cardiac-geometriesx 0.4.5__py3-none-any.whl → 0.4.7__py3-none-any.whl

cardiac_geometries/cli.py

@@ -24,6 +24,112 @@ def app():
     pass
 
 
+@click.command(help="Create UK Biobank geometry")
+@click.argument(
+    "outdir",
+    required=True,
+    type=click.Path(
+        file_okay=False,
+        dir_okay=True,
+        writable=True,
+        readable=True,
+        resolve_path=True,
+    ),
+)
+@click.option(
+    "--mode",
+    default=-1,
+    type=int,
+    help="Mode of the geometry",
+    show_default=True,
+)
+@click.option(
+    "--std",
+    default=1.5,
+    type=float,
+    help="Standard deviation of the geometry",
+    show_default=True,
+)
+@click.option(
+    "--case",
+    default="ED",
+    type=str,
+    help="Case of the geometry",
+    show_default=True,
+)
+@click.option(
+    "--char-length-max",
+    default=2.0,
+    type=float,
+    help="Maximum characteristic length of the mesh",
+    show_default=True,
+)
+@click.option(
+    "--char-length-min",
+    default=2.0,
+    type=float,
+    help="Minimum characteristic length of the mesh",
+    show_default=True,
+)
+@click.option(
+    "--fiber-angle-endo",
+    default=60,
+    type=float,
+    help="Angle for the endocardium",
+    show_default=True,
+)
+@click.option(
+    "--fiber-angle-epi",
+    default=-60,
+    type=float,
+    help="Angle for the epicardium",
+    show_default=True,
+)
+@click.option(
+    "--fiber-space",
+    default="P_1",
+    type=str,
+    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,
+    std: float = 1.5,
+    case: str = "ED",
+    char_length_max: float = 2.0,
+    char_length_min: float = 2.0,
+    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)
+
+    geo = mesh.ukb(
+        outdir=outdir,
+        mode=mode,
+        std=std,
+        case=case,
+        char_length_max=char_length_max,
+        char_length_min=char_length_min,
+        fiber_angle_endo=fiber_angle_endo,
+        fiber_angle_epi=fiber_angle_epi,
+        fiber_space=fiber_space,
+        clipped=clipped,
+    )
+    geo.save(outdir / "ukb.bp")
+
+
 @click.command(help="Create LV ellipsoidal geometry")
 @click.argument(
     "outdir",
@@ -382,6 +488,7 @@ def biv_ellipsoid(
     geo = mesh.biv_ellipsoid(
         outdir=outdir,
         char_length=char_length,
+        center_lv_x=center_lv_x,
         center_lv_y=center_lv_y,
         center_lv_z=center_lv_z,
         a_endo_lv=a_endo_lv,
@@ -390,6 +497,7 @@ def biv_ellipsoid(
         a_epi_lv=a_epi_lv,
         b_epi_lv=b_epi_lv,
         c_epi_lv=c_epi_lv,
+        center_rv_x=center_rv_x,
         center_rv_y=center_rv_y,
         center_rv_z=center_rv_z,
         a_endo_rv=a_endo_rv,
@@ -457,7 +565,7 @@ def biv_ellipsoid(
     default=math.pi / 6,
     type=float,
     help=(
-        "Angle to rotate the torso in order to object realistic" " position of the heart in a torso"
+        "Angle to rotate the torso in order to object realistic position of the heart in a torso"
     ),
     show_default=True,
 )
@@ -886,3 +994,4 @@ app.add_command(biv_ellipsoid_torso)
 app.add_command(slab)
 app.add_command(slab_in_bath)
 app.add_command(gui)
+app.add_command(ukb)

cardiac_geometries/geometry.py

@@ -1,4 +1,5 @@
 import json
+import logging
 import shutil
 from dataclasses import dataclass, field
 from pathlib import Path
@@ -13,6 +14,8 @@ from packaging.version import Version
 
 from . import utils
 
+logger = logging.getLogger(__name__)
+
 
 @dataclass  # (frozen=True, slots=True)
 class Geometry:
@@ -139,15 +142,17 @@ class Geometry:
     @classmethod
     def from_folder(cls, comm: MPI.Intracomm, folder: str | Path) -> "Geometry":
         folder = Path(folder)
-
+        logger.info(f"Reading geometry from {folder}")
         # Read mesh
         if (folder / "mesh.xdmf").exists():
+            logger.debug("Reading mesh")
             mesh, tags = utils.read_mesh(comm=comm, filename=folder / "mesh.xdmf")
         else:
             raise ValueError("No mesh file found")
 
         # Read markers
         if (folder / "markers.json").exists():
+            logger.debug("Reading markers")
             if comm.rank == 0:
                 markers = json.loads((folder / "markers.json").read_text())
             else:
@@ -168,10 +173,12 @@ class Geometry:
         functions = {}
         microstructure_path = folder / "microstructure.bp"
         if microstructure_path.exists():
+            logger.debug("Reading microstructure")
             # function_space = adios4dolfinx.read_attributes(
             #     comm=MPI.COMM_WORLD, filename=microstructure_path, name="function_space"
             # )
             for name, el in microstructure.items():
+                logger.debug(f"Reading {name}")
                 element = utils.array2element(el)
                 V = dolfinx.fem.functionspace(mesh, element)
                 f = dolfinx.fem.Function(V, name=name)

cardiac_geometries/mesh.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import datetime
 import json
 import math
@@ -7,9 +9,11 @@ from pathlib import Path
 from mpi4py import MPI
 
 import cardiac_geometries_core as cgc
+import dolfinx
 from structlog import get_logger
 
 from . import utils
+from .fibers.utils import save_microstructure
 from .geometry import Geometry
 
 meta = metadata("cardiac-geometriesx")
@@ -18,6 +22,137 @@ __version__ = meta["Version"]
 logger = get_logger()
 
 
+def ukb(
+    outdir: str | Path,
+    mode: int = -1,
+    std: float = 1.5,
+    case: str = "ED",
+    char_length_max: float = 2.0,
+    char_length_min: float = 2.0,
+    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:
+        import ukb.cli
+    except ImportError as e:
+        msg = (
+            "To create the UKB mesh you need to install the ukb package "
+            "which you can install with pip install ukb-atlas"
+        )
+        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(mesh_args)
+    comm.barrier()
+    outdir = Path(outdir)
+    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)
+
+    if comm.rank == 0:
+        (outdir / "markers.json").write_text(
+            json.dumps(geometry.markers, default=utils.json_serial)
+        )
+        (outdir / "info.json").write_text(
+            json.dumps(
+                {
+                    "mode": mode,
+                    "std": std,
+                    "case": case,
+                    "char_length_max": char_length_max,
+                    "char_length_min": char_length_min,
+                    "fiber_angle_endo": fiber_angle_endo,
+                    "fiber_angle_epi": fiber_angle_epi,
+                    "fiber_space": fiber_space,
+                    "cardiac_geometry_version": __version__,
+                    "type": "ukb",
+                    "timestamp": datetime.datetime.now().isoformat(),
+                }
+            )
+        )
+
+    try:
+        import ldrb
+    except ImportError:
+        msg = (
+            "To create fibers you need to install the ldrb package "
+            "which you can install with pip install fenicsx-ldrb"
+        )
+        raise ImportError(msg)
+
+    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,
+        markers=markers,
+        alpha_endo_lv=fiber_angle_endo,
+        alpha_epi_lv=fiber_angle_epi,
+        beta_endo_lv=0,
+        beta_epi_lv=0,
+        fiber_space=fiber_space,
+    )
+
+    save_microstructure(
+        mesh=geometry.mesh,
+        functions=(system.f0, system.s0, system.n0),
+        outdir=outdir,
+    )
+
+    for k, v in system._asdict().items():
+        if v is None:
+            continue
+        if fiber_space.startswith("Q"):
+            # Cannot visualize Quadrature spaces yet
+            continue
+
+        logger.debug(f"Write {k}: {v}")
+        with dolfinx.io.VTXWriter(comm, outdir / f"{k}-viz.bp", [v], engine="BP4") as vtx:
+            vtx.write(0.0)
+
+    geo = Geometry.from_folder(comm=comm, folder=outdir)
+    return geo
+
+
 def biv_ellipsoid(
     outdir: str | Path,
     char_length: float = 0.5,
@@ -199,10 +334,11 @@ def biv_ellipsoid(
             beta_epi_lv=0,
             fiber_space=fiber_space,
         )
-        from .fibers.utils import save_microstructure
 
         save_microstructure(
-            mesh=geometry.mesh, functions=(system.f0, system.s0, system.n0), outdir=outdir
+            mesh=geometry.mesh,
+            functions=(system.f0, system.s0, system.n0),
+            outdir=outdir,
         )
 
     geo = Geometry.from_folder(comm=comm, folder=outdir)

cardiac_geometries/utils.py

@@ -422,6 +422,7 @@ def read_mesh(
 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
+    outdir.mkdir(parents=True, exist_ok=True)
 
     if Version(dolfinx.__version__) >= Version("0.10.0"):
         mesh_data = dolfinx.io.gmshio.read_from_msh(comm=comm, filename=msh_file)
@@ -454,6 +455,7 @@ def gmsh2dolfin(comm: MPI.Intracomm, msh_file, rank: int = 0) -> GMshGeometry:
 
     else:
         import gmsh
+
         # We could make this work in parallel in the future
 
         if comm.rank == rank:
@@ -482,19 +484,27 @@ def gmsh2dolfin(comm: MPI.Intracomm, msh_file, rank: int = 0) -> GMshGeometry:
     with dolfinx.io.XDMFFile(comm, outdir / "mesh.xdmf", "w") as xdmf:
         xdmf.write_mesh(mesh)
         xdmf.write_meshtags(
-            ct, mesh.geometry, geometry_xpath=f"/Xdmf/Domain/Grid[@Name='{mesh.name}']/Geometry"
+            ct,
+            mesh.geometry,
+            geometry_xpath=f"/Xdmf/Domain/Grid[@Name='{mesh.name}']/Geometry",
         )
         mesh.topology.create_connectivity(2, 3)
         xdmf.write_meshtags(
-            ft, mesh.geometry, geometry_xpath=f"/Xdmf/Domain/Grid[@Name='{mesh.name}']/Geometry"
+            ft,
+            mesh.geometry,
+            geometry_xpath=f"/Xdmf/Domain/Grid[@Name='{mesh.name}']/Geometry",
         )
         mesh.topology.create_connectivity(1, 3)
         xdmf.write_meshtags(
-            et, mesh.geometry, geometry_xpath=f"/Xdmf/Domain/Grid[@Name='{mesh.name}']/Geometry"
+            et,
+            mesh.geometry,
+            geometry_xpath=f"/Xdmf/Domain/Grid[@Name='{mesh.name}']/Geometry",
         )
         mesh.topology.create_connectivity(0, 3)
         xdmf.write_meshtags(
-            vt, mesh.geometry, geometry_xpath=f"/Xdmf/Domain/Grid[@Name='{mesh.name}']/Geometry"
+            vt,
+            mesh.geometry,
+            geometry_xpath=f"/Xdmf/Domain/Grid[@Name='{mesh.name}']/Geometry",
         )
 
     return GMshGeometry(mesh, ct, ft, et, vt, markers)

{cardiac_geometriesx-0.4.5.dist-info → cardiac_geometriesx-0.4.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: cardiac-geometriesx
-Version: 0.4.5
+Version: 0.4.7
 Summary: A python library for cardiac geometries
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License: MIT
@@ -38,6 +38,8 @@ Provides-Extra: test
 Requires-Dist: pre-commit; extra == "test"
 Requires-Dist: pytest; extra == "test"
 Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: ukb-atlas[pyvista]; extra == "test"
+Requires-Dist: fenicsx-ldrb; extra == "test"
 Provides-Extra: gui
 Requires-Dist: streamlit; extra == "gui"
 Requires-Dist: stpyvista; extra == "gui"
@@ -45,6 +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-0.4.7.dist-info/RECORD

@@ -0,0 +1,16 @@
+cardiac_geometries/__init__.py,sha256=2W_ywAeLjyRk5MqSPAodHa4UN2lOnW1h8tmGLQ3gaJ0,150
+cardiac_geometries/cli.py,sha256=Um8iYayrjinNiPkqq7PZC_8GRqzXc_eFswIcrRHOdeU,22007
+cardiac_geometries/geometry.py,sha256=y-V4DyksNCqPwK7-NQIjcS6ldlvh1ub2p7lj9FZJHWw,6795
+cardiac_geometries/gui.py,sha256=9WYR850wLrqsUrVUC37E2SaO0OWA_oagSe-YNrsxz3k,8376
+cardiac_geometries/mesh.py,sha256=jLHTujz_38SQ5loN94nuN6pMG8IVPmlCdwOJhzuMxy4,30922
+cardiac_geometries/utils.py,sha256=nJE-gyV7NIAmgl5JGlG5Vl7XsIcYS8Y20bVjYcd4R6c,21964
+cardiac_geometries/fibers/__init__.py,sha256=WpRrn9Iakl-3m8IGtFkqP0LXGjw5EZHZ8Eg9JCnCdrg,137
+cardiac_geometries/fibers/lv_ellipsoid.py,sha256=LZNhxzTsn-h88xXGP5bNfnWKhdvBROUjWjt8yrQFW48,6010
+cardiac_geometries/fibers/slab.py,sha256=TYQhckJ8mwXz_08Cx3QsPQMtemkaxZ955SnSMrDfBPE,3898
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+cardiac_geometriesx-0.4.7.dist-info/licenses/LICENSE,sha256=lo5K2rJPZOSv6luutGHbzzi3IpXNaB9E2UWq60qvNx0,1111
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+cardiac_geometriesx-0.4.7.dist-info/RECORD,,

{cardiac_geometriesx-0.4.5.dist-info → cardiac_geometriesx-0.4.7.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.6.0)
+Generator: setuptools (78.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

cardiac_geometriesx-0.4.5.dist-info/RECORD

@@ -1,16 +0,0 @@
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-cardiac_geometries/cli.py,sha256=GKcsMNhVFoxWDr-o3jiDCXmTvPgCSEB9Kws8AvYIK4Q,19678
-cardiac_geometries/geometry.py,sha256=JSsLKfXej4DSgzRbivC-_jvyjiY6zkXcRCRL93IIys8,6504
-cardiac_geometries/gui.py,sha256=9WYR850wLrqsUrVUC37E2SaO0OWA_oagSe-YNrsxz3k,8376
-cardiac_geometries/mesh.py,sha256=_vNNMpQWyLEZ3TmsHAUh0l3Z2TYuQBy6Os-6nB9_Z9A,26908
-cardiac_geometries/utils.py,sha256=tMn_XQRYbP1__c0QPHZeiCRJun3TZiH80OwJDESTPzY,21817
-cardiac_geometries/fibers/__init__.py,sha256=WpRrn9Iakl-3m8IGtFkqP0LXGjw5EZHZ8Eg9JCnCdrg,137
-cardiac_geometries/fibers/lv_ellipsoid.py,sha256=LZNhxzTsn-h88xXGP5bNfnWKhdvBROUjWjt8yrQFW48,6010
-cardiac_geometries/fibers/slab.py,sha256=TYQhckJ8mwXz_08Cx3QsPQMtemkaxZ955SnSMrDfBPE,3898
-cardiac_geometries/fibers/utils.py,sha256=pCoXkaUbidLGPY0Ty8uWCU1siDkHcv2qP8rZtdxMf0k,3475
-cardiac_geometriesx-0.4.5.dist-info/LICENSE,sha256=lo5K2rJPZOSv6luutGHbzzi3IpXNaB9E2UWq60qvNx0,1111
-cardiac_geometriesx-0.4.5.dist-info/METADATA,sha256=VcogZHS3ECHMoAQ-ei54PSdGCOi6-bviY8KjEYbPgaw,4202
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-cardiac_geometriesx-0.4.5.dist-info/top_level.txt,sha256=J0gQxkWR2my5Vf7Qt8buDY8ZOjYdVfIweVunCGXWKNE,19
-cardiac_geometriesx-0.4.5.dist-info/RECORD,,