PyVoxSurf

Originally from: https://github.com/sylefeb/VoxSurf A Python C++ extension based on VoxSurf for voxelization of 3D meshes.

Principle

1. Rasterize triangles using three 2D axis aligned grids, using integer arithmetic (fixed floating point) for robust triangle interior checks
2. [Optional] Fill interior of voxelized surface with either of two schemes: Inside - fastest method evaluates whether a voxel is inside from only one direction or Robust - evaluates whether a voxel is inside from all three directions and a voting determines final status

Installation For RELU

For VirtualEnv: prerequisites: LibSSL, Cmake, libjpg,libpng

  sudo apt-get install libssl-dev
  sudo apt-get install libjpeg-dev
  sudo apt-get install libpng-dev
  wget https://github.com/Kitware/CMake/releases/download/v3.17.3/cmake-3.17.3.tar.gz
  tar -zxvf cmake-3.17.3.tar.gz
  cd cmake-3.17.3
  sudo ./bootstrap
  sudo make
  sudo make install

Activate your virtual environment

  pip install git+ssh://git@github.com/Relu-bv/PyVoxSurf.git

If that does not work, you can try to clone the repo and install it from python

git clone git@github.com:Relu-bv/PyVoxSurf.git
git submodule update --init
source <env>/bin/activate
python setup.py install

Usage

pyvoxsurf.voxelize_stl

Argument	Type	Default	Description
filename	string		Filename of .stl file
resolution	integer		Number of voxel slices in the z-axis
bounds	[2x3] array		[Optional] Min and max bounds in (x, y, z) coordinates of desired voxel volume
voxel_fill	string	"None"	[Optional] "None", "Inside", or "Robust" type of filling

import pyvoxsurf
from mayavi import mlab

volume1 = pyvoxsurf.voxelize_stl("model.stl",200,[],"Robust")
print(volume1.shape)

# Visualize voxelized model
from tvtk.util.ctf import PiecewiseFunction
mlab.figure(size=(800,800))
vol = mlab.pipeline.volume(mlab.pipeline.scalar_field(volume1))
mlab.title('Voxelized model',height=0.9,size=0.5)
mlab.orientation_axes()
otf = PiecewiseFunction()
otf.add_point(0,0)
otf.add_point(0.001, 1)
otf.add_point(1,1)
vol._otf = otf
vol._volume_property.set_scalar_opacity(otf)
mlab.show()

pyvoxsurf.voxelize

Argument	Type	Default	Description
vertices	[nx3] array		Vertex positions in (x, y, z) coordinates
triangle_indices	[nx3] array		Indices of connected vertices forming triangles of mesh
bounds	[2x3] array		Min and max bounds in (x, y, z) coordinates of desired voxel volume
resolution	integer		Number of voxel slices in the z-axis
voxel_fill	string	"None"	[Optional] "None", "Inside", or "Robust" type of filling

import pyvoxsurf
import trimesh
import numpy as np
from mayavi import mlab

mesh = trimesh.load("model.stl") # Load stl file

# Find the max and min coordinates of the mesh to form a bounding box
mesh_min_corner = [np.min(mesh.vertices[:,0]), np.min(mesh.vertices[:,1]), np.min(mesh.vertices[:,2])]
mesh_max_corner = [np.max(mesh.vertices[:,0]), np.max(mesh.vertices[:,1]), np.max(mesh.vertices[:,2])]
bounds = np.stack((mesh_min_corner,mesh_max_corner))

volume2 = pyvoxsurf.voxelize(mesh.vertices,mesh.faces,bounds,100,"Inside")
print(volume2.shape)

# Visualize voxelized model
from tvtk.util.ctf import PiecewiseFunction
mlab.figure(size=(800,800))
vol = mlab.pipeline.volume(mlab.pipeline.scalar_field(volume2))
mlab.title('Voxelized model',height=0.9,size=0.5)
mlab.orientation_axes()
otf = PiecewiseFunction()
otf.add_point(0,0)
otf.add_point(0.001, 1)
otf.add_point(1,1)
vol._otf = otf
vol._volume_property.set_scalar_opacity(otf)
mlab.show()

Credits

• VoxSurf by sylefeb
• VoxSurf Pybind11 bindings by mjgalindo
• PyVoxSurf packaging and documentation by jttoombs
• STL model of 3D knot by chylld