Geometry tools

The module vmtk_wrapper is largely a wrapper for vmtkscripts, incorporating the ease-of-use of PyVista.

Moving forward, it would be nice to re-write this using vtkvmtk and PyVista directly, but wrapping vmtkscripts works for now.

• surface contains the Surfer() class, which incorporates surface-based operations.
• meshing contains the Mesher() class for generating volume meshes and files necessary for simulation. Inherits from Surfer(). Note: VMTK TetGen is reallly buggy, YMMV.
• resample_surface contains Resampler() to sample ugly meshes to an image, then re-contour the image to get a surface.
• make_submission_file makes the bash submission file formatted for the BSL solver on Mehdi's niagara.
• common contains some useful odds and ends.

VMTK has a lot of out-of-date requirements, so surface, meshing, and vmtk_wrapper rely on VMTK, but common and resample_surface may have different requirements.

Requirements:

• vtk
• numpy
• pyvista=0.29
• scipy
• h5py
• pymeshfix
• vmtk
• networkx
• matplotlib
• TubeClipper (https://github.com/Biomedical-Simulation-Lab/tubeclipper)

Environment

First, conda env as here: http://www.vmtk.org/download/

Then conda install -c conda-forge pyvista networkx scipy ipython h5py matplotlib

Then clone and install tubeclipper using pip.

When installing on workstation (ubuntu), also had to conda install llvm=3.3 and make sure pyvista=0.29

Meshing

For an example of using this for meshing, see the meshing_example.sh file in scripts.