cardiac-geometriesx 0.0.1__py3-none-any.whl

cardiac_geometries/mesh.py

@@ -0,0 +1,727 @@
+from pathlib import Path
+import math
+import json
+import datetime
+from importlib.metadata import metadata
+from structlog import get_logger
+
+from mpi4py import MPI
+import cardiac_geometries_core as cgc
+
+from . import utils
+from .geometry import Geometry
+
+meta = metadata("cardiac-geometriesx")
+__version__ = meta["Version"]
+
+logger = get_logger()
+
+
+def biv_ellipsoid(
+    outdir: str | 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",
+) -> Geometry:
+    """Create BiV ellipsoidal geometry
+
+    Parameters
+    ----------
+    outdir : str | Path
+        Directory where to save the results.
+    char_length : float, optional
+        Characteristic length of mesh, by default 0.5
+    center_lv_y : float, optional
+        X-coordinate for the center of the lv, by default 0.0
+    center_lv_y : float, optional
+        Y-coordinate for the center of the lv, by default 0.0
+    center_lv_z : float, optional
+        Z-coordinate for the center of the lv, by default 0.0
+    a_endo_lv : float, optional
+        Dilation of lv endo ellipsoid in the x-direction, by default 2.5
+    b_endo_lv : float, optional
+       Dilation of lv endo ellipsoid in the y-direction, by default 1.0
+    c_endo_lv : float, optional
+       Dilation of lv endo ellipsoid in the z-direction, by default 1.0
+    a_epi_lv : float, optional
+        Dilation of lv epi ellipsoid in the x-direction, by default 3.0
+    b_epi_lv : float, optional
+        Dilation of lv epi ellipsoid in the y-direction, by default 1.5
+    c_epi_lv : float, optional
+        Dilation of lv epi ellipsoid in the z-direction, by default 1.5
+    center_rv_x : float, optional
+        X-coordinate for the center of the rv, by default 0.0
+    center_rv_y : float, optional
+        Y-coordinate for the center of the rv, by default 0.5
+    center_rv_z : float, optional
+        Z-coordinate for the center of the rv, by default 0.0
+    a_endo_rv : float, optional
+       Dilation of rv endo ellipsoid in the x-direction, by default 3.0
+    b_endo_rv : float, optional
+       Dilation of rv endo ellipsoid in the y-direction, by default 1.5
+    c_endo_rv : float, optional
+       Dilation of rv endo ellipsoid in the z-direction, by default 1.5
+    a_epi_rv : float, optional
+        Dilation of rv epi ellipsoid in the x-direction, by default 4.0
+    b_epi_rv : float, optional
+        Dilation of rv epi ellipsoid in the y-direction, by default 2.5
+    c_epi_rv : float, optional
+        Dilation of rv epi ellipsoid in the z-direction, by default 2.0
+    create_fibers : bool, optional
+        If True create analytic fibers, by default False
+    fiber_angle_endo : float, optional
+        Angle for the endocardium, by default -60
+    fiber_angle_epi : float, optional
+        Angle for the epicardium, by default +60
+    fiber_space : str, optional
+        Function space for fibers of the form family_degree, by default "P_1"
+
+    Returns
+    -------
+    Geometry
+        A Geometry with the mesh, markers, markers functions and fibers.
+
+    """
+    comm = MPI.COMM_WORLD
+    outdir = Path(outdir)
+    mesh_name = outdir / "biv_ellipsoid.msh"
+    if comm.rank == 0:
+        outdir.mkdir(exist_ok=True, parents=True)
+
+        with open(outdir / "info.json", "w") as f:
+            json.dump(
+                {
+                    "char_length": char_length,
+                    "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,
+                    "fibers_angle_endo": fiber_angle_endo,
+                    "fibers_angle_epi": fiber_angle_epi,
+                    "fiber_space": fiber_space,
+                    # "mesh_type": MeshTypes.biv_ellipsoid.value,
+                    "cardiac_geometry_version": __version__,
+                    "timestamp": datetime.datetime.now().isoformat(),
+                },
+                f,
+                indent=2,
+                default=utils.json_serial,
+            )
+
+        cgc.biv_ellipsoid(
+            mesh_name=mesh_name.as_posix(),
+            char_length=char_length,
+            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,
+        )
+    comm.barrier()
+    geometry = utils.gmsh2dolfin(comm=comm, msh_file=mesh_name, unlink=False)
+
+    if comm.rank == 0:
+        with open(outdir / "markers.json", "w") as f:
+            json.dump(geometry.markers, f, default=utils.json_serial)
+    comm.barrier()
+    if create_fibers:
+        raise NotImplementedError("Fibers not implemented yet for biv ellipsoid.")
+        # from .fibers._biv_ellipsoid import create_biv_fibers
+
+        # create_biv_fibers(
+        #     mesh=geometry.mesh,
+        #     ffun=geometry.marker_functions.ffun,
+        #     markers=geometry.markers,
+        #     fiber_space=fiber_space,
+        #     alpha_endo=fiber_angle_endo,
+        #     alpha_epi=fiber_angle_epi,
+        #     outdir=outdir,
+        # )
+
+    geo = Geometry.from_folder(comm=comm, folder=outdir)
+    return geo
+
+
+def biv_ellipsoid_torso(
+    outdir: str | Path,
+    char_length: float = 0.5,
+    heart_as_surface: bool = False,
+    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",
+) -> Geometry:
+    """Create BiV ellipsoidal geometry
+
+    Parameters
+    ----------
+    outdir : str | Path
+        Directory where to save the results.
+    char_length : float, optional
+        Characteristic length of mesh, by default 0.5
+    heart_as_surface: bool
+        If true, create the heart as a a surface inside the torso,
+        otherwise let the heart be a volume, by default True.
+    torso_length : float, optional
+        Length of torso in the x-direction, by default 20.0
+    torso_width : float, optional
+        Length of torso in the y-direction, by default 20.0
+    torso_height : float, optional
+        Length of torso in the z-direction, by default 20.0
+    rotation_angle: float, optional
+        Angle to rotate the torso in order to object realistic position of
+        the heart in a torso, by default pi / 6
+    center_lv_x : float, optional
+        X-coordinate for the center of the lv, by default 0.0
+    center_lv_y : float, optional
+        Y-coordinate for the center of the lv, by default 0.0
+    center_lv_z : float, optional
+        Z-coordinate for the center of the lv, by default 0.0
+    a_endo_lv : float, optional
+        Dilation of lv endo ellipsoid in the x-direction, by default 2.5
+    b_endo_lv : float, optional
+       Dilation of lv endo ellipsoid in the y-direction, by default 1.0
+    c_endo_lv : float, optional
+       Dilation of lv endo ellipsoid in the z-direction, by default 1.0
+    a_epi_lv : float, optional
+        Dilation of lv epi ellipsoid in the x-direction, by default 3.0
+    b_epi_lv : float, optional
+        Dilation of lv epi ellipsoid in the y-direction, by default 1.5
+    c_epi_lv : float, optional
+        Dilation of lv epi ellipsoid in the z-direction, by default 1.5
+    center_rv_x : float, optional
+        X-coordinate for the center of the rv, by default 0.0
+    center_rv_y : float, optional
+        Y-coordinate for the center of the rv, by default 0.5
+    center_rv_z : float, optional
+        Z-coordinate for the center of the rv, by default 0.0
+    a_endo_rv : float, optional
+       Dilation of rv endo ellipsoid in the x-direction, by default 3.0
+    b_endo_rv : float, optional
+       Dilation of rv endo ellipsoid in the y-direction, by default 1.5
+    c_endo_rv : float, optional
+       Dilation of rv endo ellipsoid in the z-direction, by default 1.5
+    a_epi_rv : float, optional
+        Dilation of rv epi ellipsoid in the x-direction, by default 4.0
+    b_epi_rv : float, optional
+        Dilation of rv epi ellipsoid in the y-direction, by default 2.5
+    c_epi_rv : float, optional
+        Dilation of rv epi ellipsoid in the z-direction, by default 2.0
+    create_fibers : bool, optional
+        If True create analytic fibers, by default False
+    fiber_angle_endo : float, optional
+        Angle for the endocardium, by default -60
+    fiber_angle_epi : float, optional
+        Angle for the epicardium, by default +60
+    fiber_space : str, optional
+        Function space for fibers of the form family_degree, by default "P_1"
+
+    Returns
+    -------
+    Geometry
+        A Geometry with the mesh, markers, markers functions and fibers.
+
+    """
+    comm = MPI.COMM_WORLD
+    outdir = Path(outdir)
+    mesh_name = outdir / "biv_ellipsoid_torso.msh"
+    if comm.rank == 0:
+        outdir.mkdir(exist_ok=True, parents=True)
+
+        with open(outdir / "info.json", "w") as f:
+            json.dump(
+                {
+                    "char_length": char_length,
+                    "heart_as_surface": heart_as_surface,
+                    "torso_length": torso_length,
+                    "torso_width": torso_width,
+                    "torso_height": torso_height,
+                    "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,
+                    "fibers_angle_endo": fiber_angle_endo,
+                    "fibers_angle_epi": fiber_angle_epi,
+                    "fiber_space": fiber_space,
+                    # "mesh_type": MeshTypes.biv_ellipsoid.value,
+                    "cardiac_geometry_version": __version__,
+                    "timestamp": datetime.datetime.now().isoformat(),
+                },
+                f,
+                indent=2,
+                default=utils.json_serial,
+            )
+
+        cgc.biv_ellipsoid_torso(
+            mesh_name=mesh_name.as_posix(),
+            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,
+        )
+    comm.barrier()
+
+    geometry = utils.gmsh2dolfin(comm=comm, msh_file=mesh_name, unlink=False)
+
+    if comm.rank == 0:
+        with open(outdir / "markers.json", "w") as f:
+            json.dump(geometry.markers, f, default=utils.json_serial)
+    comm.barrier()
+
+    if create_fibers:
+        if heart_as_surface:
+            logger.warning("Can only create fibers when heart is a volume.")
+        else:
+            raise NotImplementedError("Fibers not implemented yet for biv ellipsoid.")
+            # from .fibers._biv_ellipsoid import create_biv_in_torso_fibers
+
+            # create_biv_in_torso_fibers(
+            #     mesh=geometry.mesh,
+            #     ffun=geometry.marker_functions.ffun,
+            #     cfun=geometry.marker_functions.cfun,
+            #     markers=geometry.markers,
+            #     fiber_space=fiber_space,
+            #     alpha_endo=fiber_angle_endo,
+            #     alpha_epi=fiber_angle_epi,
+            #     outdir=outdir,
+            # )
+
+    geo = Geometry.from_folder(comm=comm, folder=outdir)
+    return geo
+
+
+def lv_ellipsoid(
+    outdir: Path | str,
+    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,
+) -> Geometry:
+    """Create an LV ellipsoidal geometry
+
+    Parameters
+    ----------
+    outdir : Optional[Path], optional
+        Directory where to save the results.
+    r_short_endo : float, optional
+        Shortest radius on the endocardium layer, by default 7.0
+    r_short_epi : float, optional
+       Shortest radius on the epicardium layer, by default 10.0
+    r_long_endo : float, optional
+        Longest radius on the endocardium layer, by default 17.0
+    r_long_epi : float, optional
+        Longest radius on the epicardium layer, by default 20.0
+    psize_ref : float, optional
+        The reference point size (smaller values yield as finer mesh, by default 3
+    mu_apex_endo : float, optional
+        Angle for the endocardial apex, by default -math.pi
+    mu_base_endo : float, optional
+        Angle for the endocardial base, by default -math.acos(5 / 17)
+    mu_apex_epi : float, optional
+        Angle for the epicardial apex, by default -math.pi
+    mu_base_epi : float, optional
+        Angle for the epicardial apex, by default -math.acos(5 / 20)
+    create_fibers : bool, optional
+        If True create analytic fibers, by default False
+    fiber_angle_endo : float, optional
+        Angle for the endocardium, by default -60
+    fiber_angle_epi : float, optional
+        Angle for the epicardium, by default +60
+    fiber_space : str, optional
+        Function space for fibers of the form family_degree, by default "P_1"
+    aha : bool, optional
+        If True create 17-segment AHA regions
+
+    Returns
+    -------
+    Geometry
+        A Geometry with the mesh, markers, markers functions and fibers.
+
+    """
+    comm = MPI.COMM_WORLD
+    outdir = Path(outdir)
+    mesh_name = outdir / "lv_ellipsoid.msh"
+    if comm.rank == 0:
+        outdir.mkdir(exist_ok=True, parents=True)
+
+        with open(outdir / "info.json", "w") as f:
+            json.dump(
+                {
+                    "r_short_endo": r_short_endo,
+                    "r_short_epi": r_short_epi,
+                    "r_long_endo": r_long_endo,
+                    "r_long_epi": r_long_epi,
+                    "psize_ref": psize_ref,
+                    "mu_apex_endo": mu_apex_endo,
+                    "mu_base_endo": mu_base_endo,
+                    "mu_apex_epi": mu_apex_epi,
+                    "mu_base_epi": mu_base_epi,
+                    "create_fibers": create_fibers,
+                    "fibers_angle_endo": fiber_angle_endo,
+                    "fibers_angle_epi": fiber_angle_epi,
+                    "fiber_space": fiber_space,
+                    "aha": aha,
+                    # "mesh_type": MeshTypes.lv_ellipsoid.value,
+                    "cardiac_geometry_version": __version__,
+                    "timestamp": datetime.datetime.now().isoformat(),
+                },
+                f,
+                indent=2,
+                default=utils.json_serial,
+            )
+
+        cgc.lv_ellipsoid(
+            mesh_name=mesh_name.as_posix(),
+            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,
+        )
+    comm.barrier()
+
+    geometry = utils.gmsh2dolfin(comm=comm, msh_file=mesh_name, unlink=False)
+
+    # if aha:
+    #     from .aha import lv_aha
+
+    #     geometry = lv_aha(
+    #         geometry=geometry,
+    #         r_long_endo=r_long_endo,
+    #         r_short_endo=r_short_endo,
+    #         mu_base=mu_base_endo,
+    #     )
+    #     from dolfin import XDMFFile
+
+    #     with XDMFFile((outdir / "cfun.xdmf").as_posix()) as xdmf:
+    #         xdmf.write(geometry.marker_functions.cfun)
+
+    if comm.rank == 0:
+        with open(outdir / "markers.json", "w") as f:
+            json.dump(geometry.markers, f, default=utils.json_serial)
+
+    if create_fibers:
+        from .fibers.lv_ellipsoid import create_microstructure
+
+        create_microstructure(
+            mesh=geometry.mesh,
+            ffun=geometry.ffun,
+            markers=geometry.markers,
+            function_space=fiber_space,
+            r_short_endo=r_short_endo,
+            r_short_epi=r_short_epi,
+            r_long_endo=r_long_endo,
+            r_long_epi=r_long_epi,
+            alpha_endo=fiber_angle_endo,
+            alpha_epi=fiber_angle_epi,
+            outdir=outdir,
+        )
+
+    geo = Geometry.from_folder(comm=comm, folder=outdir)
+    # if aha:
+    #     # Update schema
+    #     from .geometry import H5Path
+
+    #     cfun = geo.schema["cfun"].to_dict()
+    #     cfun["fname"] = "cfun.xdmf:f"
+    #     geo.schema["cfun"] = H5Path(**cfun)
+
+    return geo
+
+
+def slab(
+    outdir: Path | str,
+    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",
+) -> Geometry:
+    """Create slab geometry
+
+    Parameters
+    ----------
+    outdir : Optional[Path], optional
+        Directory where to save the results.
+    lx : float, optional
+        Length of slab the x-direction, by default 20.0
+    ly : float, optional
+        Length of slab the x-direction, by default 7.0
+    lz : float, optional
+        Length of slab the z-direction, by default 3.0
+    dx : float, optional
+        Element size, by default 1.0
+    create_fibers : bool, optional
+        If True create analytic fibers, by default True
+    fiber_angle_endo : float, optional
+        Angle for the endocardium, by default -60
+    fiber_angle_epi : float, optional
+        Angle for the epicardium, by default +60
+    fiber_space : str, optional
+        Function space for fibers of the form family_degree, by default "P_1"
+
+    Returns
+    -------
+    Geometry
+        A Geometry with the mesh, markers, markers functions and fibers.
+
+    """
+    comm = MPI.COMM_WORLD
+    outdir = Path(outdir)
+    mesh_name = outdir / "slab.msh"
+    if comm.rank == 0:
+        outdir.mkdir(exist_ok=True, parents=True)
+
+        with open(outdir / "info.json", "w") as f:
+            json.dump(
+                {
+                    "lx": lx,
+                    "ly": ly,
+                    "lz": lz,
+                    "dx": dx,
+                    "create_fibers": create_fibers,
+                    "fibers_angle_endo": fiber_angle_endo,
+                    "fibers_angle_epi": fiber_angle_epi,
+                    "fiber_space": fiber_space,
+                    # "mesh_type": MeshTypes.slab.value,
+                    "cardiac_geometry_version": __version__,
+                    "timestamp": datetime.datetime.now().isoformat(),
+                },
+                f,
+                indent=2,
+                default=utils.json_serial,
+            )
+
+        cgc.slab(mesh_name=mesh_name.as_posix(), lx=lx, ly=ly, lz=lz, dx=dx)
+    comm.barrier()
+
+    geometry = utils.gmsh2dolfin(comm=comm, msh_file=mesh_name, unlink=False)
+
+    if comm.rank == 0:
+        with open(outdir / "markers.json", "w") as f:
+            json.dump(geometry.markers, f, default=utils.json_serial)
+
+    if create_fibers:
+        from .fibers.slab import create_microstructure
+
+        create_microstructure(
+            mesh=geometry.mesh,
+            ffun=geometry.ffun,
+            markers=geometry.markers,
+            function_space=fiber_space,
+            alpha_endo=fiber_angle_endo,
+            alpha_epi=fiber_angle_epi,
+            outdir=outdir,
+        )
+
+    geo = Geometry.from_folder(comm=comm, folder=outdir)
+
+    return geo
+
+
+def slab_in_bath(
+    outdir: Path | str,
+    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 = 0.001,
+) -> Geometry:
+    """Create slab geometry
+
+    Parameters
+    ----------
+    outdir : Path
+        Directory where to save the results.
+    lx : float, optional
+        Length of slab the x-direction, by default 1.0
+    ly : float, optional
+        Length of slab the x-direction, by default 0.5
+    lz : float, optional
+        Length of slab the z-direction, by default 0.01
+    bx : float, optional
+        Thickness of bath the x-direction, by default 0.0
+    by : float, optional
+        Thickness of bath the x-direction, by default 0.0
+    bz : float, optional
+        Thickness of bath the z-direction, by default 0.1
+    dx : float, optional
+        Element size, by default 0.001
+
+    Returns
+    -------
+    Geometry
+        A Geometry with the mesh, markers, markers functions and fibers.
+
+    """
+    comm = MPI.COMM_WORLD
+
+    outdir = Path(outdir)
+    mesh_name = outdir / "slab_in_bath.msh"
+    if comm.rank == 0:
+        outdir.mkdir(exist_ok=True, parents=True)
+
+        with open(outdir / "info.json", "w") as f:
+            json.dump(
+                {
+                    "lx": lx,
+                    "ly": ly,
+                    "lz": lz,
+                    "bx": bx,
+                    "by": by,
+                    "bz": bz,
+                    "dx": dx,
+                    # "mesh_type": MeshTypes.slab.value,
+                    "cardiac_geometry_version": __version__,
+                    "timestamp": datetime.datetime.now().isoformat(),
+                },
+                f,
+                indent=2,
+                default=utils.json_serial,
+            )
+
+        cgc.slab_in_bath(
+            mesh_name=mesh_name.as_posix(),
+            lx=lx,
+            ly=ly,
+            lz=lz,
+            bx=bx,
+            by=by,
+            bz=bz,
+            dx=dx,
+        )
+
+    geometry = utils.gmsh2dolfin(comm=comm, msh_file=mesh_name, unlink=False)
+
+    if comm.rank == 0:
+        with open(outdir / "markers.json", "w") as f:
+            json.dump(geometry.markers, f, default=utils.json_serial)
+
+    geo = Geometry.from_folder(comm=comm, folder=outdir)
+
+    return geo