cardiac-geometriesx 0.0.1__py3-none-any.whl → 0.0.3__py3-none-any.whl

cardiac_geometries/mesh.py

@@ -166,7 +166,7 @@ def biv_ellipsoid(
             c_epi_rv=c_epi_rv,
         )
     comm.barrier()
-    geometry = utils.gmsh2dolfin(comm=comm, msh_file=mesh_name, unlink=False)
+    geometry = utils.gmsh2dolfin(comm=comm, msh_file=mesh_name)
 
     if comm.rank == 0:
         with open(outdir / "markers.json", "w") as f:
@@ -367,7 +367,7 @@ def biv_ellipsoid_torso(
         )
     comm.barrier()
 
-    geometry = utils.gmsh2dolfin(comm=comm, msh_file=mesh_name, unlink=False)
+    geometry = utils.gmsh2dolfin(comm=comm, msh_file=mesh_name)
 
     if comm.rank == 0:
         with open(outdir / "markers.json", "w") as f:
@@ -500,7 +500,7 @@ def lv_ellipsoid(
         )
     comm.barrier()
 
-    geometry = utils.gmsh2dolfin(comm=comm, msh_file=mesh_name, unlink=False)
+    geometry = utils.gmsh2dolfin(comm=comm, msh_file=mesh_name)
 
     # if aha:
     #     from .aha import lv_aha
@@ -618,7 +618,7 @@ def slab(
         cgc.slab(mesh_name=mesh_name.as_posix(), lx=lx, ly=ly, lz=lz, dx=dx)
     comm.barrier()
 
-    geometry = utils.gmsh2dolfin(comm=comm, msh_file=mesh_name, unlink=False)
+    geometry = utils.gmsh2dolfin(comm=comm, msh_file=mesh_name)
 
     if comm.rank == 0:
         with open(outdir / "markers.json", "w") as f:
@@ -716,7 +716,7 @@ def slab_in_bath(
             dx=dx,
         )
 
-    geometry = utils.gmsh2dolfin(comm=comm, msh_file=mesh_name, unlink=False)
+    geometry = utils.gmsh2dolfin(comm=comm, msh_file=mesh_name)
 
     if comm.rank == 0:
         with open(outdir / "markers.json", "w") as f:

cardiac_geometries/utils.py

@@ -8,7 +8,6 @@ from mpi4py import MPI
 from structlog import get_logger
 import basix
 import dolfinx
-import meshio
 
 
 logger = get_logger()
@@ -68,106 +67,57 @@ class GMshGeometry(NamedTuple):
     markers: dict[str, tuple[int, int]]
 
 
-def create_mesh(mesh, cell_type):
-    # From http://jsdokken.com/converted_files/tutorial_pygmsh.html
-    cells = mesh.get_cells_type(cell_type)
-    if cells.size == 0:
-        return None
-
-    cells = mesh.get_cells_type(cell_type)
-    cell_data = mesh.get_cell_data("gmsh:physical", cell_type)
-    out_mesh = meshio.Mesh(
-        points=mesh.points,
-        cells={cell_type: cells},
-        cell_data={"name_to_read": [cell_data]},
-    )
-    return out_mesh
-
-
 def read_ffun(mesh, filename: str | Path) -> dolfinx.mesh.MeshTags | None:
     mesh.topology.create_connectivity(mesh.topology.dim - 1, mesh.topology.dim)
     with dolfinx.io.XDMFFile(mesh.comm, filename, "r") as xdmf:
-        ffun = xdmf.read_meshtags(mesh, name="Grid")
-    ffun.name = "Facet tags"
+        ffun = xdmf.read_meshtags(mesh, name="Facet tags")
+
     return ffun
 
 
 def read_mesh(comm, filename: str | Path) -> tuple[dolfinx.mesh.Mesh, dolfinx.mesh.MeshTags | None]:
     with dolfinx.io.XDMFFile(comm, filename, "r") as xdmf:
-        mesh = xdmf.read_mesh(name="Grid")
-        cfun = xdmf.read_meshtags(mesh, name="Grid")
+        mesh = xdmf.read_mesh(name="Mesh")
+        cfun = xdmf.read_meshtags(mesh, name="Cell tags")
     return mesh, cfun
 
 
-def gmsh2dolfin(comm: MPI.Intracomm, msh_file, unlink: bool = False) -> GMshGeometry:
+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
 
-    vertex_mesh_name = outdir / "vertex_mesh.xdmf"
-    line_mesh_name = outdir / "line_mesh.xdmf"
-    triangle_mesh_name = outdir / "triangle_mesh.xdmf"
-    tetra_mesh_name = outdir / "mesh.xdmf"
-
-    if comm.rank == 0:
-        msh = meshio.gmsh.read(msh_file)
-        vertex_mesh = create_mesh(msh, "vertex")
-        line_mesh = create_mesh(msh, "line")
-        triangle_mesh = create_mesh(msh, "triangle")
-        tetra_mesh = create_mesh(msh, "tetra")
-
-        if vertex_mesh is not None:
-            meshio.write(vertex_mesh_name, vertex_mesh)
-
-        if line_mesh is not None:
-            meshio.write(line_mesh_name, line_mesh)
-
-        if triangle_mesh is not None:
-            meshio.write(triangle_mesh_name, triangle_mesh)
-
-        if tetra_mesh is not None:
-            meshio.write(
-                tetra_mesh_name,
-                tetra_mesh,
-            )
-        markers = msh.field_data
-    else:
-        markers = {}
-    # Broadcast markers
-    markers = comm.bcast(markers, root=0)
-    comm.barrier()
-
-    mesh, cfun = read_mesh(comm, tetra_mesh_name)
-
-    if triangle_mesh_name.is_file():
-        ffun = read_ffun(mesh, triangle_mesh_name)
-    else:
-        ffun = None
+    import gmsh
 
-    if line_mesh_name.is_file():
-        mesh.topology.create_connectivity(mesh.topology.dim - 2, mesh.topology.dim)
-        with dolfinx.io.XDMFFile(comm, line_mesh_name, "r") as xdmf:
-            efun = xdmf.read_meshtags(mesh, name="Grid")
-    else:
-        efun = None
+    # We could make this work in parallel in the future
 
-    if vertex_mesh_name.is_file():
-        mesh.topology.create_connectivity(mesh.topology.dim - 3, mesh.topology.dim)
-        with dolfinx.io.XDMFFile(comm, vertex_mesh_name, "r") as xdmf:
-            vfun = xdmf.read_meshtags(mesh, name="Grid")
+    if comm.rank == rank:
+        gmsh.initialize()
+        gmsh.model.add("Mesh from file")
+        gmsh.merge(str(msh_file))
+        mesh, ct, ft = dolfinx.io.gmshio.model_to_mesh(gmsh.model, comm, 0)
+        markers = {gmsh.model.getPhysicalName(*v): v for v in gmsh.model.getPhysicalGroups()}
+        gmsh.finalize()
     else:
-        vfun = None
-
-    if unlink:
-        # Wait for all processes to finish reading
-        comm.barrier()
-        if comm.rank == 0:
-            vertex_mesh_name.unlink(missing_ok=True)
-            line_mesh_name.unlink(missing_ok=True)
-            triangle_mesh_name.unlink(missing_ok=True)
-            tetra_mesh_name.unlink(missing_ok=True)
-            vertex_mesh_name.with_suffix(".h5").unlink(missing_ok=True)
-            line_mesh_name.with_suffix(".h5").unlink(missing_ok=True)
-            triangle_mesh_name.with_suffix(".h5").unlink(missing_ok=True)
-            tetra_mesh_name.with_suffix(".h5").unlink(missing_ok=True)
-
-    return GMshGeometry(mesh, cfun, ffun, efun, vfun, markers)
+        mesh, ct, ft = dolfinx.io.gmshio.model_to_mesh(gmsh.model, comm, 0)
+        markers = {}
+    mesh.name = "Mesh"
+    ct.name = "Cell tags"
+    ft.name = "Facet 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)
+        mesh.topology.create_connectivity(2, 3)
+        xdmf.write_meshtags(
+            ct, mesh.geometry, geometry_xpath=f"/Xdmf/Domain/Grid[@Name='{mesh.name}']/Geometry"
+        )
+        xdmf.write_meshtags(
+            ft, mesh.geometry, geometry_xpath=f"/Xdmf/Domain/Grid[@Name='{mesh.name}']/Geometry"
+        )
+
+    vfun = None
+    efun = None
+
+    return GMshGeometry(mesh, ct, ft, efun, vfun, markers)

{cardiac_geometriesx-0.0.1.dist-info → cardiac_geometriesx-0.0.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cardiac-geometriesx
-Version: 0.0.1
+Version: 0.0.3
 Summary: A python library for cardiac geometries
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License: MIT
@@ -12,8 +12,6 @@ Classifier: Programming Language :: Python :: 3 :: Only
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 Requires-Dist: fenics-dolfinx >=0.8.0
-Requires-Dist: meshio
-Requires-Dist: h5py
 Requires-Dist: structlog
 Requires-Dist: cardiac-geometries-core
 Requires-Dist: rich-click

{cardiac_geometriesx-0.0.1.dist-info → cardiac_geometriesx-0.0.3.dist-info}/RECORD

@@ -1,14 +1,14 @@
 cardiac_geometries/__init__.py,sha256=-I-0nXbVFRgfZ-mbXeC-OMg2jh7WnTch6_DkBbAGnGg,202
 cardiac_geometries/cli.py,sha256=nOI56WV1fXstL3vxhux90qPnmZ69y1r-PGDYgFMgNeA,19324
 cardiac_geometries/geometry.py,sha256=MYF9diZl9igayAuptSyOsHf7-3zJHFd8UgfWtXJgrHk,4849
-cardiac_geometries/mesh.py,sha256=K-EEJcJNgxubnLnMkPrysnKfNe7HCfLf26lxI1lCosA,25250
-cardiac_geometries/utils.py,sha256=cg42PP56UIVoDyur0lp6nJ3dAuZiHQB9kvYShKti1Bk,5452
+cardiac_geometries/mesh.py,sha256=tAB9A6J-C4do-pvwShr20s8iQzUm4YfYmXqzGRmYW8Q,25180
+cardiac_geometries/utils.py,sha256=BXEpU6qYylE3y7rabBvTXGhNZYbiT177UjJ8assiuXE,3693
 cardiac_geometries/fibers/__init__.py,sha256=p6d-3uql8pFailBcLPPGLfRDQs38wefnarS3aSQV0FE,151
 cardiac_geometries/fibers/lv_ellipsoid.py,sha256=DWDUV0sGrsZH9O-EtN3veSkE96U6XuHko3WUW9Ce_uc,3695
 cardiac_geometries/fibers/slab.py,sha256=sY9VXv-J1D2wSPTcB_6opRmGMLqUXb5ix7C3gJlSJOU,3867
 cardiac_geometries/fibers/utils.py,sha256=iozqorgu2KcxbzR52b2Not2IyJ-DrPyqn2Ds-QX2QLE,2584
-cardiac_geometriesx-0.0.1.dist-info/METADATA,sha256=MNi78FcH9sKYLiDVgW9J_y-A45MJ-XxMxNKv1iQaHlA,1437
-cardiac_geometriesx-0.0.1.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-cardiac_geometriesx-0.0.1.dist-info/entry_points.txt,sha256=xOBnlc6W-H9oCDYLNz3kpki26OmpfYSoFSrmi_4V-Ec,52
-cardiac_geometriesx-0.0.1.dist-info/top_level.txt,sha256=J0gQxkWR2my5Vf7Qt8buDY8ZOjYdVfIweVunCGXWKNE,19
-cardiac_geometriesx-0.0.1.dist-info/RECORD,,
+cardiac_geometriesx-0.0.3.dist-info/METADATA,sha256=5PZwkcOwkoz-4euqoXoRhUsEcS2UlgIagPk2sJRu8Zw,1395
+cardiac_geometriesx-0.0.3.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+cardiac_geometriesx-0.0.3.dist-info/entry_points.txt,sha256=xOBnlc6W-H9oCDYLNz3kpki26OmpfYSoFSrmi_4V-Ec,52
+cardiac_geometriesx-0.0.3.dist-info/top_level.txt,sha256=J0gQxkWR2my5Vf7Qt8buDY8ZOjYdVfIweVunCGXWKNE,19
+cardiac_geometriesx-0.0.3.dist-info/RECORD,,