cardiac-geometriesx 0.4.3__py3-none-any.whl → 0.4.5__py3-none-any.whl

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
@@ -27,9 +30,11 @@ def save_microstructure(
     # Save for paraview visualization
 
     if functions[0].function_space.ufl_element().family_name == "quadrature":
-        from scifem.xdmf import create_pointcloud
+        from scifem.xdmf import XDMFFile
+
+        with XDMFFile(Path(outdir) / "microstructure-viz.xdmf", functions) as xdmf:
+            xdmf.write(0.0)
 
-        create_pointcloud(functions=functions, filename=Path(outdir) / "microstructure-viz.xdmf")
     else:
         try:
             with dolfinx.io.VTXWriter(
@@ -99,7 +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_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-0.4.3.dist-info → cardiac_geometriesx-0.4.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cardiac-geometriesx
-Version: 0.4.3
+Version: 0.4.5
 Summary: A python library for cardiac geometries
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License: MIT
@@ -12,38 +12,39 @@ Classifier: Programming Language :: Python :: 3 :: Only
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: fenics-dolfinx >=0.8.0
+Requires-Dist: fenics-dolfinx>=0.8.0
 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'
-Requires-Dist: pdbpp ; extra == 'dev'
-Requires-Dist: pre-commit ; extra == 'dev'
-Requires-Dist: twine ; extra == 'dev'
-Requires-Dist: wheel ; extra == 'dev'
+Requires-Dist: bump-my-version; extra == "dev"
+Requires-Dist: ipython; extra == "dev"
+Requires-Dist: pdbpp; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Requires-Dist: wheel; extra == "dev"
 Provides-Extra: docs
-Requires-Dist: jupyter-book ; extra == 'docs'
-Requires-Dist: jupytext ; extra == 'docs'
-Requires-Dist: jupyter ; extra == 'docs'
-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'
-Provides-Extra: gui
-Requires-Dist: streamlit ; extra == 'gui'
-Requires-Dist: stpyvista ; extra == 'gui'
-Requires-Dist: pyvista[all] >=0.43.0 ; extra == 'gui'
-Requires-Dist: trame-vuetify ; extra == 'gui'
-Requires-Dist: ipywidgets ; extra == 'gui'
-Requires-Dist: fenicsx-ldrb ; extra == 'gui'
+Requires-Dist: jupyter-book; extra == "docs"
+Requires-Dist: jupytext; extra == "docs"
+Requires-Dist: jupyter; extra == "docs"
+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'
-Requires-Dist: pytest-cov ; extra == 'test'
+Requires-Dist: pre-commit; extra == "test"
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Provides-Extra: gui
+Requires-Dist: streamlit; extra == "gui"
+Requires-Dist: stpyvista; extra == "gui"
+Requires-Dist: pyvista[all]>=0.43.0; extra == "gui"
+Requires-Dist: trame-vuetify; extra == "gui"
+Requires-Dist: ipywidgets; extra == "gui"
+Requires-Dist: fenicsx-ldrb; extra == "gui"
 
 ![_](docs/_static/logo.png)
 

{cardiac_geometriesx-0.4.3.dist-info → cardiac_geometriesx-0.4.5.dist-info}/RECORD

@@ -3,14 +3,14 @@ cardiac_geometries/cli.py,sha256=GKcsMNhVFoxWDr-o3jiDCXmTvPgCSEB9Kws8AvYIK4Q,196
 cardiac_geometries/geometry.py,sha256=JSsLKfXej4DSgzRbivC-_jvyjiY6zkXcRCRL93IIys8,6504
 cardiac_geometries/gui.py,sha256=9WYR850wLrqsUrVUC37E2SaO0OWA_oagSe-YNrsxz3k,8376
 cardiac_geometries/mesh.py,sha256=_vNNMpQWyLEZ3TmsHAUh0l3Z2TYuQBy6Os-6nB9_Z9A,26908
-cardiac_geometries/utils.py,sha256=hR-uV9lzmfM_kQkqHY9MmJ_b3-Lv5oTsNOKCb-0nn_U,20616
+cardiac_geometries/utils.py,sha256=tMn_XQRYbP1__c0QPHZeiCRJun3TZiH80OwJDESTPzY,21817
 cardiac_geometries/fibers/__init__.py,sha256=WpRrn9Iakl-3m8IGtFkqP0LXGjw5EZHZ8Eg9JCnCdrg,137
 cardiac_geometries/fibers/lv_ellipsoid.py,sha256=LZNhxzTsn-h88xXGP5bNfnWKhdvBROUjWjt8yrQFW48,6010
 cardiac_geometries/fibers/slab.py,sha256=TYQhckJ8mwXz_08Cx3QsPQMtemkaxZ955SnSMrDfBPE,3898
-cardiac_geometries/fibers/utils.py,sha256=bEz2MMSRhzYhiRSFahdqQRsOWzCCauERKU2V6tdgSkQ,3239
-cardiac_geometriesx-0.4.3.dist-info/LICENSE,sha256=lo5K2rJPZOSv6luutGHbzzi3IpXNaB9E2UWq60qvNx0,1111
-cardiac_geometriesx-0.4.3.dist-info/METADATA,sha256=mpSvjuPehah4Z-XxkLrZkcq7U-HUxg66uPFpAFD2BTM,4185
-cardiac_geometriesx-0.4.3.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
-cardiac_geometriesx-0.4.3.dist-info/entry_points.txt,sha256=xOBnlc6W-H9oCDYLNz3kpki26OmpfYSoFSrmi_4V-Ec,52
-cardiac_geometriesx-0.4.3.dist-info/top_level.txt,sha256=J0gQxkWR2my5Vf7Qt8buDY8ZOjYdVfIweVunCGXWKNE,19
-cardiac_geometriesx-0.4.3.dist-info/RECORD,,
+cardiac_geometries/fibers/utils.py,sha256=pCoXkaUbidLGPY0Ty8uWCU1siDkHcv2qP8rZtdxMf0k,3475
+cardiac_geometriesx-0.4.5.dist-info/LICENSE,sha256=lo5K2rJPZOSv6luutGHbzzi3IpXNaB9E2UWq60qvNx0,1111
+cardiac_geometriesx-0.4.5.dist-info/METADATA,sha256=VcogZHS3ECHMoAQ-ei54PSdGCOi6-bviY8KjEYbPgaw,4202
+cardiac_geometriesx-0.4.5.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+cardiac_geometriesx-0.4.5.dist-info/entry_points.txt,sha256=xOBnlc6W-H9oCDYLNz3kpki26OmpfYSoFSrmi_4V-Ec,52
+cardiac_geometriesx-0.4.5.dist-info/top_level.txt,sha256=J0gQxkWR2my5Vf7Qt8buDY8ZOjYdVfIweVunCGXWKNE,19
+cardiac_geometriesx-0.4.5.dist-info/RECORD,,

{cardiac_geometriesx-0.4.3.dist-info → cardiac_geometriesx-0.4.5.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.3.0)
+Generator: setuptools (75.6.0)
 Root-Is-Purelib: true
 Tag: py3-none-any