cardiac-geometriesx 0.0.1__tar.gz → 0.0.3__tar.gz

{cardiac_geometriesx-0.0.1 → cardiac_geometriesx-0.0.3}/PKG-INFO

@@ -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 → cardiac_geometriesx-0.0.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cardiac-geometriesx"
-version = "0.0.1"
+version = "0.0.3"
 description = "A python library for cardiac geometries"
 authors = [{name = "Henrik Finsberg", email = "henriknf@simula.no"}]
 license = {text = "MIT"}
@@ -18,8 +18,6 @@ urls = {Homepage = "https://github.com/finsberg/cardiac-geometriesx" }
 requires-python = ">=3.8"
 dependencies = [
     "fenics-dolfinx>=0.8.0",
-    "meshio",
-    "h5py",
     "structlog",
     "cardiac-geometries-core",
     "rich-click",
@@ -136,7 +134,7 @@ tag = true
 sign_tags = false
 tag_name = "v{new_version}"
 tag_message = "Bump version: {current_version} → {new_version}"
-current_version = "0.0.1"
+current_version = "0.0.3"
 
 
 [[tool.bumpversion.files]]

{cardiac_geometriesx-0.0.1 → cardiac_geometriesx-0.0.3}/src/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_geometriesx-0.0.3/src/cardiac_geometries/utils.py

@@ -0,0 +1,123 @@
+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
+
+
+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 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="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="Mesh")
+        cfun = xdmf.read_meshtags(mesh, name="Cell tags")
+    return mesh, cfun
+
+
+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
+
+    # 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 = 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:
+        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 → cardiac_geometriesx-0.0.3}/src/cardiac_geometriesx.egg-info/PKG-INFO

@@ -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 → cardiac_geometriesx-0.0.3}/src/cardiac_geometriesx.egg-info/requires.txt

@@ -1,6 +1,4 @@
 fenics-dolfinx>=0.8.0
-meshio
-h5py
 structlog
 cardiac-geometries-core
 rich-click

cardiac_geometriesx-0.0.1/src/cardiac_geometries/utils.py

@@ -1,173 +0,0 @@
-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)