gel.scripts.create_cell_surf_normals_mesh

Compute nodal cell surface normals, save as .vtk file

For all arguments, run create_cell_surf_normals_mesh --help

Uses Tensorflow (must be installed) to compute nodal normals on cell surface mesh, saves in provided directory.

 1"""Compute nodal cell surface normals, save as .vtk file
 2
 3For all arguments, run `create_cell_surf_normals_mesh --help`
 4
 5Uses Tensorflow (must be installed) to compute nodal normals on cell
 6surface mesh, saves in provided directory.
 7"""
 8import sys
 9if "pdoc" not in sys.modules:
10    from tensorflow_graphics.geometry.representation.mesh.normals import vertex_normals
11import argparse
12import os
13import numpy as np
14import meshio
15
16
17def create_cell_surf_normals_mesh(cell_mesh_file, dest_dir):
18    """Creates mesh .vtk file with nodal normals.
19
20    * `cell_mesh_file`: str path to mesh file with downsampled,
21    centered cell surface (for instance, an .stl)
22    * `dest_dir`: str path to directory in which to create new mesh file
23
24    Side-effects: writes `cell_surf_with_normal.vtk` under `dest_dir`
25    """
26    cell_surf_mesh = meshio.read(cell_mesh_file)
27    
28    cell_vertices = cell_surf_mesh.points
29    cell_conn = cell_surf_mesh.cells[0].data
30    
31    # Outward normal
32    cell_normals = -vertex_normals(cell_vertices, cell_conn) 
33    
34    cell_surf_mesh.point_data["n"] = cell_normals.numpy()
35    
36    cell_surf_mesh.write(os.path.join(dest_dir, "cell_surf_with_normal.vtk"))
37
38
39def create_cell_surf_normals_mesh_main():
40    """The function invoked by the command. Parses arguments and passes
41    to `create_cell_surf_with_normals_mesh`.
42    """
43    parser = argparse.ArgumentParser(
44        description="Uses Tensorflow (must be installed) to compute nodal normals on cell surface mesh, saves in provided directory."
45    )
46    parser.add_argument(
47        "-c",
48        type=str,
49        metavar="CELL_MESH_FILE",
50        help="input cell mesh file"
51    )
52    parser.add_argument(
53        "-d",
54        type=str,
55        metavar="DEST_DIR",
56        help="directory in which cell_surf_with_normal.vtk will be "
57        "placed"
58    )
59    args = parser.parse_args()
60
61    create_cell_surf_normals_mesh(args.c, args.d)
62
63
64if __name__=="__main__":
65    create_cell_surf_normals_mesh_main()
def create_cell_surf_normals_mesh(cell_mesh_file, dest_dir): 
18def create_cell_surf_normals_mesh(cell_mesh_file, dest_dir):
19    """Creates mesh .vtk file with nodal normals.
20
21    * `cell_mesh_file`: str path to mesh file with downsampled,
22    centered cell surface (for instance, an .stl)
23    * `dest_dir`: str path to directory in which to create new mesh file
24
25    Side-effects: writes `cell_surf_with_normal.vtk` under `dest_dir`
26    """
27    cell_surf_mesh = meshio.read(cell_mesh_file)
28    
29    cell_vertices = cell_surf_mesh.points
30    cell_conn = cell_surf_mesh.cells[0].data
31    
32    # Outward normal
33    cell_normals = -vertex_normals(cell_vertices, cell_conn) 
34    
35    cell_surf_mesh.point_data["n"] = cell_normals.numpy()
36    
37    cell_surf_mesh.write(os.path.join(dest_dir, "cell_surf_with_normal.vtk"))

Creates mesh .vtk file with nodal normals.

  • cell_mesh_file: str path to mesh file with downsampled, centered cell surface (for instance, an .stl)
  • dest_dir: str path to directory in which to create new mesh file

Side-effects: writes cell_surf_with_normal.vtk under dest_dir

def create_cell_surf_normals_mesh_main(): 
40def create_cell_surf_normals_mesh_main():
41    """The function invoked by the command. Parses arguments and passes
42    to `create_cell_surf_with_normals_mesh`.
43    """
44    parser = argparse.ArgumentParser(
45        description="Uses Tensorflow (must be installed) to compute nodal normals on cell surface mesh, saves in provided directory."
46    )
47    parser.add_argument(
48        "-c",
49        type=str,
50        metavar="CELL_MESH_FILE",
51        help="input cell mesh file"
52    )
53    parser.add_argument(
54        "-d",
55        type=str,
56        metavar="DEST_DIR",
57        help="directory in which cell_surf_with_normal.vtk will be "
58        "placed"
59    )
60    args = parser.parse_args()
61
62    create_cell_surf_normals_mesh(args.c, args.d)

The function invoked by the command. Parses arguments and passes to create_cell_surf_with_normals_mesh.