How can I create mesh from a 3D binary mask?

[zhang-qiang-github]

The mask means the pixel inside of object is 1, and the pixel outside of object is 0.

If I have a 3D binary mask, how can I create the mesh?

[wd15]

I'm not sure exactly what you're asking for here. Some clarification might help.

My guess is that you could either base the material properties on the mask and use a grid mesh, which often works well (e.g. have a null region without diffusion) or somehow use the mask to generate a mesh using Gmsh. I'm not sure about the latter. Gmsh does have a Python API (maybe it's just a Python tool that interfaces with the CLI), which might make programming it easier. I can imagine generating a geometry for Gmsh based on the masked array using Python.