Techniques to smooth 3D mesh from labeled image

[oarcelus]

When trying to build a 3D tetrahedral mesh from labeled image I use the examples shown in the webpage (https://doc.cgal.org/latest/Mesh_3/index.html)

The meshes I am dealing with are quite complex with pretty amorphous shapes. The issue I am having is that the domain boundaries sometimes come up pretty 'spiky'. Some tetrahedra go into other domains instead of being bound to their surface.

I guess that one way of making these shapes smoother is to increase the resolution of the underlying 3D image (make smaller voxels). But I wonder if there is some better way to inprove this withing CGAL.

Best regards,
Oier.

[janetournois]

Hello,

you should try meshing from weighted images, as done in this example

Then, reducing your facet_distance criterion should help.

Best regards,
Jane

[oarcelus]

Thanks! This improves a little bit. I just discovered that the reason these spikes appear is because I am also meshing the surrounding 'air' volume for my simulations. If I exclude the surrounding volume from the meshing, my particles are much smoother.

So, I wonder if there is a way of first meshing the particles alone (even individually since I have labels for each of them), and then keep these surface polyhedral features to mesh the whole structure.

I have tried to include feature detection as a partial solution, to at least improve the meshin in the contact between 3 subdomains. But I find some errors when compiling.

CGAL::Image_3 image;
  const bool success = image.read(inr_filename.c_str());
  if (!success) {
  throw "Could not read image file";
  }

  // Create weights with gaussian smoothing with sigma = sig * max_voxel_size
  const float sigma = sig * (std::max)(image.vx(), (std::max)(image.vy(), image.vz()));
  CGAL::Image_3 img_weights = CGAL::Mesh_3::generate_label_weights(image, sigma);

  Mesh_domain cgal_domain = Mesh_domain::create_labeled_image_mesh_domain(image,
                                                                          CGAL::parameters::weights(img_weights).relative_error_bound(relative_error_bound_weights),
                                                                          CGAL::parameters::features_detector = CGAL::Mesh_3::Detect_features_in_image());

I see an error of the type:
C:\dev\vcpkg\installed\x64-windows\include\CGAL/Labeled_mesh_domain_3.h(848,66): error C2672: 'CGAL::internal_np::combine_named_parameters': no matching overloaded funct
ion found [C:\Users\oarcelus\ElectrodeBuilder\meshing_cgal\build\mesh_from_labeled_3d_array_with_weights_detect.vcxproj]
C:\Users\oarcelus\ElectrodeBuilder\meshing_cgal\mesh_from_labeled_3d_array_with_weights_detect.cpp(76): message : see reference to function template instantiation 'auto
CGAL::Labeled_mesh_domain_3<K,int,std::pair<int,int>>::create_labeled_image_mesh_domain<double,CGAL::internal_np::error_bound_t,CGAL::Named_function_parameters<std::refe
rence_wrapperCGAL::Image_3,Tag,CGAL::internal_np::No_property>,CGAL::Mesh_3::Detect_features_in_image,CGAL::internal_np::features_detector_param_t,CGAL::internal_np::N
o_property,>(const CGAL::Image_3 &,const CGAL::Named_function_parameters<double,CGAL::internal_np::error_bound_t,CGAL::Named_function_parameters<std::reference_wrapper,Tag,CGAL::internal_np::No_property>> &,const CGAL::Named_function_parameters<CGAL::Mesh_3::Detect_features_in_image,CGAL::internal_np::features_detector_pa
ram_t,CGAL::internal_np::No_property> &)' being compiled [C:\Users\oarcelus\ElectrodeBuilder\meshing_cgal\build\mesh_from_labeled_3d_array_with_weights_detect.vcxproj]
with
[
Tag=CGAL::internal_np::weights_param_t
]
C:\dev\vcpkg\installed\x64-windows\include\CGAL/Labeled_mesh_domain_3.h(847,1): error C2784: 'auto CGAL::internal_np::combine_named_parameters(const CGAL::Named_function
parameters<K,Tag,CGAL::internal_np::No_property> &,const NPS &...)': could not deduce template argument for 'const CGAL::Named_function_parameters<K,Tag,CGAL::internal
np::No_property> &' from 'const CGAL::Named_function_parameters<double,CGAL::internal_np::error_bound_t,CGAL::Named_function_parameters<std::reference_wrapper<CGAL::Imag
e_3>,Tag,CGAL::internal_np::No_property>>' [C:\Users\oarcelus\ElectrodeBuilder\meshing_cgal\build\mesh_from_labeled_3d_array_with_weights_detect.vcxproj]
with
[
Tag=CGAL::internal_np::weights_param_t
]
C:\dev\vcpkg\installed\x64-windows\include\CGAL/Named_function_parameters.h(329): message : see declaration of 'CGAL::internal_np::combine_named_parameters' [C:\Users\oa
rcelus\ElectrodeBuilder\meshing_cgal\build\mesh_from_labeled_3d_array_with_weights_detect.vcxproj]
C:\dev\vcpkg\installed\x64-windows\include\CGAL/Labeled_mesh_domain_3.h(847,1): error C2782: 'auto CGAL::internal_np::combine_named_parameters(const CGAL::Named_function
_parameters<K,Tag,CGAL::internal_np::No_property> &,const NPS &...)': template parameter 'K' is ambiguous [C:\Users\oarcelus\ElectrodeBuilder\meshing_cgal\build\mesh_fro
m_labeled_3d_array_with_weights_detect.vcxproj]
C:\dev\vcpkg\installed\x64-windows\include\CGAL/Named_function_parameters.h(329): message : see declaration of 'CGAL::internal_np::combine_named_parameters' [C:\Users\oa
rcelus\ElectrodeBuilder\meshing_cgal\build\mesh_from_labeled_3d_array_with_weights_detect.vcxproj]
C:\dev\vcpkg\installed\x64-windows\include\CGAL/Labeled_mesh_domain_3.h(847,1): message : could be 'std::reference_wrapperCGAL::Image_3' [C:\Users\oarcelus\ElectrodeBu
ilder\meshing_cgal\build\mesh_from_labeled_3d_array_with_weights_detect.vcxproj]
C:\dev\vcpkg\installed\x64-windows\include\CGAL/Labeled_mesh_domain_3.h(847,1): message : or 'double' [C:\Users\oarcelus\ElectrodeBuilder\meshing_cgal\build\mesh_f
rom_labeled_3d_array_with_weights_detect.vcxproj]

[janetournois]

You probably can't mix the named parameters , and . separators together.
Try

esh_domain cgal_domain = Mesh_domain::create_labeled_image_mesh_domain(image,
                                                                          CGAL::parameters::weights(img_weights).relative_error_bound(relative_error_bound_weights)
                                                                          .features_detector(CGAL::Mesh_3::Detect_features_in_image()));

[oarcelus]

Hi, I now get a linking error.

mesh_from_labeled_3d_array_with_weights_detect.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) v
oid __cdecl itk::OutputWindowDisplayWarningText(char const *)" (_imp?OutputWindowDisplayWarningText@itk@@YAXPEBD@Z) r
eferenced in function "protected: virtual class std::vector<double,class std::allocator > __cdecl itk::Gaussian
Operator<unsigned char,3,class itk::NeighborhoodAllocator >::GenerateCoefficients(void)" (?GenerateCoeff
icients@?$GaussianOperator@E$02V?$NeighborhoodAllocator@E@itk@@@itk@@Meaa?AV?$vector@NV?$allocator@N@std@@@std@@xz) [C:
\Users\oarcelus\ElectrodeBuilder\meshing_cgal\build\mesh_from_labeled_3d_array_with_weights_detect.vcxproj]

It is strange because when I include feature detection only or weights only it works. But combining both not. Any idea how could I keep advancing here?

Best regardsm
Oier.

[janetournois]

Hello,

You can have a look at the example mesh_3D_weighted_image_with_detection_of_features.cpp which combines weights and features detection as you are trying to do.

The corresponding CMakeLists prepares the proper setup for all examples of Mesh_3, including this one.

[oarcelus]

Oh, there was an example all along. I did not see that! Thanks!

[janetournois]

The example was there but not listed in the documentation.
The PR ##8373 adds it to the doc