cardiac-geometriesx 0.4.4__tar.gz → 0.4.5__tar.gz

{cardiac_geometriesx-0.4.4/src/cardiac_geometriesx.egg-info → cardiac_geometriesx-0.4.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cardiac-geometriesx
-Version: 0.4.4
+Version: 0.4.5
 Summary: A python library for cardiac geometries
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License: MIT
@@ -33,6 +33,7 @@ Requires-Dist: pyvista[all]>=0.43.0; extra == "docs"
 Requires-Dist: trame-vuetify; extra == "docs"
 Requires-Dist: ipywidgets; extra == "docs"
 Requires-Dist: fenicsx-ldrb; extra == "docs"
+Requires-Dist: ukb-atlas; extra == "docs"
 Provides-Extra: test
 Requires-Dist: pre-commit; extra == "test"
 Requires-Dist: pytest; extra == "test"

{cardiac_geometriesx-0.4.4 → cardiac_geometriesx-0.4.5}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cardiac-geometriesx"
-version = "0.4.4"
+version = "0.4.5"
 description = "A python library for cardiac geometries"
 authors = [{name = "Henrik Finsberg", email = "henriknf@simula.no"}]
 license = {text = "MIT"}
@@ -46,6 +46,7 @@ docs = [
     "trame-vuetify",
     "ipywidgets",
     "fenicsx-ldrb",
+    "ukb-atlas",
 ]
 test = [
     "pre-commit",
@@ -174,7 +175,7 @@ tag = true
 sign_tags = false
 tag_name = "v{new_version}"
 tag_message = "Bump version: {current_version} → {new_version}"
-current_version = "0.4.4"
+current_version = "0.4.5"
 
 
 [[tool.bumpversion.files]]

{cardiac_geometriesx-0.4.4 → cardiac_geometriesx-0.4.5}/src/cardiac_geometries/fibers/utils.py

@@ -7,9 +7,12 @@ import dolfinx
 import numpy as np
 import ufl
 from dolfinx.fem.petsc import LinearProblem
+from packaging.version import Version
 
 from ..utils import space_from_string
 
+_dolfinx_version = Version(dolfinx.__version__)
+
 
 class Microstructure(NamedTuple):
     f0: dolfinx.fem.Function
@@ -101,7 +104,12 @@ def laplace(
     if function_space != "P_1":
         W = space_from_string(function_space, mesh, dim=1)
         t = dolfinx.fem.Function(W)
-        expr = dolfinx.fem.Expression(uh, W.element.interpolation_points())
+        if _dolfinx_version >= Version("0.10"):
+            points = W.element.interpolation_points
+        else:
+            points = W.element.interpolation_points()
+
+        expr = dolfinx.fem.Expression(uh, points)
         t.interpolate(expr)
     else:
         t = uh

{cardiac_geometriesx-0.4.4 → cardiac_geometriesx-0.4.5}/src/cardiac_geometries/utils.py

@@ -10,6 +10,7 @@ from mpi4py import MPI
 import basix
 import dolfinx
 import numpy as np
+from dolfinx.graph import adjacencylist
 from packaging.version import Version
 from structlog import get_logger
 
@@ -184,7 +185,8 @@ def model_to_mesh(
     )
 
     mesh.topology.create_connectivity(mesh.topology.dim, 0)
-    adj = dolfinx.cpp.graph.AdjacencyList_int32(local_entities)
+    # adj = dolfinx.cpp.graph.AdjacencyList_int32(local_entities)
+    adj = adjacencylist(local_entities)
     ct = dolfinx.mesh.meshtags_from_entities(
         mesh, mesh.topology.dim, adj, local_values.astype(np.int32, copy=False)
     )
@@ -213,7 +215,7 @@ def model_to_mesh(
         )
 
         mesh.topology.create_connectivity(topology.dim - 1, tdim)
-        adj = dolfinx.cpp.graph.AdjacencyList_int32(local_entities)
+        adj = adjacencylist(local_entities)
 
         ft = dolfinx.io.gmshio.meshtags_from_entities(
             mesh, tdim - 1, adj, local_values.astype(np.int32, copy=False)
@@ -236,7 +238,7 @@ def model_to_mesh(
             mesh, tdim - 2, marked_edges, edge_values
         )
         mesh.topology.create_connectivity(topology.dim - 2, tdim)
-        adj = dolfinx.cpp.graph.AdjacencyList_int32(local_entities)
+        adj = adjacencylist(local_entities)
         et = dolfinx.io.gmshio.meshtags_from_entities(
             mesh, tdim - 2, adj, local_values.astype(np.int32, copy=False)
         )
@@ -258,7 +260,7 @@ def model_to_mesh(
             mesh, tdim - 3, marked_vertices, vertex_values
         )
         mesh.topology.create_connectivity(topology.dim - 3, tdim)
-        adj = dolfinx.cpp.graph.AdjacencyList_int32(local_entities)
+        adj = adjacencylist(local_entities)
         vt = dolfinx.io.gmshio.meshtags_from_entities(
             mesh, tdim - 3, adj, local_values.astype(np.int32, copy=False)
         )
@@ -421,31 +423,61 @@ def gmsh2dolfin(comm: MPI.Intracomm, msh_file, rank: int = 0) -> GMshGeometry:
     logger.debug(f"Convert file {msh_file} to dolfin")
     outdir = Path(msh_file).parent
 
-    import gmsh
+    if Version(dolfinx.__version__) >= Version("0.10.0"):
+        mesh_data = dolfinx.io.gmshio.read_from_msh(comm=comm, filename=msh_file)
+        mesh = mesh_data.mesh
+        markers_ = mesh_data.physical_groups
+        ct = mesh_data.cell_tags
+        tdim = mesh.topology.dim
+        if ct is None:
+            ct = dolfinx.mesh.meshtags(
+                mesh, tdim, np.empty(0, dtype=np.int32), np.empty(0, dtype=np.int32)
+            )
+
+        ft = mesh_data.facet_tags
+        if ft is None:
+            ft = dolfinx.mesh.meshtags(
+                mesh, tdim - 1, np.empty(0, dtype=np.int32), np.empty(0, dtype=np.int32)
+            )
+        et = mesh_data.edge_tags
+        if et is None:
+            et = dolfinx.mesh.meshtags(
+                mesh, tdim - 2, np.empty(0, dtype=np.int32), np.empty(0, dtype=np.int32)
+            )
+        vt = mesh_data.vertex_tags
+        if vt is None:
+            vt = dolfinx.mesh.meshtags(
+                mesh, tdim - 3, np.empty(0, dtype=np.int32), np.empty(0, dtype=np.int32)
+            )
+
+        markers = {k: tuple(reversed(v)) for k, v in markers_.items()}
 
-    # We could make this work in parallel in the future
-
-    if comm.rank == rank:
-        gmsh.initialize()
-        gmsh.model.add("Mesh from file")
-        gmsh.merge(str(msh_file))
-        mesh, ct, ft, et, vt = model_to_mesh(gmsh.model, comm, 0)
-        markers = {
-            gmsh.model.getPhysicalName(*v): tuple(reversed(v))
-            for v in gmsh.model.getPhysicalGroups()
-        }
-        gmsh.finalize()
     else:
-        mesh, ct, ft, et, vt = model_to_mesh(gmsh.model, comm, 0)
-        markers = {}
+        import gmsh
+        # We could make this work in parallel in the future
+
+        if comm.rank == rank:
+            gmsh.initialize()
+            gmsh.model.add("Mesh from file")
+            gmsh.merge(str(msh_file))
+            mesh, ct, ft, et, vt = model_to_mesh(gmsh.model, comm, 0)
+            markers = {
+                gmsh.model.getPhysicalName(*v): tuple(reversed(v))
+                for v in gmsh.model.getPhysicalGroups()
+            }
+            gmsh.finalize()
+        else:
+            mesh, ct, ft, et, vt = model_to_mesh(gmsh.model, comm, 0)
+            markers = {}
+
+        markers = comm.bcast(markers, root=rank)
+
     mesh.name = "Mesh"
     ct.name = "Cell tags"
     ft.name = "Facet tags"
     et.name = "Edge tags"
     vt.name = "Vertex tags"
 
-    markers = comm.bcast(markers, root=rank)
-
     # Save tags to xdmf
     with dolfinx.io.XDMFFile(comm, outdir / "mesh.xdmf", "w") as xdmf:
         xdmf.write_mesh(mesh)

{cardiac_geometriesx-0.4.4 → cardiac_geometriesx-0.4.5/src/cardiac_geometriesx.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cardiac-geometriesx
-Version: 0.4.4
+Version: 0.4.5
 Summary: A python library for cardiac geometries
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License: MIT
@@ -33,6 +33,7 @@ Requires-Dist: pyvista[all]>=0.43.0; extra == "docs"
 Requires-Dist: trame-vuetify; extra == "docs"
 Requires-Dist: ipywidgets; extra == "docs"
 Requires-Dist: fenicsx-ldrb; extra == "docs"
+Requires-Dist: ukb-atlas; extra == "docs"
 Provides-Extra: test
 Requires-Dist: pre-commit; extra == "test"
 Requires-Dist: pytest; extra == "test"

{cardiac_geometriesx-0.4.4 → cardiac_geometriesx-0.4.5}/src/cardiac_geometriesx.egg-info/requires.txt

@@ -21,6 +21,7 @@ pyvista[all]>=0.43.0
 trame-vuetify
 ipywidgets
 fenicsx-ldrb
+ukb-atlas
 
 [gui]
 streamlit