cardiac-geometriesx 0.6.0__py3-none-any.whl → 0.6.2__py3-none-any.whl

cardiac_geometries/fibers/slab.py

@@ -48,6 +48,13 @@ def compute_system(
                 np.sin(alpha(t)),
             ],
         )
+        n0 = np.array(
+            [
+                np.zeros_like(t),
+                np.ones_like(t),
+                np.zeros_like(t),
+            ],
+        )
     elif endo_epi_axis == "z":
         f0 = np.array(
             [
@@ -56,6 +63,13 @@ def compute_system(
                 np.zeros_like(t),
             ],
         )
+        n0 = np.array(
+            [
+                np.zeros_like(t),
+                np.zeros_like(t),
+                np.ones_like(t),
+            ],
+        )
     elif endo_epi_axis == "x":
         f0 = np.array(
             [
@@ -64,19 +78,18 @@ def compute_system(
                 np.sin(alpha(t)),
             ],
         )
+        n0 = np.array(
+            [
+                np.ones_like(t),
+                np.zeros_like(t),
+                np.zeros_like(t),
+            ],
+        )
     else:
         raise ValueError(f"Unknown endo_epi_axis: {endo_epi_axis}")
 
-    s0 = np.array(
-        [
-            np.zeros_like(t),
-            np.ones_like(t),
-            np.zeros_like(t),
-        ],
-    )
-
-    n0 = np.cross(f0, s0, axis=0)
-    n0 = utils.normalize(n0)
+    s0 = np.cross(f0, n0, axis=0)
+    s0 = utils.normalize(s0)
 
     Vv = space_from_string(
         space_string=f"{element.family_name}_{element.degree}",

cardiac_geometries/utils.py

@@ -14,6 +14,11 @@ from dolfinx.graph import adjacencylist
 from packaging.version import Version
 from structlog import get_logger
 
+try:
+    import dolfinx.io.gmsh as gmshio
+except ImportError:
+    import dolfinx.io.gmshio as gmshio  # type: ignore[import]
+
 logger = get_logger()
 
 quads = ("Quadrature", "Q", "Quad", "quadrature", "q", "quad")
@@ -90,8 +95,8 @@ def model_to_mesh(
     if comm.rank == rank:
         assert model is not None, "Gmsh model is None on rank responsible for mesh creation."
         # Get mesh geometry and mesh topology for each element
-        x = dolfinx.io.gmshio.extract_geometry(model)
-        topologies = dolfinx.io.gmshio.extract_topology_and_markers(model)
+        x = gmshio.extract_geometry(model)
+        topologies = gmshio.extract_topology_and_markers(model)
 
         # Extract Gmsh cell id, dimension of cell and number of nodes to
         # cell for each
@@ -170,8 +175,8 @@ def model_to_mesh(
             vertex_values = np.empty((0,), dtype=np.int32)
 
     # Create distributed mesh
-    ufl_domain = dolfinx.io.gmshio.ufl_mesh(cell_id, gdim, dtype=dtype)
-    gmsh_cell_perm = dolfinx.io.gmshio.cell_perm_array(
+    ufl_domain = gmshio.ufl_mesh(cell_id, gdim, dtype=dtype)
+    gmsh_cell_perm = gmshio.cell_perm_array(
         dolfinx.cpp.mesh.to_type(str(ufl_domain.ufl_cell())), num_nodes
     )
     cells = cells[:, gmsh_cell_perm].copy()
@@ -207,7 +212,7 @@ def model_to_mesh(
         facet_type = dolfinx.cpp.mesh.cell_entity_type(
             dolfinx.cpp.mesh.to_type(str(ufl_domain.ufl_cell())), tdim - 1, 0
         )
-        gmsh_facet_perm = dolfinx.io.gmshio.cell_perm_array(facet_type, num_facet_nodes)
+        gmsh_facet_perm = gmshio.cell_perm_array(facet_type, num_facet_nodes)
         marked_facets = marked_facets[:, gmsh_facet_perm]
 
         local_entities, local_values = distribute_entity_data(
@@ -217,7 +222,7 @@ def model_to_mesh(
         mesh.topology.create_connectivity(topology.dim - 1, tdim)
         adj = adjacencylist(local_entities)
 
-        ft = dolfinx.io.gmshio.meshtags_from_entities(
+        ft = gmshio.meshtags_from_entities(
             mesh, tdim - 1, adj, local_values.astype(np.int32, copy=False)
         )
         ft.name = "Facet tags"
@@ -231,7 +236,7 @@ def model_to_mesh(
         edge_type = dolfinx.cpp.mesh.cell_entity_type(
             dolfinx.cpp.mesh.to_type(str(ufl_domain.ufl_cell())), tdim - 2, 0
         )
-        gmsh_edge_perm = dolfinx.io.gmshio.cell_perm_array(edge_type, num_edge_nodes)
+        gmsh_edge_perm = gmshio.cell_perm_array(edge_type, num_edge_nodes)
         marked_edges = marked_edges[:, gmsh_edge_perm]
 
         local_entities, local_values = distribute_entity_data(
@@ -239,7 +244,7 @@ def model_to_mesh(
         )
         mesh.topology.create_connectivity(topology.dim - 2, tdim)
         adj = adjacencylist(local_entities)
-        et = dolfinx.io.gmshio.meshtags_from_entities(
+        et = gmshio.meshtags_from_entities(
             mesh, tdim - 2, adj, local_values.astype(np.int32, copy=False)
         )
         et.name = "Edge tags"
@@ -253,7 +258,7 @@ def model_to_mesh(
         vertex_type = dolfinx.cpp.mesh.cell_entity_type(
             dolfinx.cpp.mesh.to_type(str(ufl_domain.ufl_cell())), tdim - 3, 0
         )
-        gmsh_vertex_perm = dolfinx.io.gmshio.cell_perm_array(vertex_type, num_vertex_nodes)
+        gmsh_vertex_perm = gmshio.cell_perm_array(vertex_type, num_vertex_nodes)
         marked_vertices = marked_vertices[:, gmsh_vertex_perm]
 
         local_entities, local_values = distribute_entity_data(
@@ -261,7 +266,7 @@ def model_to_mesh(
         )
         mesh.topology.create_connectivity(topology.dim - 3, tdim)
         adj = adjacencylist(local_entities)
-        vt = dolfinx.io.gmshio.meshtags_from_entities(
+        vt = gmshio.meshtags_from_entities(
             mesh, tdim - 3, adj, local_values.astype(np.int32, copy=False)
         )
         vt.name = "Vertex tags"
@@ -425,7 +430,7 @@ def gmsh2dolfin(comm: MPI.Intracomm, msh_file, rank: int = 0) -> GMshGeometry:
     outdir.mkdir(parents=True, exist_ok=True)
 
     if Version(dolfinx.__version__) >= Version("0.10.0"):
-        mesh_data = dolfinx.io.gmshio.read_from_msh(comm=comm, filename=msh_file)
+        mesh_data = gmshio.read_from_msh(comm=comm, filename=msh_file)
         mesh = mesh_data.mesh
         markers_ = mesh_data.physical_groups
         ct = mesh_data.cell_tags

{cardiac_geometriesx-0.6.0.dist-info → cardiac_geometriesx-0.6.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cardiac-geometriesx
-Version: 0.6.0
+Version: 0.6.2
 Summary: A python library for cardiac geometries
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License: MIT

{cardiac_geometriesx-0.6.0.dist-info → cardiac_geometriesx-0.6.2.dist-info}/RECORD

@@ -3,16 +3,16 @@ cardiac_geometries/cli.py,sha256=a4LTlphEl_ODGFRhHjhg-RHqWNTQYgbA_apora0NuY4,293
 cardiac_geometries/geometry.py,sha256=b-JbxV1wTgrjgQaNNG4NiGmXLs3nqRabsUUtYDnyKKA,13616
 cardiac_geometries/gui.py,sha256=9WYR850wLrqsUrVUC37E2SaO0OWA_oagSe-YNrsxz3k,8376
 cardiac_geometries/mesh.py,sha256=4aqzrPMgpV1gapRAFPHIYuroSZvcEFxtMefOpgIdhfc,48224
-cardiac_geometries/utils.py,sha256=6H0tZif7GPINdrxfPm3HQH1T4_DfDvWMejjpXPb8mLY,22206
+cardiac_geometries/utils.py,sha256=y-uQVSUDnlsAr8W60ranpQi6-B7ysUybyBIouDqVwTY,22211
 cardiac_geometries/fibers/__init__.py,sha256=iggELqJBQySc6ihph1-yaweOfxNvvTE2670RnUnOgDw,2229
 cardiac_geometries/fibers/cylinder.py,sha256=Q1GIuVvntPQ7pW6Z4UYSC8-8WfkClbakiW81Fl9dvk0,3345
 cardiac_geometries/fibers/cylinder_flat.py,sha256=h8ZeyQdZJAOTU456TIumh3eWkZkhzf7R7CpKki5HNrk,5304
 cardiac_geometries/fibers/lv_ellipsoid.py,sha256=KMVOHg2VPg1tF2R9TKIX-vQr6dDM4HThh12WW_diNfU,6024
-cardiac_geometries/fibers/slab.py,sha256=FVcfQ4AxaOFppc9YOlkQ1BUZvlLEUp3x810ma4YmfYQ,4452
+cardiac_geometries/fibers/slab.py,sha256=vQ9nYoAnoeBevEYkY3Hsy7o4tZ_gfBWaZI_p5UH_PgM,4805
 cardiac_geometries/fibers/utils.py,sha256=Uy0xWpQXNpOLqCYaSFmJ2rKcCeP3lXCLlQnZR1S2KKQ,3852
-cardiac_geometriesx-0.6.0.dist-info/licenses/LICENSE,sha256=lo5K2rJPZOSv6luutGHbzzi3IpXNaB9E2UWq60qvNx0,1111
-cardiac_geometriesx-0.6.0.dist-info/METADATA,sha256=ZWIUMPP6Cl8K8nazTGC-6EIBVDChwadVezhsbnuTuhY,4390
-cardiac_geometriesx-0.6.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-cardiac_geometriesx-0.6.0.dist-info/entry_points.txt,sha256=xOBnlc6W-H9oCDYLNz3kpki26OmpfYSoFSrmi_4V-Ec,52
-cardiac_geometriesx-0.6.0.dist-info/top_level.txt,sha256=J0gQxkWR2my5Vf7Qt8buDY8ZOjYdVfIweVunCGXWKNE,19
-cardiac_geometriesx-0.6.0.dist-info/RECORD,,
+cardiac_geometriesx-0.6.2.dist-info/licenses/LICENSE,sha256=lo5K2rJPZOSv6luutGHbzzi3IpXNaB9E2UWq60qvNx0,1111
+cardiac_geometriesx-0.6.2.dist-info/METADATA,sha256=Dq6kbzra8mbFrVtypK5rDWhzDyf3vjsHjqgOI9mHamI,4390
+cardiac_geometriesx-0.6.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+cardiac_geometriesx-0.6.2.dist-info/entry_points.txt,sha256=xOBnlc6W-H9oCDYLNz3kpki26OmpfYSoFSrmi_4V-Ec,52
+cardiac_geometriesx-0.6.2.dist-info/top_level.txt,sha256=J0gQxkWR2my5Vf7Qt8buDY8ZOjYdVfIweVunCGXWKNE,19
+cardiac_geometriesx-0.6.2.dist-info/RECORD,,