cardiac-geometriesx 0.0.4__py3-none-any.whl → 0.1.1__py3-none-any.whl

cardiac_geometries/fibers/utils.py

@@ -1,5 +1,5 @@
 from pathlib import Path
-from typing import NamedTuple
+from typing import NamedTuple, Sequence
 
 import adios4dolfinx
 import dolfinx
@@ -15,28 +15,25 @@ class Microstructure(NamedTuple):
 
 
 def save_microstructure(
-    mesh: dolfinx.mesh.Mesh, system: Microstructure, outdir: str | Path
+    mesh: dolfinx.mesh.Mesh, functions: Sequence[dolfinx.fem.Function], outdir: str | Path
 ) -> None:
     from ..utils import element2array
 
     # Save for paraview visualization
-    with dolfinx.io.XDMFFile(mesh.comm, Path(outdir) / "microstructure.xdmf", "w") as file:
-        file.write_mesh(mesh)
-        file.write_function(system.f0)
-        file.write_function(system.s0)
-        file.write_function(system.n0)
-
+    with dolfinx.io.VTXWriter(mesh.comm, Path(outdir) / "microstructure-viz.bp", functions, engine="BP4") as file:
+        file.write(0.0)
+        
     # Save with proper function space
     filename = Path(outdir) / "microstructure.bp"
-    adios4dolfinx.write_function(u=system.f0, filename=filename)
-    adios4dolfinx.write_function(u=system.s0, filename=filename)
-    adios4dolfinx.write_function(u=system.n0, filename=filename)
-    arr = element2array(system.f0.ufl_element().basix_element)
+    for function in functions:
+        adios4dolfinx.write_function(u=function, filename=filename)
+
+    attributes = {f.name: element2array(f.ufl_element().basix_element) for f in functions}
     adios4dolfinx.write_attributes(
         comm=mesh.comm,
         filename=filename,
         name="function_space",
-        attributes={k: arr for k in ("f0", "s0", "n0")},
+        attributes=attributes,
     )
 
 

cardiac_geometries/geometry.py

@@ -12,7 +12,7 @@ import numpy as np
 from . import utils
 
 
-@dataclass(frozen=True, slots=True)
+@dataclass#(frozen=True, slots=True)
 class Geometry:
     mesh: dolfinx.mesh.Mesh
     markers: dict[str, tuple[str, str]] = field(default_factory=dict)

{cardiac_geometriesx-0.0.4.dist-info → cardiac_geometriesx-0.1.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cardiac-geometriesx
-Version: 0.0.4
+Version: 0.1.1
 Summary: A python library for cardiac geometries
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License: MIT
@@ -29,13 +29,14 @@ 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
+python3 -m pip install cardiac-geometriesx
 ```
 
 Example usage

{cardiac_geometriesx-0.0.4.dist-info → cardiac_geometriesx-0.1.1.dist-info}/RECORD

@@ -1,14 +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/geometry.py,sha256=rhtq219q06ta1ZS_WIyqfjr00rN1L099bfX_Fwhe29g,4656
 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_geometries/fibers/utils.py,sha256=K_C_G1az_SnwBAeKvvvZN4V4M_6z0DAAqOsV7M3T5aI,2428
+cardiac_geometriesx-0.1.1.dist-info/METADATA,sha256=w_cEg_5ZBV2Ptl9OxH2VN4Psll0wjlLU0WTR4GIaB8o,1349
+cardiac_geometriesx-0.1.1.dist-info/WHEEL,sha256=cpQTJ5IWu9CdaPViMhC9YzF8gZuS5-vlfoFihTBC86A,91
+cardiac_geometriesx-0.1.1.dist-info/entry_points.txt,sha256=xOBnlc6W-H9oCDYLNz3kpki26OmpfYSoFSrmi_4V-Ec,52
+cardiac_geometriesx-0.1.1.dist-info/top_level.txt,sha256=J0gQxkWR2my5Vf7Qt8buDY8ZOjYdVfIweVunCGXWKNE,19
+cardiac_geometriesx-0.1.1.dist-info/RECORD,,

{cardiac_geometriesx-0.0.4.dist-info → cardiac_geometriesx-0.1.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (70.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any