cardiac-geometriesx 0.0.1__py3-none-any.whl → 0.0.4__py3-none-any.whl

cardiac_geometries/__init__.py

@@ -1,8 +1,4 @@
-from . import fibers
-from . import geometry
+from . import cli, fibers, geometry, mesh, utils
 from .geometry import Geometry
-from . import mesh
-from . import utils
-from . import cli
 
 __all__ = ["mesh", "fibers", "geometry", "Geometry", "utils", "cli"]

cardiac_geometries/cli.py

@@ -6,7 +6,6 @@ import rich_click as click
 
 from . import mesh
 
-
 meta = metadata("cardiac-geometriesx")
 __version__ = meta["Version"]
 __author__ = meta["Author"]

cardiac_geometries/fibers/__init__.py

@@ -1,6 +1,4 @@
-from . import lv_ellipsoid, slab
-from . import utils
-
+from . import lv_ellipsoid, slab, utils
 from .utils import Microstructure
 
 __all__ = ["lv_ellipsoid", "slab", "utils", "Microstructure"]

cardiac_geometries/fibers/lv_ellipsoid.py

@@ -1,8 +1,8 @@
 from pathlib import Path
+
+import basix
 import dolfinx
 import numpy as np
-import basix
-
 
 from . import utils
 

cardiac_geometries/fibers/slab.py

@@ -1,8 +1,8 @@
 from pathlib import Path
 
+import basix
 import dolfinx
 import numpy as np
-import basix
 
 from . import utils
 

cardiac_geometries/fibers/utils.py

@@ -1,11 +1,11 @@
-from typing import NamedTuple
 from pathlib import Path
+from typing import NamedTuple
 
+import adios4dolfinx
 import dolfinx
-from dolfinx.fem.petsc import LinearProblem
-import ufl
 import numpy as np
-import adios4dolfinx
+import ufl
+from dolfinx.fem.petsc import LinearProblem
 
 
 class Microstructure(NamedTuple):

cardiac_geometries/geometry.py

@@ -1,10 +1,12 @@
-from dataclasses import dataclass, field
 import json
+import shutil
+from dataclasses import dataclass, field
 from pathlib import Path
-import dolfinx
+
 from mpi4py import MPI
-import shutil
+
 import adios4dolfinx
+import dolfinx
 import numpy as np
 
 from . import utils
@@ -85,16 +87,10 @@ class Geometry:
 
         # Read mesh
         if (folder / "mesh.xdmf").exists():
-            mesh, cfun = utils.read_mesh(comm=comm, filename=folder / "mesh.xdmf")
+            mesh, cfun, ffun = utils.read_mesh(comm=comm, filename=folder / "mesh.xdmf")
         else:
             raise ValueError("No mesh file found")
 
-        # Read meshtags
-        if (folder / "triangle_mesh.xdmf").exists():
-            ffun = utils.read_ffun(mesh=mesh, filename=folder / "triangle_mesh.xdmf")
-        else:
-            ffun = None
-
         # Read markers
         if (folder / "markers.json").exists():
             if comm.rank == 0:

cardiac_geometries/mesh.py

@@ -1,12 +1,13 @@
-from pathlib import Path
-import math
-import json
 import datetime
+import json
+import math
 from importlib.metadata import metadata
-from structlog import get_logger
+from pathlib import Path
 
 from mpi4py import MPI
+
 import cardiac_geometries_core as cgc
+from structlog import get_logger
 
 from . import utils
 from .geometry import Geometry
@@ -42,6 +43,7 @@ def biv_ellipsoid(
     fiber_angle_endo: float = -60,
     fiber_angle_epi: float = +60,
     fiber_space: str = "P_1",
+    verbose: bool = False,
 ) -> Geometry:
     """Create BiV ellipsoidal geometry
 
@@ -95,6 +97,8 @@ def biv_ellipsoid(
         Angle for the epicardium, by default +60
     fiber_space : str, optional
         Function space for fibers of the form family_degree, by default "P_1"
+    verbose : bool, optional
+        If True print information from gmsh, by default False
 
     Returns
     -------
@@ -164,9 +168,10 @@ def biv_ellipsoid(
             a_epi_rv=a_epi_rv,
             b_epi_rv=b_epi_rv,
             c_epi_rv=c_epi_rv,
+            verbose=verbose,
         )
     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:
@@ -220,6 +225,7 @@ def biv_ellipsoid_torso(
     fiber_angle_endo: float = -60,
     fiber_angle_epi: float = +60,
     fiber_space: str = "P_1",
+    verbose: bool = False,
 ) -> Geometry:
     """Create BiV ellipsoidal geometry
 
@@ -285,6 +291,8 @@ def biv_ellipsoid_torso(
         Angle for the epicardium, by default +60
     fiber_space : str, optional
         Function space for fibers of the form family_degree, by default "P_1"
+    verbose : bool, optional
+        If True print information from gmsh, by default False
 
     Returns
     -------
@@ -364,10 +372,11 @@ def biv_ellipsoid_torso(
             a_epi_rv=a_epi_rv,
             b_epi_rv=b_epi_rv,
             c_epi_rv=c_epi_rv,
+            verbose=verbose,
         )
     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:
@@ -412,6 +421,7 @@ def lv_ellipsoid(
     fiber_angle_epi: float = +60,
     fiber_space: str = "P_1",
     aha: bool = True,
+    verbose: bool = False,
 ) -> Geometry:
     """Create an LV ellipsoidal geometry
 
@@ -447,6 +457,8 @@ def lv_ellipsoid(
         Function space for fibers of the form family_degree, by default "P_1"
     aha : bool, optional
         If True create 17-segment AHA regions
+    verbose : bool, optional
+        If True print information from gmsh, by default False
 
     Returns
     -------
@@ -497,10 +509,11 @@ def lv_ellipsoid(
             mu_apex_endo=mu_apex_endo,
             mu_apex_epi=mu_apex_epi,
             psize_ref=psize_ref,
+            verbose=verbose,
         )
     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
@@ -559,6 +572,7 @@ def slab(
     fiber_angle_endo: float = -60,
     fiber_angle_epi: float = +60,
     fiber_space: str = "P_1",
+    verbose: bool = False,
 ) -> Geometry:
     """Create slab geometry
 
@@ -582,6 +596,8 @@ def slab(
         Angle for the epicardium, by default +60
     fiber_space : str, optional
         Function space for fibers of the form family_degree, by default "P_1"
+    verbose : bool, optional
+        If True print information from gmsh, by default False
 
     Returns
     -------
@@ -615,10 +631,17 @@ def slab(
                 default=utils.json_serial,
             )
 
-        cgc.slab(mesh_name=mesh_name.as_posix(), lx=lx, ly=ly, lz=lz, dx=dx)
+        cgc.slab(
+            mesh_name=mesh_name.as_posix(),
+            lx=lx,
+            ly=ly,
+            lz=lz,
+            dx=dx,
+            verbose=verbose,
+        )
     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:
@@ -651,6 +674,7 @@ def slab_in_bath(
     by: float = 0.0,
     bz: float = 0.1,
     dx: float = 0.001,
+    verbose: bool = False,
 ) -> Geometry:
     """Create slab geometry
 
@@ -672,6 +696,8 @@ def slab_in_bath(
         Thickness of bath the z-direction, by default 0.1
     dx : float, optional
         Element size, by default 0.001
+    verbose : bool, optional
+        If True print information from gmsh, by default False
 
     Returns
     -------
@@ -714,9 +740,10 @@ def slab_in_bath(
             by=by,
             bz=bz,
             dx=dx,
+            verbose=verbose,
         )
 
-    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

@@ -1,15 +1,14 @@
-from pathlib import Path
 import tempfile
-from typing import NamedTuple, Iterable
 from enum import Enum
+from pathlib import Path
+from typing import Iterable, NamedTuple
 
-import numpy as np
 from mpi4py import MPI
-from structlog import get_logger
+
 import basix
 import dolfinx
-import meshio
-
+import numpy as np
+from structlog import get_logger
 
 logger = get_logger()
 
@@ -68,106 +67,56 @@ 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"
-    return ffun
-
-
-def read_mesh(comm, filename: str | Path) -> tuple[dolfinx.mesh.Mesh, dolfinx.mesh.MeshTags | None]:
+def read_mesh(
+    comm, filename: str | Path
+) -> tuple[dolfinx.mesh.Mesh, dolfinx.mesh.MeshTags | None, 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
+        mesh = xdmf.read_mesh(name="Mesh")
+        cfun = xdmf.read_meshtags(mesh, name="Cell tags")
+        mesh.topology.create_connectivity(2, 3)
+        ffun = xdmf.read_meshtags(mesh, name="Facet tags")
+    return mesh, cfun, ffun
 
 
-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)
+    import gmsh
 
-    if triangle_mesh_name.is_file():
-        ffun = read_ffun(mesh, triangle_mesh_name)
-    else:
-        ffun = None
+    # We could make this work in parallel in the future
 
-    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")
+    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): tuple(reversed(v))
+            for v in gmsh.model.getPhysicalGroups()
+        }
+        gmsh.finalize()
     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)
+        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-0.0.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cardiac-geometriesx
-Version: 0.0.1
+Version: 0.0.4
 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-0.0.4.dist-info/RECORD

@@ -0,0 +1,14 @@
+cardiac_geometries/__init__.py,sha256=2W_ywAeLjyRk5MqSPAodHa4UN2lOnW1h8tmGLQ3gaJ0,150
+cardiac_geometries/cli.py,sha256=2-99xmcBltdotzxp4aDZLrh46gyA5U_PZc6lHen7LIM,19323
+cardiac_geometries/geometry.py,sha256=XRacH519WbrLK0V_Ec6rbxAZFK-n39fUsEzdK3ulbJg,4655
+cardiac_geometries/mesh.py,sha256=cJAcwdDaYmO8MlfocaxvV6pkBcfEWybMSBAaycr6q3s,25987
+cardiac_geometries/utils.py,sha256=-fH13vimCYrirDZubQdxRpX-7I9iCFsOJ8Xo1NL5Nvc,3596
+cardiac_geometries/fibers/__init__.py,sha256=WpRrn9Iakl-3m8IGtFkqP0LXGjw5EZHZ8Eg9JCnCdrg,137
+cardiac_geometries/fibers/lv_ellipsoid.py,sha256=zcCTcst08-xcG5c2j8rPLFp0cgNjXt1Q0mVGhs5r5Ps,3695
+cardiac_geometries/fibers/slab.py,sha256=-EWG4cHjtFYo4VyoFfVnsbHhfdf8qKWphYimJ1jB56o,3867
+cardiac_geometries/fibers/utils.py,sha256=hra9OKKNJhhTkgx4Xs4Oc2FoX8kzY-Eyu6KjQ74FNh4,2584
+cardiac_geometriesx-0.0.4.dist-info/METADATA,sha256=nSeHEbLKF9sIbjc18m0hYcMSAfy7db05NZaFyFioIRA,1395
+cardiac_geometriesx-0.0.4.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+cardiac_geometriesx-0.0.4.dist-info/entry_points.txt,sha256=xOBnlc6W-H9oCDYLNz3kpki26OmpfYSoFSrmi_4V-Ec,52
+cardiac_geometriesx-0.0.4.dist-info/top_level.txt,sha256=J0gQxkWR2my5Vf7Qt8buDY8ZOjYdVfIweVunCGXWKNE,19
+cardiac_geometriesx-0.0.4.dist-info/RECORD,,

cardiac_geometriesx-0.0.1.dist-info/RECORD

@@ -1,14 +0,0 @@
-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,,