cardiac-geometriesx 0.2.0__py3-none-any.whl → 0.3.1__py3-none-any.whl

cardiac_geometries/fibers/lv_ellipsoid.py

@@ -7,6 +7,58 @@ from ..utils import space_from_string
 from . import utils
 
 
+def mu_theta(
+    x: np.ndarray, y: np.ndarray, z: np.ndarray, long_axis: int = 0
+) -> tuple[np.ndarray, np.ndarray, list[int]]:
+    """Get the angles mu and theta from the coordinates x, y, z
+    given the long axis.
+
+    Parameters
+    ----------
+    x : np.ndarray
+        The x-coordinates
+    y : np.ndarray
+        The y-coordinates
+    z : np.ndarray
+        The z-coordinates
+    long_axis : int, optional
+        The long axis, by default 0 (x-axis)
+
+    Returns
+    -------
+    tuple[np.ndarray, np.ndarray, list[int]]
+        The angles mu and theta and the permutation of the axes
+
+    Raises
+    ------
+    ValueError
+        If the long axis is not 0, 1 or 2
+    """
+    if long_axis == 0:
+        a = np.sqrt(y**2 + z**2)
+        b = x
+        theta = np.pi - np.arctan2(z, -y)
+        perm = [0, 1, 2]
+    elif long_axis == 1:
+        a = np.sqrt(x**2 + z**2)
+        b = y
+        theta = np.pi - np.arctan2(z, -x)
+        perm = [1, 0, 2]
+    elif long_axis == 2:
+        a = np.sqrt(x**2 + y**2)
+        b = z
+        theta = np.pi - np.arctan2(x, -y)
+        perm = [2, 1, 0]
+    else:
+        raise ValueError("Invalid long_axis")
+
+    mu = np.arctan2(a, b)
+
+    theta[mu < 1e-7] = 0.0
+
+    return mu, theta, perm
+
+
 def compute_system(
     t_func: dolfinx.fem.Function,
     r_short_endo=0.025,
@@ -15,8 +67,36 @@ def compute_system(
     r_long_epi=0.097,
     alpha_endo: float = -60,
     alpha_epi: float = 60,
+    long_axis: int = 0,
     **kwargs,
 ) -> utils.Microstructure:
+    """Compute the microstructure for the given time function.
+
+    Parameters
+    ----------
+    t_func : dolfinx.fem.Function
+        Solution of the Laplace equation
+    r_short_endo : float, optional
+        Short radius at the endocardium, by default 0.025
+    r_short_epi : float, optional
+        Short radius at the epicardium, by default 0.035
+    r_long_endo : float, optional
+        Long radius at the endocardium, by default 0.09
+    r_long_epi : float, optional
+        Long radius at the epicardium, by default 0.097
+    alpha_endo : float, optional
+        Angle at the endocardium, by default -60
+    alpha_epi : float, optional
+        Angle at the epicardium, by default 60
+    long_axis : int, optional
+        Long axis, by default 0 (x-axis)
+
+    Returns
+    -------
+    utils.Microstructure
+        The microstructure
+    """
+
     V = t_func.function_space
     element = V.ufl_element()
     mesh = V.mesh
@@ -40,11 +120,7 @@ def compute_system(
     y = dof_coordinates[:, 1]
     z = dof_coordinates[:, 2]
 
-    a = np.sqrt(y**2 + z**2) / rs
-    b = x / rl
-    mu = np.arctan2(a, b)
-    theta = np.pi - np.arctan2(z, -y)
-    theta[mu < 1e-7] = 0.0
+    mu, theta, perm = mu_theta(x, y, z, long_axis=long_axis)
 
     e_t = np.array(
         [
@@ -52,7 +128,7 @@ def compute_system(
             drs_dt * np.sin(mu) * np.cos(theta),
             drs_dt * np.sin(mu) * np.sin(theta),
         ],
-    )
+    )[perm]
     e_t = utils.normalize(e_t)
 
     e_mu = np.array(
@@ -61,7 +137,7 @@ def compute_system(
             rs * np.cos(mu) * np.cos(theta),
             rs * np.cos(mu) * np.sin(theta),
         ],
-    )
+    )[perm]
     e_mu = utils.normalize(e_mu)
 
     e_theta = np.array(
@@ -70,7 +146,7 @@ def compute_system(
             -rs * np.sin(mu) * np.sin(theta),
             rs * np.sin(mu) * np.cos(theta),
         ],
-    )
+    )[perm]
     e_theta = utils.normalize(e_theta)
 
     f0 = np.sin(al) * e_mu + np.cos(al) * e_theta
@@ -113,6 +189,7 @@ def create_microstructure(
     r_long_epi=0.097,
     alpha_endo: float = -60,
     alpha_epi: float = 60,
+    long_axis: int = 0,
     outdir: str | Path | None = None,
 ):
     endo_marker = markers["ENDO"][0]
@@ -143,6 +220,7 @@ def create_microstructure(
         r_long_epi=r_long_epi,
         alpha_endo=alpha_endo,
         alpha_epi=alpha_epi,
+        long_axis=long_axis,
     )
     if outdir is not None:
         utils.save_microstructure(mesh, system, outdir)

cardiac_geometries/mesh.py

@@ -44,6 +44,7 @@ def biv_ellipsoid(
     fiber_angle_epi: float = -60,
     fiber_space: str = "P_1",
     verbose: bool = False,
+    comm: MPI.Comm = MPI.COMM_WORLD,
 ) -> Geometry:
     """Create BiV ellipsoidal geometry
 
@@ -99,6 +100,8 @@ def biv_ellipsoid(
         Function space for fibers of the form family_degree, by default "P_1"
     verbose : bool, optional
         If True print information from gmsh, by default False
+    comm : MPI.Comm, optional
+        MPI communicator, by default MPI.COMM_WORLD
 
     Returns
     -------
@@ -106,7 +109,6 @@ def biv_ellipsoid(
         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:
@@ -202,17 +204,6 @@ def biv_ellipsoid(
         save_microstructure(
             mesh=geometry.mesh, functions=(system.f0, system.s0, system.n0), outdir=outdir
         )
-        # 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
@@ -249,6 +240,7 @@ def biv_ellipsoid_torso(
     fiber_angle_epi: float = -60,
     fiber_space: str = "P_1",
     verbose: bool = False,
+    comm: MPI.Comm = MPI.COMM_WORLD,
 ) -> Geometry:
     """Create BiV ellipsoidal geometry
 
@@ -316,6 +308,8 @@ def biv_ellipsoid_torso(
         Function space for fibers of the form family_degree, by default "P_1"
     verbose : bool, optional
         If True print information from gmsh, by default False
+    comm : MPI.Comm, optional
+        MPI communicator, by default MPI.COMM_WORLD
 
     Returns
     -------
@@ -323,7 +317,6 @@ def biv_ellipsoid_torso(
         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:
@@ -445,6 +438,7 @@ def lv_ellipsoid(
     fiber_space: str = "P_1",
     aha: bool = True,
     verbose: bool = False,
+    comm: MPI.Comm = MPI.COMM_WORLD,
 ) -> Geometry:
     """Create an LV ellipsoidal geometry
 
@@ -482,6 +476,8 @@ def lv_ellipsoid(
         If True create 17-segment AHA regions
     verbose : bool, optional
         If True print information from gmsh, by default False
+    comm : MPI.Comm, optional
+        MPI communicator, by default MPI.COMM_WORLD
 
     Returns
     -------
@@ -489,7 +485,7 @@ def lv_ellipsoid(
         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:
@@ -596,6 +592,7 @@ def slab(
     fiber_angle_epi: float = -60,
     fiber_space: str = "P_1",
     verbose: bool = False,
+    comm: MPI.Comm = MPI.COMM_WORLD,
 ) -> Geometry:
     """Create slab geometry
 
@@ -621,6 +618,8 @@ def slab(
         Function space for fibers of the form family_degree, by default "P_1"
     verbose : bool, optional
         If True print information from gmsh, by default False
+    comm : MPI.Comm, optional
+        MPI communicator, by default MPI.COMM_WORLD
 
     Returns
     -------
@@ -628,7 +627,6 @@ def slab(
         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:
@@ -698,6 +696,7 @@ def slab_in_bath(
     bz: float = 0.1,
     dx: float = 0.001,
     verbose: bool = False,
+    comm: MPI.Comm = MPI.COMM_WORLD,
 ) -> Geometry:
     """Create slab geometry
 
@@ -721,6 +720,8 @@ def slab_in_bath(
         Element size, by default 0.001
     verbose : bool, optional
         If True print information from gmsh, by default False
+    comm : MPI.Comm, optional
+        MPI communicator, by default MPI.COMM_WORLD
 
     Returns
     -------
@@ -728,7 +729,6 @@ def slab_in_bath(
         A Geometry with the mesh, markers, markers functions and fibers.
 
     """
-    comm = MPI.COMM_WORLD
 
     outdir = Path(outdir)
     mesh_name = outdir / "slab_in_bath.msh"

{cardiac_geometriesx-0.2.0.dist-info → cardiac_geometriesx-0.3.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cardiac-geometriesx
-Version: 0.2.0
+Version: 0.3.1
 Summary: A python library for cardiac geometries
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License: MIT

{cardiac_geometriesx-0.2.0.dist-info → cardiac_geometriesx-0.3.1.dist-info}/RECORD

@@ -2,15 +2,15 @@ cardiac_geometries/__init__.py,sha256=2W_ywAeLjyRk5MqSPAodHa4UN2lOnW1h8tmGLQ3gaJ
 cardiac_geometries/cli.py,sha256=GKcsMNhVFoxWDr-o3jiDCXmTvPgCSEB9Kws8AvYIK4Q,19678
 cardiac_geometries/geometry.py,sha256=iK8lydZEqU3sz0983yucW9IzQ2VqSXSy4D5ubdl9bOs,5636
 cardiac_geometries/gui.py,sha256=9WYR850wLrqsUrVUC37E2SaO0OWA_oagSe-YNrsxz3k,8376
-cardiac_geometries/mesh.py,sha256=JSm69BTS7WRUldwaQ9-Gnjq_KbX66FTnl2ouFKRtFhA,26825
+cardiac_geometries/mesh.py,sha256=Ejciny48mnKKN20RrY9DwLY7_Lh1jb6Kldj4CW1wr1o,26909
 cardiac_geometries/utils.py,sha256=EwEXAuB4XiJaqlZaGZ1cc6sIBSPJLCx-43As1NUcJrA,16488
 cardiac_geometries/fibers/__init__.py,sha256=WpRrn9Iakl-3m8IGtFkqP0LXGjw5EZHZ8Eg9JCnCdrg,137
-cardiac_geometries/fibers/lv_ellipsoid.py,sha256=jFloAhrFRkKrhsWVKcOiZrGioPLBN3_yiIXiyr1mHCQ,3665
+cardiac_geometries/fibers/lv_ellipsoid.py,sha256=KuWnx9yZ5KDyoeoYyDnXLZYb82DRiNveZyNIboD3uJ8,5768
 cardiac_geometries/fibers/slab.py,sha256=5tMvOSqXQ4_nbdUUtho_tQjDrmICxZfN7SXNq4FKdlY,3836
 cardiac_geometries/fibers/utils.py,sha256=j1ERqXcdaWCwO2yjbYGlgTt2G1DxZCVzbNHuDhh_QrM,2541
-cardiac_geometriesx-0.2.0.dist-info/LICENSE,sha256=lo5K2rJPZOSv6luutGHbzzi3IpXNaB9E2UWq60qvNx0,1111
-cardiac_geometriesx-0.2.0.dist-info/METADATA,sha256=VHm0LNhB1GsjrcY8fPTJH0C6UzvV01FW07kIxgmVAwc,4163
-cardiac_geometriesx-0.2.0.dist-info/WHEEL,sha256=y4mX-SOX4fYIkonsAGA5N0Oy-8_gI4FXw5HNI1xqvWg,91
-cardiac_geometriesx-0.2.0.dist-info/entry_points.txt,sha256=xOBnlc6W-H9oCDYLNz3kpki26OmpfYSoFSrmi_4V-Ec,52
-cardiac_geometriesx-0.2.0.dist-info/top_level.txt,sha256=J0gQxkWR2my5Vf7Qt8buDY8ZOjYdVfIweVunCGXWKNE,19
-cardiac_geometriesx-0.2.0.dist-info/RECORD,,
+cardiac_geometriesx-0.3.1.dist-info/LICENSE,sha256=lo5K2rJPZOSv6luutGHbzzi3IpXNaB9E2UWq60qvNx0,1111
+cardiac_geometriesx-0.3.1.dist-info/METADATA,sha256=maN2Wb_hCkroXXzBdl-_UX0BxQW9jvNAQkqb38YAb40,4163
+cardiac_geometriesx-0.3.1.dist-info/WHEEL,sha256=cVxcB9AmuTcXqmwrtPhNK88dr7IR_b6qagTj0UvIEbY,91
+cardiac_geometriesx-0.3.1.dist-info/entry_points.txt,sha256=xOBnlc6W-H9oCDYLNz3kpki26OmpfYSoFSrmi_4V-Ec,52
+cardiac_geometriesx-0.3.1.dist-info/top_level.txt,sha256=J0gQxkWR2my5Vf7Qt8buDY8ZOjYdVfIweVunCGXWKNE,19
+cardiac_geometriesx-0.3.1.dist-info/RECORD,,

{cardiac_geometriesx-0.2.0.dist-info → cardiac_geometriesx-0.3.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (70.2.0)
+Generator: setuptools (74.1.2)
 Root-Is-Purelib: true
 Tag: py3-none-any