cardiac-geometriesx 0.4.0__tar.gz → 0.4.2__tar.gz

{cardiac_geometriesx-0.4.0/src/cardiac_geometriesx.egg-info → cardiac_geometriesx-0.4.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cardiac-geometriesx
-Version: 0.4.0
+Version: 0.4.2
 Summary: A python library for cardiac geometries
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License: MIT
@@ -17,6 +17,7 @@ Requires-Dist: structlog
 Requires-Dist: cardiac-geometries-core
 Requires-Dist: rich-click
 Requires-Dist: adios4dolfinx
+Requires-Dist: scifem
 Provides-Extra: dev
 Requires-Dist: bump-my-version; extra == "dev"
 Requires-Dist: ipython; extra == "dev"

{cardiac_geometriesx-0.4.0 → cardiac_geometriesx-0.4.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cardiac-geometriesx"
-version = "0.4.0"
+version = "0.4.2"
 description = "A python library for cardiac geometries"
 authors = [{name = "Henrik Finsberg", email = "henriknf@simula.no"}]
 license = {text = "MIT"}
@@ -22,6 +22,7 @@ dependencies = [
     "cardiac-geometries-core",
     "rich-click",
     "adios4dolfinx",
+    "scifem",
 ]
 
 [project.readme]
@@ -173,7 +174,7 @@ tag = true
 sign_tags = false
 tag_name = "v{new_version}"
 tag_message = "Bump version: {current_version} → {new_version}"
-current_version = "0.4.0"
+current_version = "0.4.2"
 
 
 [[tool.bumpversion.files]]

{cardiac_geometriesx-0.4.0 → cardiac_geometriesx-0.4.2}/src/cardiac_geometries/fibers/lv_ellipsoid.py

@@ -8,7 +8,12 @@ from . import utils
 
 
 def mu_theta(
-    x: np.ndarray, y: np.ndarray, z: np.ndarray, long_axis: int = 0
+    x: np.ndarray,
+    y: np.ndarray,
+    z: np.ndarray,
+    rs: np.ndarray,
+    rl: 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.
@@ -21,6 +26,10 @@ def mu_theta(
         The y-coordinates
     z : np.ndarray
         The z-coordinates
+    rs : np.ndarray
+        The short radius
+    rl : np.ndarray
+        The long radius
     long_axis : int, optional
         The long axis, by default 0 (x-axis)
 
@@ -35,18 +44,18 @@ def mu_theta(
         If the long axis is not 0, 1 or 2
     """
     if long_axis == 0:
-        a = np.sqrt(y**2 + z**2)
-        b = x
+        a = np.sqrt(y**2 + z**2) / rs
+        b = x / rl
         theta = np.pi - np.arctan2(z, -y)
         perm = [0, 1, 2]
     elif long_axis == 1:
-        a = np.sqrt(x**2 + z**2)
-        b = y
+        a = np.sqrt(x**2 + z**2) / rs
+        b = y / rl
         theta = np.pi - np.arctan2(z, -x)
         perm = [1, 0, 2]
     elif long_axis == 2:
-        a = np.sqrt(x**2 + y**2)
-        b = z
+        a = np.sqrt(x**2 + y**2) / rs
+        b = z / rl
         theta = np.pi - np.arctan2(x, -y)
         perm = [2, 1, 0]
     else:
@@ -120,7 +129,7 @@ def compute_system(
     y = dof_coordinates[:, 1]
     z = dof_coordinates[:, 2]
 
-    mu, theta, perm = mu_theta(x, y, z, long_axis=long_axis)
+    mu, theta, perm = mu_theta(x, y, z, rs, rl, long_axis=long_axis)
 
     e_t = np.array(
         [
@@ -159,7 +168,10 @@ def compute_system(
     s0 = utils.normalize(s0)
 
     Vv = space_from_string(
-        space_string=f"{element.family_name}_{element.degree}", mesh=mesh, dim=mesh.geometry.dim
+        space_string=f"{element.family_name}_{element.degree}",
+        mesh=mesh,
+        dim=mesh.geometry.dim,
+        discontinuous=element.discontinuous,
     )
 
     fiber = dolfinx.fem.Function(Vv)

{cardiac_geometriesx-0.4.0 → cardiac_geometriesx-0.4.2}/src/cardiac_geometries/fibers/slab.py

@@ -60,7 +60,10 @@ def compute_system(
     n0 = utils.normalize(n0)
 
     Vv = space_from_string(
-        space_string=f"{element.family_name}_{element.degree}", mesh=mesh, dim=mesh.geometry.dim
+        space_string=f"{element.family_name}_{element.degree}",
+        mesh=mesh,
+        dim=mesh.geometry.dim,
+        discontinuous=element.discontinuous,
     )
 
     fiber = dolfinx.fem.Function(Vv)

{cardiac_geometriesx-0.4.0 → cardiac_geometriesx-0.4.2}/src/cardiac_geometries/fibers/utils.py

@@ -20,21 +20,24 @@ class Microstructure(NamedTuple):
 def save_microstructure(
     mesh: dolfinx.mesh.Mesh, functions: Sequence[dolfinx.fem.Function], outdir: str | Path
 ) -> None:
-    from ..utils import create_xdmf_pointcloud, element2array
+    from ..utils import element2array
 
     if len(functions) == 0:
         return
     # Save for paraview visualization
+
     if functions[0].function_space.ufl_element().family_name == "quadrature":
-        create_xdmf_pointcloud(us=functions, filename=Path(outdir) / "microstructure-viz.xdmf")
+        from scifem.xdmf import create_pointcloud
+
+        create_pointcloud(functions=functions, filename=Path(outdir) / "microstructure-viz.xdmf")
     else:
         try:
             with dolfinx.io.VTXWriter(
                 mesh.comm, Path(outdir) / "microstructure-viz.bp", functions, engine="BP4"
             ) as file:
                 file.write(0.0)
-        except RuntimeError:
-            pass
+        except RuntimeError as ex:
+            print(f"Failed to write microstructure: {ex}")
 
     # Save with proper function space
     filename = Path(outdir) / "microstructure.bp"

{cardiac_geometriesx-0.4.0 → cardiac_geometriesx-0.4.2}/src/cardiac_geometries/utils.py

@@ -270,7 +270,9 @@ def model_to_mesh(
     return GMshModel(mesh, ct, ft, et, vt)
 
 
-def parse_element(space_string: str, mesh: dolfinx.mesh.Mesh, dim: int) -> basix.ufl._ElementBase:
+def parse_element(
+    space_string: str, mesh: dolfinx.mesh.Mesh, dim: int, discontinuous: bool = False
+) -> basix.ufl._ElementBase:
     """
     Parse a string representation of a basix element family
     """
@@ -283,8 +285,9 @@ def parse_element(space_string: str, mesh: dolfinx.mesh.Mesh, dim: int) -> basix
         else:
             kwargs["shape"] = (dim,)
 
+    # breakpoint()
     if family_str in ["Lagrange", "P", "CG"]:
-        el = basix.ufl.element(family=basix.ElementFamily.P, discontinuous=False, **kwargs)
+        el = basix.ufl.element(family=basix.ElementFamily.P, discontinuous=discontinuous, **kwargs)
     elif family_str in ["Discontinuous Lagrange", "DG", "dP"]:
         el = basix.ufl.element(family=basix.ElementFamily.P, discontinuous=True, **kwargs)
 
@@ -298,7 +301,7 @@ def parse_element(space_string: str, mesh: dolfinx.mesh.Mesh, dim: int) -> basix
 
 
 def space_from_string(
-    space_string: str, mesh: dolfinx.mesh.Mesh, dim: int
+    space_string: str, mesh: dolfinx.mesh.Mesh, dim: int, discontinuous: bool = False
 ) -> dolfinx.fem.functionspace:
     """
     Constructed a finite elements space from a string
@@ -313,8 +316,10 @@ def space_from_string(
         The mesh
     dim : int
         1 for scalar space, 3 for vector space.
+    discontinuous: bool
+        If true force element to be discontinuous, by default False
     """
-    el = parse_element(space_string, mesh, dim)
+    el = parse_element(space_string, mesh, dim, discontinuous=discontinuous)
     return dolfinx.fem.functionspace(mesh, el)
 
 

{cardiac_geometriesx-0.4.0 → cardiac_geometriesx-0.4.2/src/cardiac_geometriesx.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cardiac-geometriesx
-Version: 0.4.0
+Version: 0.4.2
 Summary: A python library for cardiac geometries
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License: MIT
@@ -17,6 +17,7 @@ Requires-Dist: structlog
 Requires-Dist: cardiac-geometries-core
 Requires-Dist: rich-click
 Requires-Dist: adios4dolfinx
+Requires-Dist: scifem
 Provides-Extra: dev
 Requires-Dist: bump-my-version; extra == "dev"
 Requires-Dist: ipython; extra == "dev"

{cardiac_geometriesx-0.4.0 → cardiac_geometriesx-0.4.2}/src/cardiac_geometriesx.egg-info/requires.txt

@@ -3,6 +3,7 @@ structlog
 cardiac-geometries-core
 rich-click
 adios4dolfinx
+scifem
 
 [dev]
 bump-my-version

{cardiac_geometriesx-0.4.0 → cardiac_geometriesx-0.4.2}/tests/test_cli.py

@@ -16,7 +16,7 @@ from cardiac_geometries import Geometry, cli
     ],
     ids=["slab", "lv_ellipsoid"],
 )
-@pytest.mark.parametrize("fiber_space", [None, "P_1", "P_2", "Quadrature_2"])
+@pytest.mark.parametrize("fiber_space", [None, "P_1", "P_2", "Quadrature_2", "DG_1"])
 def test_script(fiber_space, script, tmp_path: Path):
     runner = CliRunner()