CGAL users discussion list

[Ramón Casero Cañas <>]

Replying to myself, I had got confused, as the CGAL::Labeled_image_mesh_domain_3 is for volumetric meshes, not surfaces meshes.

In the end, I managed to make it work following the example more closely, with a CGAL::Gray_level_image_3 and CGAL::Implicit_surface_3.

The code is here in case it's useful for somebody else (it's a Matlab MEX wrapper around  CGAL::make_surface_mesh)

https://code.google.com/p/gerardus/source/browse/trunk/matlab/CgalToolbox/CgalMeshSegmentation.cpp

Cheers,

Ramon.

On 24 September 2013 12:01, Ramón Casero Cañas <> wrote:

Dear all,

I'm trying to mesh a segmentation (labelled image). So far I've been trying with the "3D Surface Mesh Generation" package.

http://www.cgal.org/Manual/latest/doc_html/cgal_manual/Surface_mesher/Chapter_main.html

I haven't found an example for this online, so I'm trying to adapt "Example 48.3.2 Meshing Isosurfaces Defined as Gray Levels in 3D Images" to labelled images, but I'm shooting a bit in the dark.

As my image lives in Matlab memory, I have written a function to get the pointer and metainformation into a CGAL _image struct.

  // get Matlab image pointer and metadata in CGAL format

  _image *im = matlabImport->ReadCgalImageFromMatlab(inIM);

Otherwise, I'm trying to stick to the example, replacing the gray image by a labelled image, but I'm doing something wrong. The parts of my code that are relevant to CGAL are:

/* CGAL headers */

#include <CGAL/Surface_mesh_default_triangulation_3.h>

#include <CGAL/Surface_mesh_default_criteria_3.h>

#include <CGAL/Complex_2_in_triangulation_3.h>

#include <CGAL/IO/Complex_2_in_triangulation_3_file_writer.h>

#include <CGAL/make_surface_mesh.h>

//#include <CGAL/Gray_level_image_3.h>

#include <CGAL/Labeled_image_mesh_domain_3.h>

#include <CGAL/Implicit_surface_3.h>

#include <CGAL/ImageIO.h>

#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>

// default triangulation for Surface_mesher

typedef CGAL::Surface_mesh_default_triangulation_3 Tr;

// c2t3

typedef CGAL::Complex_2_in_triangulation_3<Tr> C2t3;

// labelled image

typedef Tr::Geom_traits GT;

//typedef CGAL::Gray_level_image_3<GT::FT, GT::Point_3> Gray_level_image;

typedef CGAL::Exact_predicates_inexact_constructions_kernel K;

typedef CGAL::Labeled_image_mesh_domain_3<CGAL::Image_3, K> Mesh_domain;

typedef CGAL::Implicit_surface_3<GT, Mesh_domain> Surface_3;

void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]) {

// some Matlab stuff

...

  // get Matlab image pointer and metadata in CGAL format

  _image *im = matlabImport->ReadCgalImageFromMatlab(inIM);

  // Carefully choosen bounding sphere: the center must be inside the

  // surface defined by 'image' and the radius must be high enough so that

  // the sphere actually bounds the whole image.

  GT::Point_3 bounding_sphere_center(2.0, 2.0, 2.0);

  GT::FT bounding_sphere_squared_radius = 5.0*5.0*5.0;

  GT::Sphere_3 bounding_sphere(bounding_sphere_center,

      bounding_sphere_squared_radius);

  // say that the input image is a labeled segmentation that is going

  // to be meshed

  Mesh_domain domain(im);

  // definition of the surface, with 10^-5 as relative precision

  Surface_3 surface(domain, bounding_sphere, 1e-5);

  Tr tr;            // 3D-Delaunay triangulation

  C2t3 c2t3 (tr);   // 2D-complex in 3D-Delaunay triangulation

  // Mesh criteria

  CGAL::Surface_mesh_default_criteria_3<Tr> criteria(30.,

                                                     5.,

                                                     5.);

  // Meshing

  CGAL::make_surface_mesh(c2t3, surface, criteria, CGAL::Manifold_tag());

  // Output

  std::ofstream medit_file("/tmp/out.mesh");

  c2t3.output_to_medit(medit_file);

}

But I get a compilation error in line

Surface_3 surface(domain, bounding_sphere, 1e-5);

/home/rcasero/Documents/gerardus/cpp/src/third-party/CGAL-4.2/include/CGAL/Labeled_image_mesh_domain_3.h: In function ‘void mexFunction(int, mxArray**, int, const mxArray**)’:

/home/rcasero/Documents/gerardus/cpp/src/third-party/CGAL-4.2/include/CGAL/Labeled_image_mesh_domain_3.h:79: error: ‘CGAL::Labeled_image_mesh_domain_3<Image, BGT, Wrapper>::Labeled_image_mesh_domain_3(const CGAL::Labeled_image_mesh_domain_3<Image, BGT, CGAL::Mesh_3::Image_to_labeled_function_wrapper<Image, BGT, unsigned char, int, true> >&) [with Image = CGAL::Image_3, BGT = CGAL::Epick, Wrapper = CGAL::Mesh_3::Image_to_labeled_function_wrapper<CGAL::Image_3, CGAL::Epick, unsigned char, int, true>]’ is private

/home/rcasero/Documents/gerardus/matlab/CgalToolbox/CgalMeshSegmentation.cpp:92: error: within this context

/home/rcasero/Documents/gerardus/matlab/CgalToolbox/CgalMeshSegmentation.cpp:92: error:   initializing argument 1 of ‘CGAL::Implicit_surface_3<GT, Function_>::Implicit_surface_3(Function_, typename GT::Sphere_3, typename GT::FT, GT) [with GT = CGAL::Robust_circumcenter_traits_3<CGAL::Epick>, Function_ = CGAL::Labeled_image_mesh_domain_3<CGAL::Image_3, CGAL::Epick, CGAL::Mesh_3::Image_to_labeled_function_wrapper<CGAL::Image_3, CGAL::Epick, unsigned char, int, true> >]’

/home/rcasero/Documents/gerardus/matlab/CgalToolbox/CgalMeshSegmentation.cpp:108: error: ‘class C2t3’ has no member named ‘output_to_medit’

[...other errors edited out...]

As I'm not too sure of what I'm doing, any examples or indications on how to tackle this would be welcome.

Best regards,

Ramon.

--
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/

--
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/