CGAL users discussion list

[elhassan Abdou <>]

This  snippet of code is a Part of Voreen code. I first generated binary 
image mask of the brain(I do not have a full atlas of the brain) , so my data 
are voxels with zeros and 10. 10 represents the brain mask, and zero is empty 
space.  I am sure the entire brain is totally fill with no holes inside it 
except in a region that I made.(which is the aim of my project). 
this the including part in the my .h
#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>

#include <CGAL/Mesh_triangulation_3.h>
#include <CGAL/Mesh_complex_3_in_triangulation_3.h>
#include <CGAL/Mesh_criteria_3.h>

#include <CGAL/Labeled_image_mesh_domain_3.h>
#include <CGAL/make_mesh_3.h>
#include <CGAL/Image_3.h>
// Domain
typedef CGAL::Exact_predicates_inexact_constructions_kernel K;
typedef CGAL::Labeled_image_mesh_domain_3<CGAL::Image_3,K> Mesh_domain;

// Triangulation
typedef CGAL::Mesh_triangulation_3<Mesh_domain>::type Tr;
typedef CGAL::Mesh_complex_3_in_triangulation_3<Tr> C3t3;

// Mesh Criteria
typedef CGAL::Mesh_criteria_3<Tr> Mesh_criteria;

using namespace CGAL::parameters;

using tgt::vec3;
using tgt::vec4;

 
************************************************

The actual process is starting here by putting the data in one dimensional 
array and send it to make_mesh_3
 leadadd();

            //generate tetrahedron
            const tgt::svec3 outputdim = outputVolume_->getDimensions();
            const Volume* outputVolume = 
outputVolume_->getRepresentation<Volume>();
            unsigned int i,j,k;
            uint8_t *volumearray =new uint8_t[18874368];
                       /*for (k=0; k<(outputdim.z); k++) {
                               for (j=0; j<(outputdim.y); j++) {
                                   for (i=0; i<(outputdim.x); i++) {
                                       
volumearray[k*outputdim.x*outputdim.y+j*outputdim.x+i]=outputVolume->getVoxelFloat(i,j,k);
                                   }
                               }
                           }*/
            for(size_t i=0;i<outputVolume->getNumVoxels();i++)
                
volumearray[i]=static_cast<uint8_t>(outputVolume->getVoxelFloat(i));
            std::cout<<volumearray[500];
            CGAL::Image_3 image(_createImage(outputdim.x, outputdim.y, 
outputdim.z, 1, 0.585938, 0.585938, 2, sizeof(uint8_t), 
WK_FIXED,SGN_UNSIGNED));
            ImageIO_free(image.data());
            image.set_data(volumearray);
            Mesh_domain domain(image);
            // Mesh criteria
              Mesh_criteria criteria(facet_angle=30, 
facet_distance=4,cell_radius_edge=3);

              // Mesh generation and optimization in one call
              C3t3 c3t3 = CGAL::make_mesh_3<C3t3>(domain, criteria, 
CGAL::parameters::no_features(),
                                                  lloyd(time_limit=30),
                                                  exude(time_limit=10, 
sliver_bound=10));
            std::ofstream 
medit_file("/Users/elhassanabdou/voreen/svnvoreen/trunk/out.mesh");
           c3t3.output_to_medit(medit_file);
           //end of generation
           outport_.setData(outputVolume_);

Thanks in advance
Elhassan
On Dec 8, 2011, at 11:14 AM, Laurent Rineau (GeometryFactory) wrote:

> Le jeudi 08 décembre 2011 11:08:55 elhassan Abdou a écrit :
>> Dear  ALL
>> 
>> I attached in the mail a slice from the mri volume that I need to mesh. The
>> slice has some 90 degree angles resulted from segmentation. I tried to use
>> make_mesh_3 to generate tetrahedron for this but it does not work. I did
>> not use any optimization in mesh criteria.
>> 
>> DO I miss something in the delaunay triangulation. I thought yesterday that
>> I should find away to control the divide and conquer during the mesh
>> generation. but I am not sure if this is right or wrong although I do not
>> have too much experience in the 3d delaunay triangulation.
> 
> Please, send us your code, or some parts of the code (that use CGAL), and 
> the 
> data, or at least the header fields of your data.
> 
> With that information, there is a chance that we can give you an answer.
> 
> If the files are bigger than.. say 10Ko, please do not send the files as 
> attachment to the mailing list. Post it to a dedicated web site (dropbox 
> for 
> example), or send the files directly to me (to avoid spamming the whole 
> list 
> with big attachments).
> 
> -- 
> Laurent Rineau, PhD
> R&D Engineer at GeometryFactory           http://www.geometryfactory.com/
> Release Manager of the CGAL Project       http://www.cgal.org/
> 
> 
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Elhassan Abdou
Computational Science master student
Uppsala