cardiac-geometriesx 0.0.1__py3-none-any.whl

cardiac_geometries/utils.py

@@ -0,0 +1,173 @@
+from pathlib import Path
+import tempfile
+from typing import NamedTuple, Iterable
+from enum import Enum
+
+import numpy as np
+from mpi4py import MPI
+from structlog import get_logger
+import basix
+import dolfinx
+import meshio
+
+
+logger = get_logger()
+
+
+def element2array(el: basix.finite_element.FiniteElement) -> np.ndarray:
+    return np.array(
+        [int(el.family), int(el.cell_type), int(el.degree), int(el.discontinuous)],
+        dtype=np.uint8,
+    )
+
+
+def number2Enum(num: int, enum: Iterable) -> Enum:
+    for e in enum:
+        if int(e) == num:
+            return e
+    raise ValueError(f"Invalid value {num} for enum {enum}")
+
+
+def array2element(arr: np.ndarray) -> basix.finite_element.FiniteElement:
+    family = number2Enum(arr[0], basix.ElementFamily)
+    cell_type = number2Enum(arr[1], basix.CellType)
+    degree = int(arr[2])
+    discontinuous = bool(arr[3])
+    # TODO: Shape is hardcoded to (3,) for now, but this should also be stored
+    return basix.ufl.element(
+        family=family,
+        cell=cell_type,
+        degree=degree,
+        discontinuous=discontinuous,
+        shape=(3,),
+    )
+
+
+def handle_mesh_name(mesh_name: str = "") -> Path:
+    if mesh_name == "":
+        fd, mesh_name = tempfile.mkstemp(suffix=".msh")
+    return Path(mesh_name).with_suffix(".msh")
+
+
+def json_serial(obj):
+    if isinstance(obj, (np.ndarray)):
+        return obj.tolist()
+    else:
+        try:
+            return str(obj)
+        except Exception:
+            raise TypeError("Type %s not serializable" % type(obj))
+
+
+class GMshGeometry(NamedTuple):
+    mesh: dolfinx.mesh.Mesh
+    cfun: dolfinx.mesh.MeshTags | None
+    ffun: dolfinx.mesh.MeshTags | None
+    efun: dolfinx.mesh.MeshTags | None
+    vfun: dolfinx.mesh.MeshTags | None
+    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"
+    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")
+    return mesh, cfun
+
+
+def gmsh2dolfin(comm: MPI.Intracomm, msh_file, unlink: bool = False) -> 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
+
+    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
+
+    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")
+    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)

cardiac_geometriesx-0.0.1.dist-info/METADATA

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+Metadata-Version: 2.1
+Name: cardiac-geometriesx
+Version: 0.0.1
+Summary: A python library for cardiac geometries
+Author-email: Henrik Finsberg <henriknf@simula.no>
+License: MIT
+Project-URL: Homepage, https://github.com/finsberg/cardiac-geometriesx
+Keywords: cardiac,geometry
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+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
+Requires-Dist: adios4dolfinx
+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'
+Provides-Extra: docs
+Provides-Extra: test
+Requires-Dist: pre-commit ; extra == 'test'
+Requires-Dist: pytest ; extra == 'test'
+Requires-Dist: pytest-cov ; extra == 'test'
+
+# Cardiac geometries
+
+Cardiac geometries for `dolfinx` (targeting v0.8).
+
+Install
+```
+python3 -m pip install git+https://github.com/ComputationalPhysiology/cardiac-geometriesx
+```
+
+Example usage
+```
+geox lv-ellipsoid --create-fibers lv-mesh
+```
+
+## Authors
+Henrik Finsberg (henriknf@simula.no)
+
+## License
+MIT

cardiac_geometriesx-0.0.1.dist-info/RECORD

@@ -0,0 +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/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-0.0.1.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: bdist_wheel (0.43.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

cardiac_geometriesx-0.0.1.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+geox = cardiac_geometries.cli:app

cardiac_geometriesx-0.0.1.dist-info/top_level.txt

@@ -0,0 +1 @@
+cardiac_geometries