cardiac-geometriesx 0.0.1__py3-none-any.whl

cardiac_geometries/cli.py

@@ -0,0 +1,875 @@
+import math
+from importlib.metadata import metadata
+from pathlib import Path
+
+import rich_click as click
+
+from . import mesh
+
+
+meta = metadata("cardiac-geometriesx")
+__version__ = meta["Version"]
+__author__ = meta["Author"]
+__license__ = meta["License"]
+
+
+@click.group()
+@click.version_option(__version__, prog_name="cardiac_geometriesx")
+def app():
+    """
+    Cardiac Geometries - A library for creating meshes of
+    cardiac geometries
+    """
+    pass
+
+
+@click.command(help="Create LV ellipsoidal geometry")
+@click.argument(
+    "outdir",
+    required=True,
+    type=click.Path(
+        file_okay=False,
+        dir_okay=True,
+        writable=True,
+        readable=True,
+        resolve_path=True,
+    ),
+)
+@click.option(
+    "--r-short-endo",
+    default=7.0,
+    type=float,
+    help="Shortest radius on the endocardium layer",
+    show_default=True,
+)
+@click.option(
+    "--r-short-epi",
+    default=10.0,
+    type=float,
+    help="Shortest radius on the epicardium layer",
+    show_default=True,
+)
+@click.option(
+    "--r-long-endo",
+    default=17.0,
+    type=float,
+    help="Longest radius on the endocardium layer",
+    show_default=True,
+)
+@click.option(
+    "--r-long-epi",
+    default=20.0,
+    type=float,
+    help="Longest radius on the epicardium layer",
+    show_default=True,
+)
+@click.option(
+    "--psize-ref",
+    default=3.0,
+    type=float,
+    help="The reference point size (smaller values yield as finer mesh",
+    show_default=True,
+)
+@click.option(
+    "--mu-apex-endo",
+    default=-math.pi,
+    type=float,
+    help="Angle for the endocardial apex",
+    show_default=True,
+)
+@click.option(
+    "--mu-base-endo",
+    default=-math.acos(5 / 17),
+    type=float,
+    help="Angle for the endocardial base",
+    show_default=True,
+)
+@click.option(
+    "--mu-apex-epi",
+    default=-math.pi,
+    type=float,
+    help="Angle for the epicardial apex",
+    show_default=True,
+)
+@click.option(
+    "--mu-base-epi",
+    default=-math.acos(5 / 20),
+    type=float,
+    help="Angle for the epicardial base",
+    show_default=True,
+)
+@click.option(
+    "--create-fibers",
+    default=False,
+    is_flag=True,
+    type=bool,
+    help="If True create analytic fibers",
+    show_default=True,
+)
+@click.option(
+    "--fiber-angle-endo",
+    default=-60,
+    type=float,
+    help="Angle for the endocardium",
+    show_default=True,
+)
+@click.option(
+    "--fiber-angle-epi",
+    default=+60,
+    type=float,
+    help="Angle for the epicardium",
+    show_default=True,
+)
+@click.option(
+    "--fiber-space",
+    default="P_1",
+    type=str,
+    help="Function space for fibers of the form family_degree",
+    show_default=True,
+)
+@click.option(
+    "--aha/--no-aha",
+    default=True,
+    is_flag=True,
+    type=bool,
+    help="If True create 17-segment AHA regions",
+    show_default=True,
+)
+def lv_ellipsoid(
+    outdir: Path,
+    r_short_endo: float = 7.0,
+    r_short_epi: float = 10.0,
+    r_long_endo: float = 17.0,
+    r_long_epi: float = 20.0,
+    psize_ref: float = 3,
+    mu_apex_endo: float = -math.pi,
+    mu_base_endo: float = -math.acos(5 / 17),
+    mu_apex_epi: float = -math.pi,
+    mu_base_epi: float = -math.acos(5 / 20),
+    create_fibers: bool = False,
+    fiber_angle_endo: float = -60,
+    fiber_angle_epi: float = +60,
+    fiber_space: str = "P_1",
+    aha: bool = True,
+):
+    outdir = Path(outdir)
+    outdir.mkdir(exist_ok=True)
+
+    geo = mesh.lv_ellipsoid(
+        outdir=outdir,
+        r_short_endo=r_short_endo,
+        r_short_epi=r_short_epi,
+        r_long_endo=r_long_endo,
+        r_long_epi=r_long_epi,
+        mu_base_endo=mu_base_endo,
+        mu_base_epi=mu_base_epi,
+        mu_apex_endo=mu_apex_endo,
+        mu_apex_epi=mu_apex_epi,
+        psize_ref=psize_ref,
+        create_fibers=create_fibers,
+        fiber_angle_endo=fiber_angle_endo,
+        fiber_angle_epi=fiber_angle_epi,
+        fiber_space=fiber_space,
+        aha=aha,
+    )
+    geo.save(outdir / "lv_ellipsoid.bp")
+
+
+@click.command(help="Create BiV ellipsoidal geometry")
+@click.argument(
+    "outdir",
+    required=True,
+    type=click.Path(
+        file_okay=False,
+        dir_okay=True,
+        writable=True,
+        readable=True,
+        resolve_path=True,
+    ),
+)
+@click.option(
+    "--char-length",
+    default=0.5,
+    type=float,
+    help="Characteristic length of mesh",
+    show_default=True,
+)
+@click.option(
+    "--center-lv-x",
+    default=0.0,
+    type=float,
+    help="X-coordinate for the center of the lv",
+    show_default=True,
+)
+@click.option(
+    "--center-lv-y",
+    default=0.0,
+    type=float,
+    help="Y-coordinate for the center of the lv",
+    show_default=True,
+)
+@click.option(
+    "--center-lv-z",
+    default=0.0,
+    type=float,
+    help="Z-coordinate for the center of the lv",
+    show_default=True,
+)
+@click.option(
+    "--a-endo-lv",
+    default=2.5,
+    type=float,
+    help="Dilation of lv endo ellipsoid in the x-direction",
+    show_default=True,
+)
+@click.option(
+    "--b-endo-lv",
+    default=1.0,
+    type=float,
+    help="Dilation of lv endo ellipsoid in the y-direction",
+    show_default=True,
+)
+@click.option(
+    "--c-endo-lv",
+    default=1.0,
+    type=float,
+    help="Dilation of lv endo ellipsoid in the y-direction",
+    show_default=True,
+)
+@click.option(
+    "--a-epi-lv",
+    default=3.0,
+    type=float,
+    help="Dilation of lv epi ellipsoid in the x-direction",
+    show_default=True,
+)
+@click.option(
+    "--b-epi-lv",
+    default=1.5,
+    type=float,
+    help="Dilation of lv epi ellipsoid in the y-direction",
+    show_default=True,
+)
+@click.option(
+    "--c-epi-lv",
+    default=1.5,
+    type=float,
+    help="Dilation of lv epi ellipsoid in the y-direction",
+    show_default=True,
+)
+@click.option(
+    "--center-rv-x",
+    default=0.0,
+    type=float,
+    help="X-coordinate for the center of the rv",
+    show_default=True,
+)
+@click.option(
+    "--center-rv-y",
+    default=0.5,
+    type=float,
+    help="Y-coordinate for the center of the rv",
+    show_default=True,
+)
+@click.option(
+    "--center-rv-z",
+    default=0.0,
+    type=float,
+    help="Z-coordinate for the center of the rv",
+    show_default=True,
+)
+@click.option(
+    "--a-endo-rv",
+    default=3.0,
+    type=float,
+    help="Dilation of rv endo ellipsoid in the x-direction",
+    show_default=True,
+)
+@click.option(
+    "--b-endo-rv",
+    default=1.5,
+    type=float,
+    help="Dilation of rv endo ellipsoid in the y-direction",
+    show_default=True,
+)
+@click.option(
+    "--c-endo-rv",
+    default=1.5,
+    type=float,
+    help="Dilation of rv endo ellipsoid in the y-direction",
+    show_default=True,
+)
+@click.option(
+    "--a-epi-rv",
+    default=4.0,
+    type=float,
+    help="Dilation of rv epi ellipsoid in the x-direction",
+    show_default=True,
+)
+@click.option(
+    "--b-epi-rv",
+    default=2.5,
+    type=float,
+    help="Dilation of rv epi ellipsoid in the y-direction",
+    show_default=True,
+)
+@click.option(
+    "--c-epi-rv",
+    default=2.0,
+    type=float,
+    help="Dilation of rv epi ellipsoid in the z-direction",
+    show_default=True,
+)
+@click.option(
+    "--create-fibers",
+    default=False,
+    is_flag=True,
+    type=bool,
+    help="If True create analytic fibers",
+    show_default=True,
+)
+@click.option(
+    "--fiber-angle-endo",
+    default=-60,
+    type=float,
+    help="Angle for the endocardium",
+    show_default=True,
+)
+@click.option(
+    "--fiber-angle-epi",
+    default=+60,
+    type=float,
+    help="Angle for the epicardium",
+    show_default=True,
+)
+@click.option(
+    "--fiber-space",
+    default="P_1",
+    type=str,
+    help="Function space for fibers of the form family_degree",
+    show_default=True,
+)
+def biv_ellipsoid(
+    outdir: Path,
+    char_length: float = 0.5,
+    center_lv_x: float = 0.0,
+    center_lv_y: float = 0.0,
+    center_lv_z: float = 0.0,
+    a_endo_lv: float = 2.5,
+    b_endo_lv: float = 1.0,
+    c_endo_lv: float = 1.0,
+    a_epi_lv: float = 3.0,
+    b_epi_lv: float = 1.5,
+    c_epi_lv: float = 1.5,
+    center_rv_x: float = 0.0,
+    center_rv_y: float = 0.5,
+    center_rv_z: float = 0.0,
+    a_endo_rv: float = 3.0,
+    b_endo_rv: float = 1.5,
+    c_endo_rv: float = 1.5,
+    a_epi_rv: float = 4.0,
+    b_epi_rv: float = 2.5,
+    c_epi_rv: float = 2.0,
+    create_fibers: bool = False,
+    fiber_angle_endo: float = -60,
+    fiber_angle_epi: float = +60,
+    fiber_space: str = "P_1",
+):
+    outdir = Path(outdir)
+    outdir.mkdir(exist_ok=True)
+
+    geo = mesh.biv_ellipsoid(
+        outdir=outdir,
+        char_length=char_length,
+        center_lv_y=center_lv_y,
+        center_lv_z=center_lv_z,
+        a_endo_lv=a_endo_lv,
+        b_endo_lv=b_endo_lv,
+        c_endo_lv=c_endo_lv,
+        a_epi_lv=a_epi_lv,
+        b_epi_lv=b_epi_lv,
+        c_epi_lv=c_epi_lv,
+        center_rv_y=center_rv_y,
+        center_rv_z=center_rv_z,
+        a_endo_rv=a_endo_rv,
+        b_endo_rv=b_endo_rv,
+        c_endo_rv=c_endo_rv,
+        a_epi_rv=a_epi_rv,
+        b_epi_rv=b_epi_rv,
+        c_epi_rv=c_epi_rv,
+        create_fibers=create_fibers,
+        fiber_angle_endo=fiber_angle_endo,
+        fiber_angle_epi=fiber_angle_epi,
+        fiber_space=fiber_space,
+    )
+    geo.save(outdir / "biv_ellipsoid.bp")
+
+
+@click.command(help="Create BiV ellipsoidal geometry embedded in a torso")
+@click.argument(
+    "outdir",
+    required=True,
+    type=click.Path(
+        file_okay=False,
+        dir_okay=True,
+        writable=True,
+        readable=True,
+        resolve_path=True,
+    ),
+)
+@click.option(
+    "--char-length",
+    default=0.5,
+    type=float,
+    help="Characteristic length of mesh",
+    show_default=True,
+)
+@click.option(
+    "--heart-as-surface/--heart-as-volume",
+    default=False,
+    help="Whether the heart should be a surface of a volume inside the torso",
+    show_default=True,
+)
+@click.option(
+    "--torso-length",
+    default=20,
+    type=float,
+    help="Length of torso in the x-direction",
+    show_default=True,
+)
+@click.option(
+    "--torso-width",
+    default=20,
+    type=float,
+    help="Length of torso in the y-direction",
+    show_default=True,
+)
+@click.option(
+    "--torso-height",
+    default=20,
+    type=float,
+    help="Length of torso in the z-direction",
+    show_default=True,
+)
+@click.option(
+    "--rotation-angle",
+    default=math.pi / 6,
+    type=float,
+    help=(
+        "Angle to rotate the torso in order to object realistic" " position of the heart in a torso"
+    ),
+    show_default=True,
+)
+@click.option(
+    "--center-lv-x",
+    default=0.0,
+    type=float,
+    help="X-coordinate for the center of the lv",
+    show_default=True,
+)
+@click.option(
+    "--center-lv-y",
+    default=0.0,
+    type=float,
+    help="Y-coordinate for the center of the lv",
+    show_default=True,
+)
+@click.option(
+    "--center-lv-z",
+    default=0.0,
+    type=float,
+    help="Z-coordinate for the center of the lv",
+    show_default=True,
+)
+@click.option(
+    "--a-endo-lv",
+    default=2.5,
+    type=float,
+    help="Dilation of lv endo ellipsoid in the x-direction",
+    show_default=True,
+)
+@click.option(
+    "--b-endo-lv",
+    default=1.0,
+    type=float,
+    help="Dilation of lv endo ellipsoid in the y-direction",
+    show_default=True,
+)
+@click.option(
+    "--c-endo-lv",
+    default=1.0,
+    type=float,
+    help="Dilation of lv endo ellipsoid in the y-direction",
+    show_default=True,
+)
+@click.option(
+    "--a-epi-lv",
+    default=3.0,
+    type=float,
+    help="Dilation of lv epi ellipsoid in the x-direction",
+    show_default=True,
+)
+@click.option(
+    "--b-epi-lv",
+    default=1.5,
+    type=float,
+    help="Dilation of lv epi ellipsoid in the y-direction",
+    show_default=True,
+)
+@click.option(
+    "--c-epi-lv",
+    default=1.5,
+    type=float,
+    help="Dilation of lv epi ellipsoid in the y-direction",
+    show_default=True,
+)
+@click.option(
+    "--center-rv-x",
+    default=0.0,
+    type=float,
+    help="X-coordinate for the center of the rv",
+    show_default=True,
+)
+@click.option(
+    "--center-rv-y",
+    default=0.5,
+    type=float,
+    help="Y-coordinate for the center of the rv",
+    show_default=True,
+)
+@click.option(
+    "--center-rv-z",
+    default=0.0,
+    type=float,
+    help="Z-coordinate for the center of the rv",
+    show_default=True,
+)
+@click.option(
+    "--a-endo-rv",
+    default=3.0,
+    type=float,
+    help="Dilation of rv endo ellipsoid in the x-direction",
+    show_default=True,
+)
+@click.option(
+    "--b-endo-rv",
+    default=1.5,
+    type=float,
+    help="Dilation of rv endo ellipsoid in the y-direction",
+    show_default=True,
+)
+@click.option(
+    "--c-endo-rv",
+    default=1.5,
+    type=float,
+    help="Dilation of rv endo ellipsoid in the y-direction",
+    show_default=True,
+)
+@click.option(
+    "--a-epi-rv",
+    default=4.0,
+    type=float,
+    help="Dilation of rv epi ellipsoid in the x-direction",
+    show_default=True,
+)
+@click.option(
+    "--b-epi-rv",
+    default=2.5,
+    type=float,
+    help="Dilation of rv epi ellipsoid in the y-direction",
+    show_default=True,
+)
+@click.option(
+    "--c-epi-rv",
+    default=2.0,
+    type=float,
+    help="Dilation of rv epi ellipsoid in the z-direction",
+    show_default=True,
+)
+@click.option(
+    "--create-fibers",
+    default=False,
+    is_flag=True,
+    type=bool,
+    help="If True create analytic fibers",
+    show_default=True,
+)
+@click.option(
+    "--fiber-angle-endo",
+    default=-60,
+    type=float,
+    help="Angle for the endocardium",
+    show_default=True,
+)
+@click.option(
+    "--fiber-angle-epi",
+    default=+60,
+    type=float,
+    help="Angle for the epicardium",
+    show_default=True,
+)
+@click.option(
+    "--fiber-space",
+    default="P_1",
+    type=str,
+    help="Function space for fibers of the form family_degree",
+    show_default=True,
+)
+def biv_ellipsoid_torso(
+    outdir: Path,
+    char_length: float = 0.5,
+    heart_as_surface: bool = True,
+    torso_length: float = 20.0,
+    torso_width: float = 20.0,
+    torso_height: float = 20.0,
+    rotation_angle: float = math.pi / 6,
+    center_lv_x: float = 0.0,
+    center_lv_y: float = 0.0,
+    center_lv_z: float = 0.0,
+    a_endo_lv: float = 2.5,
+    b_endo_lv: float = 1.0,
+    c_endo_lv: float = 1.0,
+    a_epi_lv: float = 3.0,
+    b_epi_lv: float = 1.5,
+    c_epi_lv: float = 1.5,
+    center_rv_x: float = 0.0,
+    center_rv_y: float = 0.5,
+    center_rv_z: float = 0.0,
+    a_endo_rv: float = 3.0,
+    b_endo_rv: float = 1.5,
+    c_endo_rv: float = 1.5,
+    a_epi_rv: float = 4.0,
+    b_epi_rv: float = 2.5,
+    c_epi_rv: float = 2.0,
+    create_fibers: bool = False,
+    fiber_angle_endo: float = -60,
+    fiber_angle_epi: float = +60,
+    fiber_space: str = "P_1",
+):
+    outdir = Path(outdir)
+    outdir.mkdir(exist_ok=True)
+
+    geo = mesh.biv_ellipsoid_torso(
+        outdir=outdir,
+        char_length=char_length,
+        heart_as_surface=heart_as_surface,
+        torso_length=torso_length,
+        torso_height=torso_height,
+        torso_width=torso_width,
+        rotation_angle=rotation_angle,
+        center_lv_x=center_lv_x,
+        center_lv_y=center_lv_y,
+        center_lv_z=center_lv_z,
+        a_endo_lv=a_endo_lv,
+        b_endo_lv=b_endo_lv,
+        c_endo_lv=c_endo_lv,
+        a_epi_lv=a_epi_lv,
+        b_epi_lv=b_epi_lv,
+        c_epi_lv=c_epi_lv,
+        center_rv_x=center_rv_x,
+        center_rv_y=center_rv_y,
+        center_rv_z=center_rv_z,
+        a_endo_rv=a_endo_rv,
+        b_endo_rv=b_endo_rv,
+        c_endo_rv=c_endo_rv,
+        a_epi_rv=a_epi_rv,
+        b_epi_rv=b_epi_rv,
+        c_epi_rv=c_epi_rv,
+        create_fibers=create_fibers,
+        fiber_angle_endo=fiber_angle_endo,
+        fiber_angle_epi=fiber_angle_epi,
+        fiber_space=fiber_space,
+    )
+
+    geo.save(outdir / "biv_ellipsoid_torso.bp")
+
+
+@click.command(help="Create slab geometry")
+@click.argument(
+    "outdir",
+    required=True,
+    type=click.Path(
+        file_okay=False,
+        dir_okay=True,
+        writable=True,
+        readable=True,
+        resolve_path=True,
+    ),
+)
+@click.option(
+    "--lx",
+    default=20.0,
+    type=float,
+    help="Length of slab in the x-direction",
+    show_default=True,
+)
+@click.option(
+    "--ly",
+    default=7.0,
+    type=float,
+    help="Length of slab in the y-direction",
+    show_default=True,
+)
+@click.option(
+    "--lz",
+    default=1.0,
+    type=float,
+    help="Length of slab in the z-direction",
+    show_default=True,
+)
+@click.option(
+    "--dx",
+    default=1.0,
+    type=float,
+    help="Element size",
+    show_default=True,
+)
+@click.option(
+    "--create-fibers",
+    default=False,
+    is_flag=True,
+    type=bool,
+    help="If True create analytic fibers",
+    show_default=True,
+)
+@click.option(
+    "--fiber-angle-endo",
+    default=-60,
+    type=float,
+    help="Angle for the endocardium",
+    show_default=True,
+)
+@click.option(
+    "--fiber-angle-epi",
+    default=+60,
+    type=float,
+    help="Angle for the epicardium",
+    show_default=True,
+)
+@click.option(
+    "--fiber-space",
+    default="P_1",
+    type=str,
+    help="Function space for fibers of the form family_degree",
+    show_default=True,
+)
+def slab(
+    outdir: Path,
+    lx: float = 20.0,
+    ly: float = 7.0,
+    lz: float = 3.0,
+    dx: float = 1.0,
+    create_fibers: bool = True,
+    fiber_angle_endo: float = -60,
+    fiber_angle_epi: float = +60,
+    fiber_space: str = "P_1",
+):
+    outdir = Path(outdir)
+    outdir.mkdir(exist_ok=True)
+
+    geo = mesh.slab(
+        outdir=outdir,
+        lx=lx,
+        ly=ly,
+        lz=lz,
+        dx=dx,
+        create_fibers=create_fibers,
+        fiber_angle_endo=fiber_angle_endo,
+        fiber_angle_epi=fiber_angle_epi,
+        fiber_space=fiber_space,
+    )
+    geo.save(outdir / "slab.bp")
+
+
+@click.command(help="Create slab in bath geometry")
+@click.argument(
+    "outdir",
+    required=True,
+    type=click.Path(
+        file_okay=False,
+        dir_okay=True,
+        writable=True,
+        readable=True,
+        resolve_path=True,
+    ),
+)
+@click.option(
+    "--lx",
+    default=1.0,
+    type=float,
+    help="Length of slab in the x-direction",
+    show_default=True,
+)
+@click.option(
+    "--ly",
+    default=0.01,
+    type=float,
+    help="Length of slab in the y-direction",
+    show_default=True,
+)
+@click.option(
+    "--lz",
+    default=0.5,
+    type=float,
+    help="Length of slab in the z-direction",
+    show_default=True,
+)
+@click.option(
+    "--bx",
+    default=0.0,
+    type=float,
+    help="Thickness of bath in the x-direction",
+    show_default=True,
+)
+@click.option(
+    "--by",
+    default=0.0,
+    type=float,
+    help="Thickness of bath in the y-direction",
+    show_default=True,
+)
+@click.option(
+    "--bz",
+    default=0.1,
+    type=float,
+    help="Thickness of bath in the z-direction",
+    show_default=True,
+)
+@click.option(
+    "--dx",
+    default=0.01,
+    type=float,
+    help="Element size",
+    show_default=True,
+)
+def slab_in_bath(
+    outdir: Path,
+    lx: float = 1.0,
+    ly: float = 0.01,
+    lz: float = 0.5,
+    bx: float = 0.0,
+    by: float = 0.0,
+    bz: float = 0.1,
+    dx: float = 0.01,
+):
+    outdir = Path(outdir)
+    outdir.mkdir(exist_ok=True)
+
+    geo = mesh.slab_in_bath(
+        outdir=outdir,
+        lx=lx,
+        ly=ly,
+        lz=lz,
+        bx=bx,
+        by=by,
+        bz=bz,
+        dx=dx,
+    )
+    geo.save(outdir / "slab_in_bath.bp")
+
+
+app.add_command(lv_ellipsoid)
+app.add_command(biv_ellipsoid)
+app.add_command(biv_ellipsoid_torso)
+app.add_command(slab)
+app.add_command(slab_in_bath)