cardiac-geometriesx 0.4.6__tar.gz → 0.4.8__tar.gz

{cardiac_geometriesx-0.4.6/src/cardiac_geometriesx.egg-info → cardiac_geometriesx-0.4.8}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: cardiac-geometriesx
-Version: 0.4.6
+Version: 0.4.8
 Summary: A python library for cardiac geometries
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License: MIT
@@ -38,7 +38,7 @@ Provides-Extra: test
 Requires-Dist: pre-commit; extra == "test"
 Requires-Dist: pytest; extra == "test"
 Requires-Dist: pytest-cov; extra == "test"
-Requires-Dist: ukb-atlas; extra == "test"
+Requires-Dist: ukb-atlas[pyvista]; extra == "test"
 Requires-Dist: fenicsx-ldrb; extra == "test"
 Provides-Extra: gui
 Requires-Dist: streamlit; extra == "gui"
@@ -47,6 +47,7 @@ Requires-Dist: pyvista[all]>=0.43.0; extra == "gui"
 Requires-Dist: trame-vuetify; extra == "gui"
 Requires-Dist: ipywidgets; extra == "gui"
 Requires-Dist: fenicsx-ldrb; extra == "gui"
+Dynamic: license-file
 
 ![_](docs/_static/logo.png)
 

{cardiac_geometriesx-0.4.6 → cardiac_geometriesx-0.4.8}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cardiac-geometriesx"
-version = "0.4.6"
+version = "0.4.8"
 description = "A python library for cardiac geometries"
 authors = [{name = "Henrik Finsberg", email = "henriknf@simula.no"}]
 license = {text = "MIT"}
@@ -52,7 +52,7 @@ test = [
     "pre-commit",
     "pytest",
     "pytest-cov",
-    "ukb-atlas",
+    "ukb-atlas[pyvista]",
     "fenicsx-ldrb",
 ]
 gui = [
@@ -177,7 +177,7 @@ tag = true
 sign_tags = false
 tag_name = "v{new_version}"
 tag_message = "Bump version: {current_version} → {new_version}"
-current_version = "0.4.6"
+current_version = "0.4.8"
 
 
 [[tool.bumpversion.files]]

{cardiac_geometriesx-0.4.6 → cardiac_geometriesx-0.4.8}/src/cardiac_geometries/cli.py

@@ -92,6 +92,14 @@ def app():
     help="Function space for fibers of the form family_degree",
     show_default=True,
 )
+@click.option(
+    "--clipped/--no-clipped",
+    default=False,
+    is_flag=True,
+    type=bool,
+    help="If True create clip away the outflow tracts",
+    show_default=True,
+)
 def ukb(
     outdir: Path | str,
     mode: int = -1,
@@ -102,6 +110,7 @@ def ukb(
     fiber_angle_endo: float = 60,
     fiber_angle_epi: float = -60,
     fiber_space: str = "P_1",
+    clipped: bool = False,
 ):
     outdir = Path(outdir)
     outdir.mkdir(exist_ok=True)
@@ -116,6 +125,7 @@ def ukb(
         fiber_angle_endo=fiber_angle_endo,
         fiber_angle_epi=fiber_angle_epi,
         fiber_space=fiber_space,
+        clipped=clipped,
     )
     geo.save(outdir / "ukb.bp")
 
@@ -199,7 +209,6 @@ def ukb(
     "--create-fibers",
     default=False,
     is_flag=True,
-    type=bool,
     help="If True create analytic fibers",
     show_default=True,
 )
@@ -421,7 +430,6 @@ def lv_ellipsoid(
     "--create-fibers",
     default=False,
     is_flag=True,
-    type=bool,
     help="If True create analytic fibers",
     show_default=True,
 )
@@ -689,7 +697,6 @@ def biv_ellipsoid(
     "--create-fibers",
     default=False,
     is_flag=True,
-    type=bool,
     help="If True create analytic fibers",
     show_default=True,
 )
@@ -827,7 +834,6 @@ def biv_ellipsoid_torso(
     "--create-fibers",
     default=False,
     is_flag=True,
-    type=bool,
     help="If True create analytic fibers",
     show_default=True,
 )

{cardiac_geometriesx-0.4.6 → cardiac_geometriesx-0.4.8}/src/cardiac_geometries/geometry.py

@@ -98,7 +98,12 @@ class Geometry:
         self.mesh.comm.barrier()
 
     @classmethod
-    def from_file(cls, comm: MPI.Intracomm, path: str | Path) -> "Geometry":
+    def from_file(
+        cls,
+        comm: MPI.Intracomm,
+        path: str | Path,
+        function_space_data: dict[str, np.ndarray] | None = None,
+    ) -> "Geometry":
         path = Path(path)
 
         mesh = adios4dolfinx.read_mesh(comm=comm, filename=path)
@@ -118,10 +123,12 @@ class Geometry:
                 tags[name] = None
 
         functions = {}
-        function_space = adios4dolfinx.read_attributes(
-            comm=comm, filename=path, name="function_space"
-        )
-        for name, el in function_space.items():
+        if function_space_data is None:
+            function_space_data = adios4dolfinx.read_attributes(
+                comm=comm, filename=path, name="function_space"
+            )
+        assert isinstance(function_space_data, dict), "function_space_data must be a dictionary"
+        for name, el in function_space_data.items():
             element = utils.array2element(el)
             V = dolfinx.fem.functionspace(mesh, element)
             f = dolfinx.fem.Function(V, name=name)

{cardiac_geometriesx-0.4.6 → cardiac_geometriesx-0.4.8}/src/cardiac_geometries/mesh.py

@@ -32,6 +32,7 @@ def ukb(
     fiber_angle_endo: float = 60,
     fiber_angle_epi: float = -60,
     fiber_space: str = "P_1",
+    clipped: bool = False,
     comm: MPI.Comm = MPI.COMM_WORLD,
 ) -> Geometry:
     try:
@@ -44,26 +45,29 @@ def ukb(
         raise ImportError(msg) from e
 
     if comm.rank == 0:
+        ukb.cli.main(["surf", str(outdir), "--mode", str(mode), "--std", str(std), "--case", case])
+        mesh_args = [
+            "mesh",
+            str(outdir),
+            "--case",
+            case,
+            "--char_length_max",
+            str(char_length_max),
+            "--char_length_min",
+            str(char_length_min),
+        ]
+        if clipped:
+            ukb.cli.main(["clip", str(outdir), "--case", case, "--smooth"])
+            mesh_args.append("--clipped")
         print(comm.rank)
-        ukb.cli.main(
-            [
-                str(outdir),
-                "--mode",
-                str(mode),
-                "--std",
-                str(std),
-                "--case",
-                case,
-                "--mesh",
-                "--char_length_max",
-                str(char_length_max),
-                "--char_length_min",
-                str(char_length_min),
-            ]
-        )
+
+        ukb.cli.main(mesh_args)
     comm.barrier()
     outdir = Path(outdir)
-    mesh_name = outdir / f"{case}.msh"
+    if clipped:
+        mesh_name = outdir / f"{case}_clipped.msh"
+    else:
+        mesh_name = outdir / f"{case}.msh"
 
     geometry = utils.gmsh2dolfin(comm=comm, msh_file=mesh_name)
 
@@ -98,24 +102,25 @@ def ukb(
         )
         raise ImportError(msg)
 
-    # base_marker = 3
-    # indices = []
-    # for k in ["PV", "TV", "AV", "MV"]:
-    #     indices.append(geometry.ffun.find(geometry.markers[k][0]))
-    # indices = np.hstack(comm.allreduce(indices, op=MPI.SUM))
-    # values = np.full(len(indices), base_marker, dtype=np.int32)
-
-    markers = {
-        "lv": [geometry.markers["LV"][0]],
-        "rv": [geometry.markers["RV"][0]],
-        "epi": [geometry.markers["EPI"][0]],
-        "base": [
-            geometry.markers["PV"][0],
-            geometry.markers["TV"][0],
-            geometry.markers["AV"][0],
-            geometry.markers["MV"][0],
-        ],
-    }
+    if clipped:
+        markers = {
+            "lv": [geometry.markers["LV"][0]],
+            "rv": [geometry.markers["RV"][0]],
+            "epi": [geometry.markers["EPI"][0]],
+            "base": [geometry.markers["BASE"][0]],
+        }
+    else:
+        markers = {
+            "lv": [geometry.markers["LV"][0]],
+            "rv": [geometry.markers["RV"][0]],
+            "epi": [geometry.markers["EPI"][0]],
+            "base": [
+                geometry.markers["PV"][0],
+                geometry.markers["TV"][0],
+                geometry.markers["AV"][0],
+                geometry.markers["MV"][0],
+            ],
+        }
     system = ldrb.dolfinx_ldrb(
         mesh=geometry.mesh,
         ffun=geometry.ffun,

{cardiac_geometriesx-0.4.6 → cardiac_geometriesx-0.4.8/src/cardiac_geometriesx.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: cardiac-geometriesx
-Version: 0.4.6
+Version: 0.4.8
 Summary: A python library for cardiac geometries
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License: MIT
@@ -38,7 +38,7 @@ Provides-Extra: test
 Requires-Dist: pre-commit; extra == "test"
 Requires-Dist: pytest; extra == "test"
 Requires-Dist: pytest-cov; extra == "test"
-Requires-Dist: ukb-atlas; extra == "test"
+Requires-Dist: ukb-atlas[pyvista]; extra == "test"
 Requires-Dist: fenicsx-ldrb; extra == "test"
 Provides-Extra: gui
 Requires-Dist: streamlit; extra == "gui"
@@ -47,6 +47,7 @@ Requires-Dist: pyvista[all]>=0.43.0; extra == "gui"
 Requires-Dist: trame-vuetify; extra == "gui"
 Requires-Dist: ipywidgets; extra == "gui"
 Requires-Dist: fenicsx-ldrb; extra == "gui"
+Dynamic: license-file
 
 ![_](docs/_static/logo.png)
 

{cardiac_geometriesx-0.4.6 → cardiac_geometriesx-0.4.8}/src/cardiac_geometriesx.egg-info/requires.txt

@@ -35,5 +35,5 @@ fenicsx-ldrb
 pre-commit
 pytest
 pytest-cov
-ukb-atlas
+ukb-atlas[pyvista]
 fenicsx-ldrb

{cardiac_geometriesx-0.4.6 → cardiac_geometriesx-0.4.8}/tests/test_cli.py

@@ -60,29 +60,36 @@ def test_script_no_fibers(script, tmp_path: Path):
     assert geo.mesh.geometry.dim == 3
 
 
+@pytest.mark.parametrize("clipped", [True, False])
 @pytest.mark.parametrize("case", ["ED", "ES"])
-def test_ukb(tmp_path: Path, case: str):
+def test_ukb(tmp_path: Path, case: str, clipped: bool):
     runner = CliRunner()
 
     comm = MPI.COMM_WORLD
     path = comm.bcast(tmp_path, root=0)
 
-    res = runner.invoke(
-        cli.ukb,
-        [
-            path.as_posix(),
-            "--case",
-            case,
-            "--char-length-max",
-            "10.0",
-            "--char-length-min",
-            "10.0",
-        ],
-    )
+    args = [
+        path.as_posix(),
+        "--case",
+        case,
+        "--char-length-max",
+        "10.0",
+        "--char-length-min",
+        "10.0",
+    ]
+    if clipped:
+        if case == "ES":
+            pytest.skip("Clipped case with default values are for ED")
+        args.append("--clipped")
+
+    res = runner.invoke(cli.ukb, args)
     assert res.exit_code == 0
     assert path.is_dir()
 
     assert (path / "mesh.xdmf").exists()
-    assert (path / f"{case}.msh").exists()
+    if clipped:
+        assert (path / f"{case}_clipped.msh").exists()
+    else:
+        assert (path / f"{case}.msh").exists()
     geo = Geometry.from_folder(comm=comm, folder=path)
     assert geo.mesh.geometry.dim == 3