cardiac-geometriesx 0.4.0__py3-none-any.whl → 0.4.1__py3-none-any.whl

cardiac_geometries/fibers/lv_ellipsoid.py

@@ -159,7 +159,10 @@ 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_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_geometries/fibers/utils.py

@@ -20,13 +20,15 @@ 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(

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.dist-info → cardiac_geometriesx-0.4.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cardiac-geometriesx
-Version: 0.4.0
+Version: 0.4.1
 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-0.4.1.dist-info/RECORD

@@ -0,0 +1,16 @@
+cardiac_geometries/__init__.py,sha256=2W_ywAeLjyRk5MqSPAodHa4UN2lOnW1h8tmGLQ3gaJ0,150
+cardiac_geometries/cli.py,sha256=GKcsMNhVFoxWDr-o3jiDCXmTvPgCSEB9Kws8AvYIK4Q,19678
+cardiac_geometries/geometry.py,sha256=s-1BIDKvP9M3uu3Sl8JpGRnTnXZAa9Aq3FfpIIEAxhY,5982
+cardiac_geometries/gui.py,sha256=9WYR850wLrqsUrVUC37E2SaO0OWA_oagSe-YNrsxz3k,8376
+cardiac_geometries/mesh.py,sha256=Ejciny48mnKKN20RrY9DwLY7_Lh1jb6Kldj4CW1wr1o,26909
+cardiac_geometries/utils.py,sha256=8QKkdK3JFZMH3qF4PzvEVfk7vMB5Ciui-KFIct2Kd2g,20560
+cardiac_geometries/fibers/__init__.py,sha256=WpRrn9Iakl-3m8IGtFkqP0LXGjw5EZHZ8Eg9JCnCdrg,137
+cardiac_geometries/fibers/lv_ellipsoid.py,sha256=nJYkwvacH1xMhuWAV06NRR4fFzyprowfWv4UIQkCPQM,5830
+cardiac_geometries/fibers/slab.py,sha256=TYQhckJ8mwXz_08Cx3QsPQMtemkaxZ955SnSMrDfBPE,3898
+cardiac_geometries/fibers/utils.py,sha256=rOGWyJTRQ7M1W5_JBOIuVPw5LGBVB0u_LGxBicfc--w,3190
+cardiac_geometriesx-0.4.1.dist-info/LICENSE,sha256=lo5K2rJPZOSv6luutGHbzzi3IpXNaB9E2UWq60qvNx0,1111
+cardiac_geometriesx-0.4.1.dist-info/METADATA,sha256=zbG7thVfZ1t_0dusLr0y8-YhOfo4pUNBD9POw9Ge2Q0,4185
+cardiac_geometriesx-0.4.1.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
+cardiac_geometriesx-0.4.1.dist-info/entry_points.txt,sha256=xOBnlc6W-H9oCDYLNz3kpki26OmpfYSoFSrmi_4V-Ec,52
+cardiac_geometriesx-0.4.1.dist-info/top_level.txt,sha256=J0gQxkWR2my5Vf7Qt8buDY8ZOjYdVfIweVunCGXWKNE,19
+cardiac_geometriesx-0.4.1.dist-info/RECORD,,

cardiac_geometriesx-0.4.0.dist-info/RECORD

@@ -1,16 +0,0 @@
-cardiac_geometries/__init__.py,sha256=2W_ywAeLjyRk5MqSPAodHa4UN2lOnW1h8tmGLQ3gaJ0,150
-cardiac_geometries/cli.py,sha256=GKcsMNhVFoxWDr-o3jiDCXmTvPgCSEB9Kws8AvYIK4Q,19678
-cardiac_geometries/geometry.py,sha256=s-1BIDKvP9M3uu3Sl8JpGRnTnXZAa9Aq3FfpIIEAxhY,5982
-cardiac_geometries/gui.py,sha256=9WYR850wLrqsUrVUC37E2SaO0OWA_oagSe-YNrsxz3k,8376
-cardiac_geometries/mesh.py,sha256=Ejciny48mnKKN20RrY9DwLY7_Lh1jb6Kldj4CW1wr1o,26909
-cardiac_geometries/utils.py,sha256=fMHlVzwxnk1lJd8XQPy8dgFB9C9ecSnJB2NzMXJGAAQ,20348
-cardiac_geometries/fibers/__init__.py,sha256=WpRrn9Iakl-3m8IGtFkqP0LXGjw5EZHZ8Eg9JCnCdrg,137
-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=x6MNtW6xN5NBGBD0Ubm4eqTDde0j_Vd-nh8agFT_AiU,3161
-cardiac_geometriesx-0.4.0.dist-info/LICENSE,sha256=lo5K2rJPZOSv6luutGHbzzi3IpXNaB9E2UWq60qvNx0,1111
-cardiac_geometriesx-0.4.0.dist-info/METADATA,sha256=rPU1WjGfdSGrlkgnkhIubCY3WzJ7nlMGsLfcuNdU2ME,4163
-cardiac_geometriesx-0.4.0.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
-cardiac_geometriesx-0.4.0.dist-info/entry_points.txt,sha256=xOBnlc6W-H9oCDYLNz3kpki26OmpfYSoFSrmi_4V-Ec,52
-cardiac_geometriesx-0.4.0.dist-info/top_level.txt,sha256=J0gQxkWR2my5Vf7Qt8buDY8ZOjYdVfIweVunCGXWKNE,19
-cardiac_geometriesx-0.4.0.dist-info/RECORD,,