - add openVDB oracle in an example

.gitignore

@@ -1,3 +1,4 @@
+build
 /*build*
 /*/*/*/build
 /*/*/*/VC*

Arrangement_on_surface_2/include/CGAL/Arr_conic_traits_2.h

@@ -2496,7 +2496,7 @@ class Arr_conic_traits_2 {
       double min_dist = -1;
       Integer aux_coeffs[6];
       for (int k = 1; k <= 2; ++k) {
-        // Get the integer coefficients of the k'th auxiliary conic curve.
+        // Get the integer coefficients of the k-th auxiliary conic curve.
         aux_rat_coeffs[0] = (k == 1) ? r_1 : r_2;
         aux_rat_coeffs[1] = (k == 1) ? s_1 : s_2;
         aux_rat_coeffs[2] = (k == 1) ? t_1 : t_2;
@@ -2512,7 +2512,7 @@ class Arr_conic_traits_2 {
                        (CGAL::sign(aux_coeffs[2]) == ZERO)) ? 1 : 2;
 
         // Compute the x- and y-coordinates of intersection points of the base
-        // conic and the k'th auxiliary conic.
+        // conic and the k-th auxiliary conic.
         int n_xs = compute_resultant_roots(*nt_traits,
                                            base_coeffs[0], base_coeffs[1],
                                            base_coeffs[2],

Arrangement_on_surface_2/include/CGAL/Arr_geometry_traits/Bezier_cache.h

@@ -590,7 +590,7 @@ bool _Bezier_cache<NtTraits>::_intersection_params
 
   // Consruct the bivariate polynomial that corresponds to Equation I.
   // Note that we represent a bivariate polynomial as a vector of univariate
-  // polynomials, whose i'th entry corresponds to the coefficient of t^i,
+  // polynomials, whose i-th entry corresponds to the coefficient of t^i,
   // which is in turn a polynomial it s.
   const int                degX_2 = nt_traits.degree (polyX_2);
   std::vector<Polynomial>  coeffsX_st (degX_2 < 0 ? 1 : (degX_2 + 1));
@@ -657,7 +657,7 @@ void _Bezier_cache<NtTraits>::_self_intersection_params
 
   // Consruct the bivariate polynomial that corresponds to Equation I.
   // Note that we represent a bivariate polynomial as a vector of univariate
-  // polynomials, whose i'th entry corresponds to the coefficient of t^i,
+  // polynomials, whose i-th entry corresponds to the coefficient of t^i,
   // which is in turn a polynomial it s.
   const int                degX = nt_traits.degree (polyX);
   CGAL_assertion(degX > 0);
@@ -771,7 +771,7 @@ _Bezier_cache<NtTraits>::_compute_resultant
     if (nt_traits.degree (mat[i][i]) < 0)
     {
       // If the current diagonal value is a zero polynomial, try to replace
-      // the current i'th row with a row with a higher index k, such that
+      // the current i-th row with a row with a higher index k, such that
       // mat[k][i] is not a zero polynomial.
 
       found_row = false;
@@ -786,7 +786,7 @@ _Bezier_cache<NtTraits>::_compute_resultant
 
       if (found_row)
       {
-        // Swap the i'th and the k'th rows (note that we start from the i'th
+        // Swap the i-th and the k-th rows (note that we start from the i-th
         // column, because the first i entries in every row with index i or
         // higher should be zero by now).
         for (j = i; j < dim; j++)
@@ -808,7 +808,7 @@ _Bezier_cache<NtTraits>::_compute_resultant
       }
     }
 
-    // Zero the whole i'th column of the following rows.
+    // Zero the whole i-th column of the following rows.
     for (k = i + 1; k < dim; k++)
     {
       if (nt_traits.degree (mat[k][i]) >= 0)
@@ -821,7 +821,7 @@ _Bezier_cache<NtTraits>::_compute_resultant
           mat[k][j] = mat[k][j] * mat[i][i] - mat[i][j] * value;
         }
 
-        // We multiplied the current row by the i'th diagonal entry, thus
+        // We multiplied the current row by the i-th diagonal entry, thus
         // multiplying the determinant value by it. We therefore increment
         // the exponent of mat[i][i] in the normalization factor.
         exp_fact[i] = exp_fact[i] + 1;

Arrangement_on_surface_2/include/CGAL/Arr_geometry_traits/Bezier_curve_2.h

@@ -411,7 +411,7 @@ class _Bezier_curve_2 :
   }
 
   /*!
-   * Get the i'th control point.
+   * Get the i-th control point.
    * \pre i must be between 0 and n - 1, where n is the number of control
    *      points.
    */
@@ -709,7 +709,7 @@ void _Bezier_curve_2_rep<RatKer, AlgKer, NtTrt,
     px = pts_begin->x();
     py = pts_begin->y();
 
-    // By simplifying (1 - t)^(n-k) we obtain that the k'th expression of
+    // By simplifying (1 - t)^(n-k) we obtain that the k-th expression of
     // the above sum is given by:
     //
     //     n-k

Arrangement_on_surface_2/include/CGAL/Arr_geometry_traits/Conic_arc_2.h

@@ -572,7 +572,7 @@ class Conic_arc_2 {
     int k;
 
     for (k = 1; k <= 2; ++k) {
-      // Get the integer coefficients of the k'th auxiliary conic curve.
+      // Get the integer coefficients of the k-th auxiliary conic curve.
       aux_rat_coeffs[0] = (k == 1) ? r_1 : r_2;
       aux_rat_coeffs[1] = (k == 1) ? s_1 : s_2;
       aux_rat_coeffs[2] = (k == 1) ? t_1 : t_2;
@@ -593,7 +593,7 @@ class Conic_arc_2 {
       }
 
       // Compute the x- and y-coordinates of intersection points of the base
-      // conic and the k'th auxiliary conic.
+      // conic and the k-th auxiliary conic.
       n_xs = compute_resultant_roots(nt_traits,
                                      base_coeffs[0], base_coeffs[1],
                                      base_coeffs[2],

Arrangement_on_surface_2/include/CGAL/Arr_geometry_traits/Conic_x_monotone_arc_2.h

@@ -1078,7 +1078,7 @@ class Conic_x_monotone_arc_2 : public ConicArc {
   }
 
 public:
-  /*! Obtain the i'th order derivative by x of the conic at the point p=(x,y).
+  /*! Obtain the i-th order derivative by x of the conic at the point p=(x,y).
    * \param p The point where we derive.
    * \param i The order of the derivatives (either 1, 2 or 3).
    * \param slope_numer The numerator of the slope.
@@ -1187,7 +1187,7 @@ class Conic_x_monotone_arc_2 : public ConicArc {
     CGAL_error();
   }
 
-  /*! Obtain the i'th order derivative by y of the conic at the point p=(x,y).
+  /*! Obtain the i-th order derivative by y of the conic at the point p=(x,y).
    * \param p The point where we derive.
    * \param i The order of the derivatives (either 1, 2 or 3).
    * \param slope_numer The numerator of the slope.

Arrangement_on_surface_2/include/CGAL/Arr_geometry_traits/de_Casteljau_2.h

@@ -77,7 +77,7 @@ bisect_control_polygon_2(InputIterator ctrl_pts_begin,
   while (last_index > 0)
   {
     // Construct (m - 1) control points from the m point we currently have,
-    // where the new i'th point is the midpoint between p[i]  and p[i + 1].
+    // where the new i-th point is the midpoint between p[i]  and p[i + 1].
     for (i = 0; i < last_index; ++i)
       vec[i] = midpoint(vec[i], vec[i + 1]);
 
@@ -134,7 +134,7 @@ typename InputIterator::value_type point_on_Bezier_curve_2
   while (last_index > 0)
   {
     // Construct (m - 1) control points from the m point we currently have,
-    // where the new i'th point is given by: (1 - t0)*p[i] + t0*p[i + 1].
+    // where the new i-th point is given by: (1 - t0)*p[i] + t0*p[i + 1].
     for (i = 0; i < last_index; ++i)
     {
       vec[i] = _Point_2(comp_t0*vec[i].x() + t0*vec[i + 1].x(),
@@ -197,7 +197,7 @@ typename InputIterator::value_type de_Casteljau_2
   while (last_index > 0)
   {
     // Construct (m - 1) control points from the m point we currently have,
-    // where the new i'th point is given by: (1 - t0)*p[i] + t0*p[i + 1].
+    // where the new i-th point is given by: (1 - t0)*p[i] + t0*p[i + 1].
     for (i = 0; i < last_index; ++i)
     {
       vec[i] = _Point_2(comp_t0*vec[i].x() + t0*vec[i + 1].x(),

Arrangement_on_surface_2/include/CGAL/Arr_polycurve_basic_traits_2.h

@@ -2704,7 +2704,7 @@ class Arr_polycurve_basic_traits_2 {
 
     if ((!is_vert(cv[0]) && (comp_x(get_min_v(cv[i]), q) == EQUAL)) ||
         (is_vert(cv[0]) && equal(get_min_v(cv[i]), q))){
-      // q is the left endpoint of the i'th subcurve:
+      // q is the left endpoint of the i-th subcurve:
       if (to_right) return i;
       else {
         // to_left
@@ -2722,7 +2722,7 @@ class Arr_polycurve_basic_traits_2 {
     if ((!is_vert(cv[0]) && (comp_x(get_max_v(cv[i]), q) == EQUAL)) ||
         (is_vert(cv[0]) && equal(get_max_v(cv[i]), q)))
     {
-      // q is the right endpoint of the i'th subcurve:
+      // q is the right endpoint of the i-th subcurve:
       if (!to_right) return i;
       else {
         if (direction == SMALLER) {

Arrangement_on_surface_2/include/CGAL/Arr_polycurve_traits_2.h

@@ -605,15 +605,15 @@ class Arr_polycurve_traits_2 :
       if (dir == SMALLER){
         // Check whether the split point is xcv[i]'s source or target.
         if (equal(max_vertex(xcv[i]), p)) {
-          // The entire i'th subcurve belongs to xcv1:
+          // The entire i-th subcurve belongs to xcv1:
           xcv1.push_back(xcv[i]);
         }
         else if (equal(min_vertex(xcv[i]), p)) {
-          // The entire i'th subcurves belongs to xcv2:
+          // The entire i-th subcurves belongs to xcv2:
           xcv2.push_back(xcv[i]);
         }
         else {
-          // The i'th subcurve should be split: The left part(seg1)
+          // The i-th subcurve should be split: The left part(seg1)
           // goes to xcv1, and the right part(seg2) goes to xcv2.
           X_monotone_subcurve_2 seg1, seg2;
           m_poly_traits.subcurve_traits_2()->split_2_object()(xcv[i], p,

Arrangement_on_surface_2/include/CGAL/CORE_algebraic_number_traits.h

@@ -541,7 +541,7 @@ class CORE_algebraic_number_traits
 
     for (i = 1; i <= n_roots; i++)
     {
-      // Get the i'th real-valued root.
+      // Get the i-th real-valued root.
       *oi = rootOf(poly, i);
       ++oi;
     }
@@ -603,7 +603,7 @@ class CORE_algebraic_number_traits
 
     for (i = 0; i < root_intervals.size(); i++)
     {
-      // Get the i'th real-valued root.
+      // Get the i-th real-valued root.
       *oi = rootOf(poly, root_intervals[i]);
       ++oi;
     }

Arrangement_on_surface_2/include/CGAL/Surface_sweep_2/Arr_construction_event_base.h

@@ -197,11 +197,11 @@ class Arr_construction_event_base :
   void init_subcurve_in_arrangement_flags(size_t n)
   { m_isCurveInArr.resize(n, false); }
 
-  /*! Check if the i'th subcurve is in the arrangement. */
+  /*! Check if the i-th subcurve is in the arrangement. */
   bool is_subcurve_in_arrangement(unsigned int i) const
   { return (m_isCurveInArr[i]); }
 
-  /*! Set the flag indicating whether the i'th subcurve is in the arrangement.
+  /*! Set the flag indicating whether the i-th subcurve is in the arrangement.
    */
   void set_subcurve_in_arrangement(unsigned int i, bool flag)
   { m_isCurveInArr[i] = flag; }

BGL/doc/BGL/BGL.txt

@@ -585,7 +585,7 @@ so that they <em>virtually</em> become border edges when exploring a seam mesh w
 The input mesh is referred to as <em>underlying</em> mesh of the seam mesh.
 We denote `tm` and `sm` the underlying mesh and the seam mesh respectively.
 
-Figure \cgalFigureRef{fig_Seam_mesh_1} shows an example of mesh on which two
+\cgalFigureRef{fig_Seam_mesh_1} shows an example of mesh on which two
 edges, defined by the halfedge pairs `h2-h3` and `h6-h7`, are marked as seams.
 The introduction of virtual borders modifies the elementary \bgl graph traversal
 operations: when we circulate around the target of `h7` in the underlying mesh,
@@ -599,7 +599,7 @@ A seam mesh with two seam edges `(h2, h3)` and `(h6, h7)`.
 \cgalFigureEnd
 
 A vertex of the underlying mesh may correspond to multiple vertices in the seam mesh.
-For example in Figure \cgalFigureRef{fig_Seam_mesh_1}, the target of `h7` corresponds to two
+For example in \cgalFigureRef{fig_Seam_mesh_1}, the target of `h7` corresponds to two
 vertices in the seam mesh, on either side of the virtual border created by the seam edges.
 For this reason, a vertex `v` of the seam mesh is internally represented as a halfedge `h`
 of the seam mesh. To obtain a canonical definition, the halfedge `h` is defined as the halfedge
@@ -611,7 +611,7 @@ For vertices `v` in the underlying mesh that are not on a seam edge, we choose
 \subsubsection BGLSeamMeshTraversal Seam Mesh Traversal
 
 Using the function `next(halfedge_descriptor, FaceGraph)`, we can walk around a face but also around
-a border of a mesh. For the seam mesh `sm` from Figure \cgalFigureRef{fig_Seam_mesh_1},
+a border of a mesh. For the seam mesh `sm` from \cgalFigureRef{fig_Seam_mesh_1},
 we have `opposite(h2, sm) == h3*`, and it holds that `face(h3*, sm) == null_face()`.
 We can walk along this virtual border: starting at `h3*` and repeatedly calling `next(..,sm)`,
 we will traverse `h6*`, `h7*`, `h2*`, before reaching `h3*` again.

CGAL_Core/include/CGAL/CORE/poly/Poly.tcc

@@ -382,7 +382,7 @@ int Polynomial<NT>::getTrueDegree() const {
   return -1;        // Zero polynomial
 }
 
-//get i'th Coeff. We check whether i is not greater than the
+//get i-th Coeff. We check whether i is not greater than the
 // true degree and if not then return coeff[i] o/w 0
 template <class NT>
 NT Polynomial<NT>::getCoeffi(int i) const {

CGAL_ImageIO/include/CGAL/IO/read_vtk_image_data.h

@@ -88,11 +88,10 @@ read_vtk_image_data(vtkImageData* vtk_image, Image_3::Own owning = Image_3::OWN_
   // If there is more than a scalar per point, vtk_image->data is not immediately
   // interpretable in Image_3->data
   CGAL_assertion(owning == Image_3::OWN_THE_DATA || cn == 1);
-
-  CGAL_assertion(vtk_image->GetPointData()->GetScalars()->GetNumberOfTuples() == dims[0]*dims[1]*dims[2]);
+  CGAL_assertion(vtk_image->GetPointData()->GetScalars()->GetNumberOfTuples() == static_cast<vtkIdType>(image->xdim*image->ydim*image->zdim));
 
   if(owning == Image_3::OWN_THE_DATA) {
-    int dims_n = dims[0]*dims[1]*dims[2];
+    std::size_t dims_n = image->xdim*image->ydim*image->zdim;
     image->data = ::ImageIO_alloc(dims_n * image->wdim);
 
     // std::cerr << "GetNumberOfTuples() = " << vtk_image->GetPointData()->GetScalars()->GetNumberOfTuples() << "\n"
@@ -110,7 +109,7 @@ read_vtk_image_data(vtkImageData* vtk_image, Image_3::Own owning = Image_3::OWN_
       char* src = static_cast<char*>(vtk_image->GetPointData()->GetScalars()->GetVoidPointer(0));
       char* dest = static_cast<char*>(image->data);
 
-      for(int i=0; i<dims_n; ++i)
+      for(std::size_t i=0; i<dims_n; ++i)
       {
         // multiply by image->wdim because we casted to char* and not the actual data type
         memcpy(dest + image->wdim*i, src + cn*image->wdim*i, image->wdim);

Circular_kernel_3/doc/Circular_kernel_3/Concepts/AlgebraicKernelForSpheres--XCriticalPoints.h

@@ -25,7 +25,7 @@ operator()(const AlgebraicKernelForSpheres::Polynomial_for_spheres_2_3 &p,
 OutputIterator res);
 
 /*!
-Computes the `i`th `x`-critical point of polynomial `p`.
+Computes the `i`-th `x`-critical point of polynomial `p`.
 */
 template < class OutputIterator >
 AlgebraicKernelForSpheres::Root_for_spheres_2_3

Circular_kernel_3/doc/Circular_kernel_3/Concepts/AlgebraicKernelForSpheres--YCriticalPoints.h

@@ -25,7 +25,7 @@ operator()(const AlgebraicKernelForSpheres::Polynomial_for_spheres_2_3 &p,
 OutputIterator res);
 
 /*!
-Computes the `i`th `y`-critical point of polynomial `p`.
+Computes the `i`-th `y`-critical point of polynomial `p`.
 */
 template < class OutputIterator >
 AlgebraicKernelForSpheres::Root_for_spheres_2_3

Circular_kernel_3/doc/Circular_kernel_3/Concepts/AlgebraicKernelForSpheres--ZCriticalPoints.h

@@ -25,7 +25,7 @@ operator()(const AlgebraicKernelForSpheres::Polynomial_for_spheres_2_3 &p,
 OutputIterator res);
 
 /*!
-Computes the `i`th `z`-critical point of polynomial `p`.
+Computes the `i`-th `z`-critical point of polynomial `p`.
 */
 template < class OutputIterator >
 AlgebraicKernelForSpheres::Root_for_spheres_2_3

Classification/doc/Classification/Classification.txt

@@ -10,7 +10,7 @@ This component implements the algorithm described in \cgalCite{cgal:lm-clscm-12}
 
 \section Classification_Organization Package Organization
 
-%Classification of data sets is achieved as follows (see Figure \cgalFigureRef{Classification_organization_fig}):
+%Classification of data sets is achieved as follows (see \cgalFigureRef{Classification_organization_fig}):
 
 - some analysis is performed on the input data set;
 - features are computed based on this analysis;
@@ -314,15 +314,15 @@ Though it is possible to set them up one by one, \cgal also provides a method [t
 
 - the same mechanism is repeated until all features' ranges have been tested. Weights are only changed one by one, the other ones are kept to the values that gave the latest best score.
 
-This usually converges to a satisfying solution (see Figure \cgalFigureRef{Classification_trainer_fig}). The number of trials is user defined, set to 300 by default. Using at least 10 times the number of features is advised (for example, at least 300 iterations if 30 features are used). If the solution is not satisfying, more inliers can be selected, for example, in a region that the user identifies as misclassified with the current configuration. The training algorithm keeps, as initialization, the best weights found at the previous round and carries on trying new weights by taking new inliers into account.
+This usually converges to a satisfying solution (see \cgalFigureRef{Classification_trainer_fig}). The number of trials is user defined, set to 300 by default. Using at least 10 times the number of features is advised (for example, at least 300 iterations if 30 features are used). If the solution is not satisfying, more inliers can be selected, for example, in a region that the user identifies as misclassified with the current configuration. The training algorithm keeps, as initialization, the best weights found at the previous round and carries on trying new weights by taking new inliers into account.
 
 \cgalFigureBegin{Classification_trainer_fig,classif_training.png}
 Example of evolution of the mean intersection-over-union. The purple curve is the score computed at the current iteration, green curve is the best score found so far.
 \cgalFigureEnd
 
 \subsubsection Classification_sowf_result Result
 
-Figure \cgalFigureRef{Classification_sowf_result_fig} shows an example of output on a defect-laden point set. The accuracy on this example is 0.97 with a mean intersection-over-union of 0.85 (see section \ref Classification_evaluation).
+\cgalFigureRef{Classification_sowf_result_fig} shows an example of output on a defect-laden point set. The accuracy on this example is 0.97 with a mean intersection-over-union of 0.85 (see section \ref Classification_evaluation).
 
 \cgalFigureBegin{Classification_sowf_result_fig,noise_outliers.png}
 Example of classification on a point set with medium noise and outliers (left: input, right: output). _Ground_ is orange, _roofs_ are pink, _vegetation_ is green. Outliers are classified with an additional label _outlier_ in black.
@@ -398,7 +398,7 @@ smoothing by providing a model of `CGAL::Classification::NeighborQuery`.
 
 - `CGAL::Classification::classify_with_graphcut()`: this method
 offers the best quality but requires longer computation time (see
-Figure \cgalFigureRef{Classification_image}, bottom-right). The
+\cgalFigureRef{Classification_image}, bottom-right). The
 total energy that is minimized is the sum of the partial data term
 \f$E_{di}(x_i)\f$ and of a pairwise interaction energy defined by the
 standard Potts model \cgalCite{cgal:l-mrfmi-09} :

Combinatorial_map/include/CGAL/Combinatorial_map/internal/Combinatorial_map_utility.h

@@ -159,7 +159,7 @@ namespace CGAL
     };
 
     //count the number of time a given type have been found
-    //within a tuple, until reaching position the k'th type of the tuple.
+    //within a tuple, until reaching position the k-th type of the tuple.
     //dim is the total size of the tuple
     template <class Type,int k,class T,
               int dim=CGAL::internal::My_length<T>::value-1>
@@ -191,7 +191,7 @@ namespace CGAL
     };
 
     //count the number of time a type different from Type have been found
-    //within a tuple, until reaching position the k'th type of the tuple.
+    //within a tuple, until reaching position the k-th type of the tuple.
     //dim is the total size of the tuple
     template <class Type, int k,class T,
               int dim=CGAL::internal::My_length<T>::value-1>
@@ -339,7 +339,7 @@ namespace CGAL
     };
 
     //Same as Foreach_static excepted that Functor
-    //is called for case k only if the k'th type in the tuple
+    //is called for case k only if the k-th type in the tuple
     //is different from Void. Note that to the converse of Foreach_static
     //Functor are called from n =0 to k
     template <class Functor,class T,int n=0, int startn=0>
@@ -365,7 +365,7 @@ namespace CGAL
     };
 
     //Same as Foreach_static_restricted excepted that Functor
-    //is called for case k only if the k'th type in the tuple
+    //is called for case k only if the k-th type in the tuple
     //is different from Void and k!=j.
     template <class Functor,int j,class T,int n=0>
     struct Foreach_static_restricted_except;

Documentation/doc/Documentation/packages.txt

@@ -93,6 +93,7 @@
 \package_listing{Skin_surface_3}
 \package_listing{SMDS_3}
 \package_listing{Mesh_3}
+\package_listing{Isosurfacing_3}
 \package_listing{Tetrahedral_remeshing}
 \package_listing{Periodic_3_mesh_3}
 \package_listing{Alpha_wrap_3}