gel.scripts.get_veh

 1"""Creates mesh with indications of which elements are in event horizon"""
 2import argparse
 3import os
 4os.environ["SUPPRESS_ADJOINT"] = "1"
 5from gel import *
 6
 7
 8def get_veh(cell_data_dir, u_exp_file, directory, cutoff=0.38,
 9            bci=None, bco=None):
10    """Creates .pvd (and support files) with event horizon indication.
11
12    * `cell_data_dir`: str path to directory with files needed by
13    `gel.geometry.Geometry`
14    * `u_exp_file`: str path to full-shape .xdmf file with displacements
15    "u" to use in determining event horizon
16    * `directory`: str path to directory within which to create new
17    files
18    * `cutoff`: float displacement magnitude in microns to use as event
19    horizon cutoff value
20    * `bci`: str or None. Override path to the inner cell-surface BC .vtk;
21    when None, `gel.geometry.Geometry` defaults to `cell_data_dir/bci.vtk`
22    * `bco`: str or None. Override path to the outer boundary BC .vtk
23
24    Side-effects: creates "u_regions_{cutoff}.pvd" and support files
25    with element-wise data having event horizon tags from
26    `gel.geometry.Geometry`
27    """
28    geo = Geometry(
29        cell_data_dir,
30        u_magnitude_subdomains_file=u_exp_file,
31        detectable_u_cutoff=cutoff,
32        bci_data=bci,
33        bco_data=bco
34    )
35    filename = os.path.join(directory, f"u_regions_{cutoff}.pvd")
36    File(filename) << geo.dx.subdomain_data()
37
38
39def get_veh_main():
40    """The function invoked by the command. Parses arguments and passes
41    to `get_veh`.
42    """
43    parser = argparse.ArgumentParser(
44        description="Obtain a mesh indicating which cells are counted"
45        " as being within the event horizon for visualization."
46    )
47    parser.add_argument(
48        "-c",
49        type=str,
50        metavar="CELL_DATA",
51        help="directory containing gel geometry"
52    )
53    parser.add_argument(
54        "-i",
55        type=str,
56        metavar="INPUT_FULL_SHAPE",
57        help="full-shape 1st order Lagrange .xdmf file with "
58        "displacements 'u'"
59    )
60    parser.add_argument(
61        "-o",
62        type=str,
63        metavar="OUTPUT_DIR",
64        help="result will be saved as "
65        "OUTPUT_DIR/u_regions_{THRESHOLD}.pvd and supporting files"
66    )
67    parser.add_argument(
68        "-t",
69        type=float,
70        metavar="THRESHOLD",
71        default=0.38,
72        help="threshold by which VEH is determined in microns"
73    )
74    parser.add_argument(
75        "--bci",
76        type=str,
77        metavar="CELL_SURF_MESH",
78        default=None,
79        help="override path to inner cell-surface BC .vtk (default: -c dir's "
80        "bci.vtk)"
81    )
82    parser.add_argument(
83        "--bco",
84        type=str,
85        metavar="OUTER_SURF_MESH",
86        default=None,
87        help="override path to outer boundary BC .vtk (default: -c dir's "
88        "bco.vtk)"
89    )
90    args = parser.parse_args()
91
92    get_veh(args.c, args.i, args.o, args.t, args.bci, args.bco)
93
94
95if __name__=="__main__":
96    get_veh_main()