CGAL users discussion list

[Mariette Yvinec <>]

-------- Message original -------- Sujet: CGAL + FEniCS integration Date : Mon, 3 Dec 2012 08:28:40 -0600 De : Shirinifard, Abbas <> Pour : <> Copie à : Thiagarajan, Suresh <>, Sablauer, Andras <>

Dear Dr. Yvinec,

My name is Abbas Shirinifard. I am a computational modeling scientist at St. Jude Children’s Research Hospital. Currently, I am working on a project to develop computational models of tumor growth in 3D based on a series of experimental observations in vivo. Here is an example of such models :

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0007190

 

In our project we use CompuCell3D as our main platform for multi-cell modeling of tumors. CompuCell3D is an open-source software package that has been actively  developed and maintained at Indiana University and has a wide spectrum of users including the Virtual Embryo Project at EPA (USA). CompuCell3D has a couple of partial-differential equation (PDE) solvers, but the integrated solvers are extremely slow for reaction diffusion problems with fast diffusing species. Improvements in PDE solvers will have a great impact on the usability of  CC3D and multi-scale modeling of tissues.

 

To solve this problem, I am trying to integrate an established PDE solver package called FEniCS (fenicsproject.org/) with CompuCell3D. This integration requires (tetrahedral)  meshing volume data that is stored in (uniform) cubic voxel lattice. This problem is similar to meshing segmented 3D medical images. I have already installed CGAL 4.0  (debian package manager) and compiled an example (mesh_3D_image.cpp) where you mesh a 3D image of liver and generated “out.mesh” file.

 

FEniCS supports .mesh file format, but it fails to import out.mesh file with the following error message:

***Unable to find cell type.

 

Also I have problems visualizing out.mesh (generated by CGAL) in gmsh package. Medit also crashes when it tries to open out.mesh.

 

-can CGAL export 3D mesh in any other format? FeniCS natively uses xml format.

 

I would greatly appreciate it if you could help me to use CGAL libraries for this integration.

 

Best Regards,

Abbas Shirinifard

 

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