Mesh

automesh mesh --help
Creates a finite element mesh from a segmentation

Usage: automesh mesh <COMMAND>

Commands:
  hex   Creates an all-hexahedral mesh from a segmentation
  tri   Creates all-triangular isosurface(s) from a segmentation
  help  Print this message or the help of the given subcommand(s)

Options:
  -h, --help  Print help

Mesh Hex

automesh mesh hex --help
Creates an all-hexahedral mesh from a segmentation

Usage: automesh mesh hex [OPTIONS] --input <FILE> --output <FILE> [COMMAND]

Commands:
  smooth  Applies smoothing to the mesh before output
  help    Print this message or the help of the given subcommand(s)

Options:
  -i, --input <FILE>      Segmentation input file (npy | spn)
  -o, --output <FILE>     Mesh output file (exo | inp | mesh | vtk)
  -d, --defeature <NUM>   Defeature clusters with less than NUM voxels
  -x, --nelx <NEL>        Number of voxels in the x-direction
  -y, --nely <NEL>        Number of voxels in the y-direction
  -z, --nelz <NEL>        Number of voxels in the z-direction
  -r, --remove <ID>...    Voxel IDs to remove from the mesh
      --xscale <SCALE>    Scaling (> 0.0) in the x-direction, applied before translation [default: 1]
      --yscale <SCALE>    Scaling (> 0.0) in the y-direction, applied before translation [default: 1]
      --zscale <SCALE>    Scaling (> 0.0) in the z-direction, applied before translation [default: 1]
      --xtranslate <VAL>  Translation in the x-direction [default: 0]
      --ytranslate <VAL>  Translation in the y-direction [default: 0]
      --ztranslate <VAL>  Translation in the z-direction [default: 0]
      --metrics <FILE>    Quality metrics output file (csv | npy)
  -q, --quiet             Pass to quiet the terminal output
  -h, --help              Print help

Mesh Tri

automesh mesh tri --help
Creates all-triangular isosurface(s) from a segmentation

Usage: automesh mesh tri [OPTIONS] --input <FILE> --output <FILE> [COMMAND]

Commands:
  smooth  Applies smoothing to the mesh before output
  help    Print this message or the help of the given subcommand(s)

Options:
  -i, --input <FILE>      Segmentation input file (npy | spn)
  -o, --output <FILE>     Mesh output file (exo | inp | mesh | stl | vtk)
  -d, --defeature <NUM>   Defeature clusters with less than NUM voxels
  -x, --nelx <NEL>        Number of voxels in the x-direction
  -y, --nely <NEL>        Number of voxels in the y-direction
  -z, --nelz <NEL>        Number of voxels in the z-direction
  -r, --remove <ID>...    Voxel IDs to remove from the mesh
      --xscale <SCALE>    Scaling (> 0.0) in the x-direction, applied before translation [default: 1]
      --yscale <SCALE>    Scaling (> 0.0) in the y-direction, applied before translation [default: 1]
      --zscale <SCALE>    Scaling (> 0.0) in the z-direction, applied before translation [default: 1]
      --xtranslate <VAL>  Translation in the x-direction [default: 0]
      --ytranslate <VAL>  Translation in the y-direction [default: 0]
      --ztranslate <VAL>  Translation in the z-direction [default: 0]
      --metrics <FILE>    Quality metrics output file (csv | npy)
  -q, --quiet             Pass to quiet the terminal output
  -h, --help              Print help

Mesh Hex Smooth

automesh mesh hex smooth --help
Applies smoothing to the mesh before output

Usage: automesh mesh hex --input <FILE> --output <FILE> smooth [OPTIONS]

Options:
  -c, --hierarchical      Pass to enable hierarchical control
  -n, --iterations <NUM>  Number of smoothing iterations [default: 20]
  -m, --method <NAME>     Smoothing method (Laplace | Taubin) [default: Taubin]
  -k, --pass-band <FREQ>  Pass-band frequency (for Taubin only) [default: 0.1]
  -s, --scale <SCALE>     Scaling parameter for all smoothing methods [default: 0.6307]
  -h, --help              Print help

Mesh Tri Smooth

automesh mesh tri smooth --help
Applies smoothing to the mesh before output

Usage: automesh mesh tri --input <FILE> --output <FILE> smooth [OPTIONS]

Options:
  -c, --hierarchical      Pass to enable hierarchical control
  -n, --iterations <NUM>  Number of smoothing iterations [default: 20]
  -m, --method <NAME>     Smoothing method (Laplace | Taubin) [default: Taubin]
  -k, --pass-band <FREQ>  Pass-band frequency (for Taubin only) [default: 0.1]
  -s, --scale <SCALE>     Scaling parameter for all smoothing methods [default: 0.6307]
  -h, --help              Print help