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[cgal-discuss] Re: Extracting triangulation from alpha shape


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  • From: rcasero <>
  • To:
  • Subject: [cgal-discuss] Re: Extracting triangulation from alpha shape
  • Date: Mon, 5 Aug 2013 07:33:15 -0700 (PDT)
Many thanks for your quick reply and fix. I have updated the alpha shape function here

https://code.google.com/p/gerardus/source/browse/trunk/matlab/CgalToolbox/CgalAlphaShape3.cpp?r=1285

and added your patched file here

https://code.google.com/p/gerardus/source/browse/trunk/cpp/src/third-party/CGAL-4.2/include/CGAL/Triangulation_hierarchy_3.h?spec=svn1285&r=1285

(As a side note, I haven't noticed a speed improvement with the 400,000 point example).

Best regards,

Ramon.

On 5 August 2013 14:08, Sebastien Loriot (GeometryFactory) [via cgal-discuss] <[hidden email]> wrote:
It's a bug.

Try with the attached file instead of the one in CGAL/.

Sebastien.

On 08/05/2013 02:20 PM, rcasero wrote:

> Hi,
>
> As a follow up, I have commited the Matlab MEX function that uses CGAL's
> Alpha_Shape_3 here [1] to share
>
> https://code.google.com/p/gerardus/source/browse/trunk/matlab/CgalToolbox/CgalAlphaShape3.cpp?r=1284
>
> That code builds and works. But as I have point sets with 400,000+
> points, I tried to add the flag CGAL::Fast_location to the Delaunay
> triangulation, replacing
>
> typedefCGAL::Delaunay_triangulation_3<K,Tds>Delaunay;
>
> with
>
> typedef CGAL::Delaunay_triangulation_3<K, Tds, CGAL::Fast_location>
> Delaunay;
>
> as in example"43.5.2   Building Basic Alpha Shapes for Many Points"
>
> http://www.cgal.org/Manual/latest/doc_html/cgal_manual/Alpha_shapes_3/Chapter_main.html#Subsection_43.5.2
>

> However, this seems to give trouble with the PointWithIndex class, and I
> get a compilation error. The full error is given below, but digging a
> bit into it, it seems that the problem is with
>
> /home/rcasero/Documents/gerardus/matlab/CgalToolbox/CgalAlphaShape3.cpp:175:
>    instantiated from here
> /usr/include/c++/4.4/bits/stl_uninitialized.h:74: error: no matching
> function for call to
> ‘CGAL::Point_3<CGAL::Epick>::Point_3(std::pair<CGAL::Point_3<CGAL::Epick>,
> long unsigned int>&)’
>
> Line 175 of CgalAlphaShape3.cpp is
>
> https://code.google.com/p/gerardus/source/browse/trunk/matlab/CgalToolbox/CgalAlphaShape3.cpp?r=1284#175
>

> <CODE>
> Delaunay delaunay(x.begin(), x.end());
> </CODE>
>
> So is this a limitation of the Delaunay triangulation class when using a
> PointWithIndex, that only happens with CGAL::Fast_location? Or am I
> reading the error the wrong way?
>
> Best regards,
>
> Ramon.
>
>
> <FULL ERROR>
> [100%] Building CXX object
> matlab/CgalToolbox/CMakeFiles/cgal_alpha_shape3.dir/CgalAlphaShape3.cpp.o
> In file included from /usr/include/c++/4.4/vector:64,
>                   from
> /usr/local/include/ITK-4.3/itkMetaDataDictionary.h:22,
>                   from /usr/local/include/ITK-4.3/itkObject.h:33,
>                   from /usr/local/include/ITK-4.3/itkDataObject.h:31,
>                   from /usr/local/include/ITK-4.3/itkProcessObject.h:31,
>                   from /usr/local/include/ITK-4.3/itkImageSource.h:31,
>                   from /usr/local/include/ITK-4.3/itkImportImageFilter.h:21,
>                   from
> /home/rcasero/Documents/gerardus/matlab/CgalToolbox/../MatlabImportFilter.h:52,
>                   from
> /home/rcasero/Documents/gerardus/matlab/CgalToolbox/CgalAlphaShape3.cpp:81:
> /usr/include/c++/4.4/bits/stl_uninitialized.h: In static member function
> ‘static _ForwardIterator std::__uninitialized_copy<<anonymous>
>  >::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator)
> [with _InputIterator =
> __gnu_cxx::__normal_iterator<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int>*, std::vector<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int>, std::allocator<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int> > > >, _ForwardIterator = CGAL::Point_3<CGAL::Epick>*,
> bool <anonymous> = false]’:
> /usr/include/c++/4.4/bits/stl_uninitialized.h:117:   instantiated from
> ‘_ForwardIterator std::uninitialized_copy(_InputIterator,
> _InputIterator, _ForwardIterator) [with _InputIterator =
> __gnu_cxx::__normal_iterator<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int>*, std::vector<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int>, std::allocator<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int> > > >, _ForwardIterator = CGAL::Point_3<CGAL::Epick>*]’
> /usr/include/c++/4.4/bits/stl_uninitialized.h:257:   instantiated from
> ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator,
> _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with
> _InputIterator =
> __gnu_cxx::__normal_iterator<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int>*, std::vector<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int>, std::allocator<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int> > > >, _ForwardIterator = CGAL::Point_3<CGAL::Epick>*, _Tp
> = CGAL::Point_3<CGAL::Epick>]’
> /usr/include/c++/4.4/bits/stl_vector.h:1024:   instantiated from ‘void
> std::vector<_Tp, _Alloc>::_M_range_initialize(_ForwardIterator,
> _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator =
> __gnu_cxx::__normal_iterator<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int>*, std::vector<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int>, std::allocator<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int> > > >, _Tp = CGAL::Point_3<CGAL::Epick>, _Alloc =
> std::allocator<CGAL::Point_3<CGAL::Epick> >]’
> /usr/include/c++/4.4/bits/stl_vector.h:1002:   instantiated from ‘void
> std::vector<_Tp, _Alloc>::_M_initialize_dispatch(_InputIterator,
> _InputIterator, std::__false_type) [with _InputIterator =
> __gnu_cxx::__normal_iterator<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int>*, std::vector<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int>, std::allocator<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int> > > >, _Tp = CGAL::Point_3<CGAL::Epick>, _Alloc =
> std::allocator<CGAL::Point_3<CGAL::Epick> >]’
> /usr/include/c++/4.4/bits/stl_vector.h:303:   instantiated from
> ‘std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const
> _Alloc&) [with _InputIterator =
> __gnu_cxx::__normal_iterator<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int>*, std::vector<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int>, std::allocator<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int> > > >, _Tp = CGAL::Point_3<CGAL::Epick>, _Alloc =
> std::allocator<CGAL::Point_3<CGAL::Epick> >]’
> /home/rcasero/Documents/gerardus/cpp/src/third-party/CGAL-4.2/include/CGAL/Triangulation_hierarchy_3.h:133:
>    instantiated from ‘ptrdiff_t
> CGAL::Triangulation_hierarchy_3<Tr>::insert(InputIterator,
> InputIterator) [with InputIterator =
> __gnu_cxx::__normal_iterator<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int>*, std::vector<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int>, std::allocator<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int> > > >, Tr = CGAL::Delaunay_triangulation_3<CGAL::Epick,
> CGAL::Triangulation_data_structure_3<CGAL::Triangulation_hierarchy_vertex_base_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick,
> CGAL::Triangulation_vertex_base_with_info_3<long unsigned int,
> CGAL::Epick, CGAL::Triangulation_vertex_base_3<CGAL::Epick,
> CGAL::Triangulation_ds_vertex_base_3<CGAL::Triangulation_data_structure_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick,
> CGAL::Triangulation_vertex_base_with_info_3<long unsigned int,
> CGAL::Epick, CGAL::Triangulation_vertex_base_3<CGAL::Epick,
> CGAL::Triangulation_ds_vertex_base_3<void> > >,
> CGAL::Boolean_tag<false>, CGAL::Boolean_tag<false> >,
> CGAL::Alpha_shape_cell_base_3<CGAL::Epick, CGAL::Default,
> CGAL::Boolean_tag<false>, CGAL::Boolean_tag<false> > > > > >,
> CGAL::Boolean_tag<false>, CGAL::Boolean_tag<false> > >,
> CGAL::Alpha_shape_cell_base_3<CGAL::Epick, CGAL::Default,
> CGAL::Boolean_tag<false>, CGAL::Boolean_tag<false> > >, CGAL::Default>]’
> /home/rcasero/Documents/gerardus/cpp/src/third-party/CGAL-4.2/include/CGAL/Triangulation_hierarchy_3.h:98:
>    instantiated from
> ‘CGAL::Triangulation_hierarchy_3<Tr>::Triangulation_hierarchy_3(InputIterator,
> InputIterator, const typename Tr::Geom_traits&) [with InputIterator =
> __gnu_cxx::__normal_iterator<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int>*, std::vector<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int>, std::allocator<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int> > > >, Tr = CGAL::Delaunay_triangulation_3<CGAL::Epick,
> CGAL::Triangulation_data_structure_3<CGAL::Triangulation_hierarchy_vertex_base_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick,
> CGAL::Triangulation_vertex_base_with_info_3<long unsigned int,
> CGAL::Epick, CGAL::Triangulation_vertex_base_3<CGAL::Epick,
> CGAL::Triangulation_ds_vertex_base_3<CGAL::Triangulation_data_structure_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick,
> CGAL::Triangulation_vertex_base_with_info_3<long unsigned int,
> CGAL::Epick, CGAL::Triangulation_vertex_base_3<CGAL::Epick,
> CGAL::Triangulation_ds_vertex_base_3<void> > >,
> CGAL::Boolean_tag<false>, CGAL::Boolean_tag<false> >,
> CGAL::Alpha_shape_cell_base_3<CGAL::Epick, CGAL::Default,
> CGAL::Boolean_tag<false>, CGAL::Boolean_tag<false> > > > > >,
> CGAL::Boolean_tag<false>, CGAL::Boolean_tag<false> > >,
> CGAL::Alpha_shape_cell_base_3<CGAL::Epick, CGAL::Default,
> CGAL::Boolean_tag<false>, CGAL::Boolean_tag<false> > >, CGAL::Default>]’
> /home/rcasero/Documents/gerardus/cpp/src/third-party/CGAL-4.2/include/CGAL/internal/Delaunay_triangulation_hierarchy_3.h:55:
>    instantiated from ‘CGAL::Delaunay_triangulation_3<Gt, Tds_,
> CGAL::Location_policy<CGAL::Fast>
>  >::Delaunay_triangulation_3(InputIterator, InputIterator, const Gt&)
> [with InputIterator =
> __gnu_cxx::__normal_iterator<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int>*, std::vector<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int>, std::allocator<std::pair<CGAL::Point_3<CGAL::Epick>, long
> unsigned int> > > >, Gt = CGAL::Epick, Tds_ =
> CGAL::Triangulation_data_structure_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick,
> CGAL::Triangulation_vertex_base_with_info_3<long unsigned int,
> CGAL::Epick, CGAL::Triangulation_vertex_base_3<CGAL::Epick,
> CGAL::Triangulation_ds_vertex_base_3<void> > >,
> CGAL::Boolean_tag<false>, CGAL::Boolean_tag<false> >,
> CGAL::Alpha_shape_cell_base_3<CGAL::Epick, CGAL::Default,
> CGAL::Boolean_tag<false>, CGAL::Boolean_tag<false> > >]’
> /home/rcasero/Documents/gerardus/matlab/CgalToolbox/CgalAlphaShape3.cpp:175:
>    instantiated from here
> /usr/include/c++/4.4/bits/stl_uninitialized.h:74: error: no matching
> function for call to
> ‘CGAL::Point_3<CGAL::Epick>::Point_3(std::pair<CGAL::Point_3<CGAL::Epick>,
> long unsigned int>&)’
> /home/rcasero/Documents/gerardus/cpp/src/third-party/CGAL-4.2/include/CGAL/Point_3.h:83:
> note: candidates are: CGAL::Point_3<R_>::Point_3(const typename R_::RT&,
> const typename R_::RT&, const typename R_::RT&, const typename R_::RT&)
> [with R_ = CGAL::Epick]
> /home/rcasero/Documents/gerardus/cpp/src/third-party/CGAL-4.2/include/CGAL/Point_3.h:75:
> note:                 CGAL::Point_3<R_>::Point_3(const typename
> R_::Kernel_base::Point_3&) [with R_ = CGAL::Epick]
> /home/rcasero/Documents/gerardus/cpp/src/third-party/CGAL-4.2/include/CGAL/Point_3.h:71:
> note:                 CGAL::Point_3<R_>::Point_3(const CGAL::Origin&)
> [with R_ = CGAL::Epick]
> /home/rcasero/Documents/gerardus/cpp/src/third-party/CGAL-4.2/include/CGAL/Point_3.h:69:
> note:                 CGAL::Point_3<R_>::Point_3() [with R_ = CGAL::Epick]
> /home/rcasero/Documents/gerardus/cpp/src/third-party/CGAL-4.2/include/CGAL/Point_3.h:40:
> note:                 CGAL::Point_3<CGAL::Epick>::Point_3(const
> CGAL::Point_3<CGAL::Epick>&)
> make[2]: ***
> [matlab/CgalToolbox/CMakeFiles/cgal_alpha_shape3.dir/CgalAlphaShape3.cpp.o]
> Error 1
> make[1]: *** [matlab/CgalToolbox/CMakeFiles/cgal_alpha_shape3.dir/all]
> Error 2
> make: *** [all] Error 2
> </FULL ERROR>
>
>
>
>
> On 2 August 2013 12:55, Ramón Casero Cañas <[hidden email]
> </user/SendEmail.jtp?type=node&node=4657880&i=0>> wrote:

>
>     Hi Sebastien,
>
>     Many thanks for your indications. I struggled a bit to find the
>     correct way to combine Triangulation_vertex_base_with_info_3
>     and Alpha_shape_3, but it seems to work in the end. Here's a code
>     snippet in case it's useful for somebody else (I'm programming a
>     Matlab MEX C++ function, so some types are specific to Matlab)
>
>     <CODE>
>     /* CGAL headers */
>     #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
>     #include <CGAL/Delaunay_triangulation_3.h>
>     #include <CGAL/Triangulation_vertex_base_with_info_3.h>
>     #include <CGAL/Alpha_shape_3.h>
>
>     typedef CGAL::Exact_predicates_inexact_constructions_kernel K;
>     // vertex
>     typedef CGAL::Triangulation_vertex_base_with_info_3<mwSize, K>  Vb;
>     typedef CGAL::Alpha_shape_vertex_base_3<K, Vb>       AsVb;
>     // cell
>     typedef CGAL::Alpha_shape_cell_base_3<K>             Fb;
>     // triangulation structure: vertex and cell
>     typedef CGAL::Triangulation_data_structure_3<AsVb, Fb> Tds;
>     typedef CGAL::Delaunay_triangulation_3<K, Tds>       Delaunay;
>     typedef CGAL::Alpha_shape_3<Delaunay>                Alpha_shape_3;
>
>     typedef K::Point_3                                   Point;
>     typedef std::pair<Point, mwIndex>                    PointWithIndex;
>     typedef Alpha_shape_3::Alpha_iterator                Alpha_iterator;
>
>     typedef Alpha_shape_3::Facet                         Facet;
>
>        // read points from function
>        std::vector<PointWithIndex> x(nrowsX);
>        for (mwIndex i = 0; i < nrowsX; ++i) {
>          x[i] = std::make_pair(
>        some_function_to_read_a_point(i),
>       i+1 // because this will be a row index in Matlab, 1, ..., Nrows
>       );
>        }
>
>        // Delaunay triangulation
>        //
>     http://www.cgal.org/Manual/latest/doc_html/cgal_manual/Triangulation_3/Chapter_main.html#Subsection_39.5.3
>        Delaunay delaunay(x.begin(), x.end());

>        CGAL_assertion(delaunay.number_of_vertices() == nrowsX);
>
>        // compute alpha shape
>        Alpha_shape_3 as(delaunay);
>     </CODE>
>
>     Best regards,
>
>     Ramón.
>
>
>
>     On 2 August 2013 06:29, Sebastien Loriot (GeometryFactory) [via
>     cgal-discuss] <[hidden email]
>     </user/SendEmail.jtp?type=node&node=4657880&i=1>> wrote:

>
>         Use one of the following examples [1] to build the triangulation
>         of your
>         points and set their indices. Then build the alpha shape from the
>         triangulation.
>
>         then you can do:
>
>         typedef CGAL::Delaunay_triangulation_3<.....> DT3;
>
>         ....
>
>         for (std::list<Facet>::iterator it = facets.begin(); it !=
>         facets.end();
>            ++it)
>         {
>             it->first->vertex( DT3::vertex_triple_index(it->second,0)
>         )->info();
>             it->first->vertex( DT3::vertex_triple_index(it->second,1)
>         )->info();
>             it->first->vertex( DT3::vertex_triple_index(it->second,2)
>         )->info();
>         }
>
>         Sebastien.
>
>         [1]
>         http://www.cgal.org/Manual/latest/doc_html/cgal_manual/Triangulation_3/Chapter_main.html#Subsection_39.5.3
>

>         On 08/01/2013 08:44 PM, rcasero wrote:
>
>          > Dear all,
>          >
>          > I'm computing alpha shapes on a set of points
>          >
>          >    // read points from function
>          >    std::vector<Point>  x =
>          >      some_function_to_read_points();
>          >
>          >    // compute alpha shape
>          >    Alpha_shape_3 as(x.begin(), x.end());
>          >
>          > based on the example from the "3D Alpha shapes" documentation:
>          >
>          >
>         http://www.cgal.org/Manual/latest/doc_html/cgal_manual/Alpha_shapes_3/Chapter_main.html#Subsection_43.5.1
>          >

>
>          > What I would like to do now is extract the triangulation of a
>         given alpha
>          > shape in index form, e.g.
>          >
>          > tri = [3 2 8
>          >          2 1 3
>          >         ...]
>          >
>          > where the indices are the indices of the points in the x
>         vector above.
>          >
>          > This is similar to a previous question I got help from
>         Sebastien Loriot to
>          >
>          >
>         http://cgal-discuss.949826.n4.nabble.com/Getting-index-of-facet-closest-to-a-point-tp4657635.html
>          >

>
>          > but I don't manage to find the right pointers in this case so
>         that I can do
>          > something like
>          >
>          >     std::distance(x.begin(), some_iterator_here);
>          >
>          > to get the index.
>          >
>          > I can get a list of the facets
>          >
>          >    // get alpha-shape surface
>          >    std::list<Facet>        facets;
>          >    as.get_alpha_shape_facets(std::back_inserter(facets),
>          >                              Alpha_shape_3::REGULAR);
>          >
>          > and I can iterate said facets
>          >
>          >    for (std::list<Facet>::iterator it = facets.begin(); it !=
>         facets.end();
>          > ++it) {
>          >
>          >    }
>          >
>          >  From the documentation and an old question replied to by
>         sloriot
>          >
>          >
>         http://stackoverflow.com/questions/7938311/cgal-help-getting-triangles-coordinates-from-delaunay-triangulation
>          >

>
>          > I know I can the coordinates of the facet vertices as
>          >
>          >    for (std::list<Facet>::iterator it = facets.begin(); it !=
>         facets.end();
>          > ++it) {
>          >
>          >      it->first->vertex((it->second+1)%4)->point();
>          >      it->first->vertex((it->second+2)%4)->point();
>          >      it->first->vertex((it->second+3)%4)->point();
>          >
>          >    }
>          >
>          > but the it->...->point(); above are not pointing to elements
>         in x, neither
>          > it->first->vertex((it->second+1)%4).
>          >
>          > Many thanks for any help or, ahem, pointers.
>          >
>          > Best regards,
>          >
>          > Ramon.
>          >
>          >
>          >
>          > --
>          > View this message in context:
>         http://cgal-discuss.949826.n4.nabble.com/Extracting-triangulation-from-alpha-shape-tp4657870.html
>          > Sent from the cgal-discuss mailing list archive at Nabble.com.

>          >
>
>
>         --
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> Dr. Ramón Casero Cañas
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> Oxford e-Research Centre (OeRC)
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> photos http://www.flickr.com/photos/rcasero/
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Dr. Ramón Casero Cañas

Oxford e-Research Centre (OeRC)
University of Oxford
7 Keble Rd
Oxford OX1 3QG

tlf     +44 (0) 1865 610739
web     http://www.cs.ox.ac.uk/people/Ramon.CaseroCanas
photos  http://www.flickr.com/photos/rcasero/

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