cardiac-geometriesx 0.6.1__tar.gz → 0.7.0__tar.gz

{cardiac_geometriesx-0.6.1/src/cardiac_geometriesx.egg-info → cardiac_geometriesx-0.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cardiac-geometriesx
-Version: 0.6.1
+Version: 0.7.0
 Summary: A python library for cardiac geometries
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License: MIT
@@ -29,11 +29,14 @@ Provides-Extra: docs
 Requires-Dist: jupyter-book; extra == "docs"
 Requires-Dist: jupytext; extra == "docs"
 Requires-Dist: jupyter; extra == "docs"
-Requires-Dist: pyvista[all]>=0.43.0; extra == "docs"
+Requires-Dist: pyvista[all]>=0.45.0; extra == "docs"
+Requires-Dist: vtk>=9.5.0; extra == "docs"
 Requires-Dist: trame-vuetify; extra == "docs"
 Requires-Dist: ipywidgets; extra == "docs"
 Requires-Dist: fenicsx-ldrb; extra == "docs"
 Requires-Dist: ukb-atlas; extra == "docs"
+Requires-Dist: sphinx-codeautolink; extra == "docs"
+Requires-Dist: sphinx-copybutton; extra == "docs"
 Provides-Extra: test
 Requires-Dist: pre-commit; extra == "test"
 Requires-Dist: pytest; extra == "test"

{cardiac_geometriesx-0.6.1 → cardiac_geometriesx-0.7.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cardiac-geometriesx"
-version = "0.6.1"
+version = "0.7.0"
 description = "A python library for cardiac geometries"
 authors = [{name = "Henrik Finsberg", email = "henriknf@simula.no"}]
 license = {text = "MIT"}
@@ -42,11 +42,14 @@ docs = [
     "jupyter-book",
     "jupytext",
     "jupyter",
-    "pyvista[all]>=0.43.0",
+    "pyvista[all]>=0.45.0",
+    "vtk>=9.5.0",
     "trame-vuetify",
     "ipywidgets",
     "fenicsx-ldrb",
     "ukb-atlas",
+    "sphinx-codeautolink",
+    "sphinx-copybutton",
 ]
 test = [
     "pre-commit",
@@ -177,7 +180,7 @@ tag = true
 sign_tags = false
 tag_name = "v{new_version}"
 tag_message = "Bump version: {current_version} → {new_version}"
-current_version = "0.6.1"
+current_version = "0.7.0"
 
 
 [[tool.bumpversion.files]]

{cardiac_geometriesx-0.6.1 → cardiac_geometriesx-0.7.0}/src/cardiac_geometries/cli.py

@@ -1,3 +1,4 @@
+import logging
 import math
 from importlib.metadata import metadata
 from pathlib import Path
@@ -6,6 +7,8 @@ import rich_click as click
 
 from . import mesh
 
+logger = logging.getLogger(__name__)
+
 meta = metadata("cardiac-geometriesx")
 __version__ = meta["Version"]
 __author__ = meta["Author-email"]
@@ -14,6 +17,13 @@ __email__ = meta["Author-email"]
 __program_name__ = meta["Name"]
 
 
+def init_logging(verbose: bool = False):
+    loglevel = logging.DEBUG if verbose else logging.INFO
+    logging.basicConfig(level=loglevel)
+    for name in ["numba"]:
+        logging.getLogger(name).setLevel(logging.WARNING)
+
+
 @click.group()
 @click.version_option(__version__, prog_name="cardiac_geometriesx")
 def app():
@@ -301,129 +311,80 @@ def lv_ellipsoid(
     show_default=True,
 )
 @click.option(
-    "--center-lv-x",
-    default=0.0,
-    type=float,
-    help="X-coordinate for the center of the lv",
-    show_default=True,
-)
-@click.option(
-    "--center-lv-y",
-    default=0.0,
-    type=float,
-    help="Y-coordinate for the center of the lv",
-    show_default=True,
-)
-@click.option(
-    "--center-lv-z",
-    default=0.0,
-    type=float,
-    help="Z-coordinate for the center of the lv",
-    show_default=True,
-)
-@click.option(
-    "--a-endo-lv",
+    "--base-cut-z",
     default=2.5,
     type=float,
-    help="Dilation of lv endo ellipsoid in the x-direction",
-    show_default=True,
-)
-@click.option(
-    "--b-endo-lv",
-    default=1.0,
-    type=float,
-    help="Dilation of lv endo ellipsoid in the y-direction",
+    help="Z-coordinate of the base cut",
     show_default=True,
 )
 @click.option(
-    "--c-endo-lv",
-    default=1.0,
+    "--box-size",
+    default=15.0,
     type=float,
-    help="Dilation of lv endo ellipsoid in the y-direction",
+    help="Size of the cutting box",
     show_default=True,
 )
 @click.option(
-    "--a-epi-lv",
-    default=3.0,
+    "--rv-wall-thickness",
+    default=0.4,
     type=float,
-    help="Dilation of lv epi ellipsoid in the x-direction",
+    help="Thickness of the right ventricle wall",
     show_default=True,
 )
 @click.option(
-    "--b-epi-lv",
-    default=1.5,
-    type=float,
-    help="Dilation of lv epi ellipsoid in the y-direction",
-    show_default=True,
-)
-@click.option(
-    "--c-epi-lv",
-    default=1.5,
-    type=float,
-    help="Dilation of lv epi ellipsoid in the y-direction",
-    show_default=True,
-)
-@click.option(
-    "--center-rv-x",
-    default=0.0,
-    type=float,
-    help="X-coordinate for the center of the rv",
-    show_default=True,
-)
-@click.option(
-    "--center-rv-y",
+    "--lv-wall-thickness",
     default=0.5,
     type=float,
-    help="Y-coordinate for the center of the rv",
+    help="Thickness of the left ventricle wall",
     show_default=True,
 )
 @click.option(
-    "--center-rv-z",
-    default=0.0,
+    "--rv-offset-x",
+    default=3.0,
     type=float,
-    help="Z-coordinate for the center of the rv",
+    help="X-offset of the right ventricle",
     show_default=True,
 )
 @click.option(
-    "--a-endo-rv",
-    default=3.0,
+    "--lv-radius-x",
+    default=2.0,
     type=float,
-    help="Dilation of rv endo ellipsoid in the x-direction",
+    help="X-radius of the left ventricle",
     show_default=True,
 )
 @click.option(
-    "--b-endo-rv",
-    default=1.5,
+    "--lv-radius-y",
+    default=1.8,
     type=float,
-    help="Dilation of rv endo ellipsoid in the y-direction",
+    help="Y-radius of the left ventricle",
     show_default=True,
 )
 @click.option(
-    "--c-endo-rv",
-    default=1.5,
+    "--lv-radius-z",
+    default=3.25,
     type=float,
-    help="Dilation of rv endo ellipsoid in the y-direction",
+    help="Z-radius of the left ventricle",
     show_default=True,
 )
 @click.option(
-    "--a-epi-rv",
-    default=4.0,
+    "--rv-radius-x",
+    default=1.9,
     type=float,
-    help="Dilation of rv epi ellipsoid in the x-direction",
+    help="X-radius of the right ventricle",
     show_default=True,
 )
 @click.option(
-    "--b-epi-rv",
+    "--rv-radius-y",
     default=2.5,
     type=float,
-    help="Dilation of rv epi ellipsoid in the y-direction",
+    help="Y-radius of the right ventricle",
     show_default=True,
 )
 @click.option(
-    "--c-epi-rv",
-    default=2.0,
+    "--rv-radius-z",
+    default=3.0,
     type=float,
-    help="Dilation of rv epi ellipsoid in the z-direction",
+    help="Z-radius of the right ventricle",
     show_default=True,
 )
 @click.option(
@@ -454,340 +415,58 @@ def lv_ellipsoid(
     help="Function space for fibers of the form family_degree",
     show_default=True,
 )
-def biv_ellipsoid(
-    outdir: Path,
-    char_length: float = 0.5,
-    center_lv_x: float = 0.0,
-    center_lv_y: float = 0.0,
-    center_lv_z: float = 0.0,
-    a_endo_lv: float = 2.5,
-    b_endo_lv: float = 1.0,
-    c_endo_lv: float = 1.0,
-    a_epi_lv: float = 3.0,
-    b_epi_lv: float = 1.5,
-    c_epi_lv: float = 1.5,
-    center_rv_x: float = 0.0,
-    center_rv_y: float = 0.5,
-    center_rv_z: float = 0.0,
-    a_endo_rv: float = 3.0,
-    b_endo_rv: float = 1.5,
-    c_endo_rv: float = 1.5,
-    a_epi_rv: float = 4.0,
-    b_epi_rv: float = 2.5,
-    c_epi_rv: float = 2.0,
-    create_fibers: bool = False,
-    fiber_angle_endo: float = -60,
-    fiber_angle_epi: float = +60,
-    fiber_space: str = "P_1",
-):
-    outdir = Path(outdir)
-    outdir.mkdir(exist_ok=True)
-
-    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,
-        b_endo_lv=b_endo_lv,
-        c_endo_lv=c_endo_lv,
-        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,
-        b_endo_rv=b_endo_rv,
-        c_endo_rv=c_endo_rv,
-        a_epi_rv=a_epi_rv,
-        b_epi_rv=b_epi_rv,
-        c_epi_rv=c_epi_rv,
-        create_fibers=create_fibers,
-        fiber_angle_endo=fiber_angle_endo,
-        fiber_angle_epi=fiber_angle_epi,
-        fiber_space=fiber_space,
-    )
-    geo.save(outdir / "biv_ellipsoid.bp")
-
-
-@click.command(help="Create BiV ellipsoidal geometry embedded in a torso")
-@click.argument(
-    "outdir",
-    required=True,
-    type=click.Path(
-        file_okay=False,
-        dir_okay=True,
-        writable=True,
-        readable=True,
-        resolve_path=True,
-    ),
-)
-@click.option(
-    "--char-length",
-    default=0.5,
-    type=float,
-    help="Characteristic length of mesh",
-    show_default=True,
-)
-@click.option(
-    "--heart-as-surface/--heart-as-volume",
-    default=False,
-    help="Whether the heart should be a surface of a volume inside the torso",
-    show_default=True,
-)
-@click.option(
-    "--torso-length",
-    default=20,
-    type=float,
-    help="Length of torso in the x-direction",
-    show_default=True,
-)
-@click.option(
-    "--torso-width",
-    default=20,
-    type=float,
-    help="Length of torso in the y-direction",
-    show_default=True,
-)
-@click.option(
-    "--torso-height",
-    default=20,
-    type=float,
-    help="Length of torso in the z-direction",
-    show_default=True,
-)
-@click.option(
-    "--rotation-angle",
-    default=math.pi / 6,
-    type=float,
-    help=(
-        "Angle to rotate the torso in order to object realistic position of the heart in a torso"
-    ),
-    show_default=True,
-)
-@click.option(
-    "--center-lv-x",
-    default=0.0,
-    type=float,
-    help="X-coordinate for the center of the lv",
-    show_default=True,
-)
 @click.option(
-    "--center-lv-y",
-    default=0.0,
-    type=float,
-    help="Y-coordinate for the center of the lv",
-    show_default=True,
-)
-@click.option(
-    "--center-lv-z",
-    default=0.0,
-    type=float,
-    help="Z-coordinate for the center of the lv",
-    show_default=True,
-)
-@click.option(
-    "--a-endo-lv",
-    default=2.5,
-    type=float,
-    help="Dilation of lv endo ellipsoid in the x-direction",
-    show_default=True,
-)
-@click.option(
-    "--b-endo-lv",
-    default=1.0,
-    type=float,
-    help="Dilation of lv endo ellipsoid in the y-direction",
-    show_default=True,
-)
-@click.option(
-    "--c-endo-lv",
-    default=1.0,
-    type=float,
-    help="Dilation of lv endo ellipsoid in the y-direction",
-    show_default=True,
-)
-@click.option(
-    "--a-epi-lv",
-    default=3.0,
-    type=float,
-    help="Dilation of lv epi ellipsoid in the x-direction",
-    show_default=True,
-)
-@click.option(
-    "--b-epi-lv",
-    default=1.5,
-    type=float,
-    help="Dilation of lv epi ellipsoid in the y-direction",
-    show_default=True,
-)
-@click.option(
-    "--c-epi-lv",
-    default=1.5,
-    type=float,
-    help="Dilation of lv epi ellipsoid in the y-direction",
-    show_default=True,
-)
-@click.option(
-    "--center-rv-x",
-    default=0.0,
-    type=float,
-    help="X-coordinate for the center of the rv",
-    show_default=True,
-)
-@click.option(
-    "--center-rv-y",
-    default=0.5,
-    type=float,
-    help="Y-coordinate for the center of the rv",
-    show_default=True,
-)
-@click.option(
-    "--center-rv-z",
-    default=0.0,
-    type=float,
-    help="Z-coordinate for the center of the rv",
-    show_default=True,
-)
-@click.option(
-    "--a-endo-rv",
-    default=3.0,
-    type=float,
-    help="Dilation of rv endo ellipsoid in the x-direction",
-    show_default=True,
-)
-@click.option(
-    "--b-endo-rv",
-    default=1.5,
-    type=float,
-    help="Dilation of rv endo ellipsoid in the y-direction",
-    show_default=True,
-)
-@click.option(
-    "--c-endo-rv",
-    default=1.5,
-    type=float,
-    help="Dilation of rv endo ellipsoid in the y-direction",
-    show_default=True,
-)
-@click.option(
-    "--a-epi-rv",
-    default=4.0,
-    type=float,
-    help="Dilation of rv epi ellipsoid in the x-direction",
-    show_default=True,
-)
-@click.option(
-    "--b-epi-rv",
-    default=2.5,
-    type=float,
-    help="Dilation of rv epi ellipsoid in the y-direction",
-    show_default=True,
-)
-@click.option(
-    "--c-epi-rv",
-    default=2.0,
-    type=float,
-    help="Dilation of rv epi ellipsoid in the z-direction",
-    show_default=True,
-)
-@click.option(
-    "--create-fibers",
-    default=False,
+    "-v",
+    "--verbose",
     is_flag=True,
-    help="If True create analytic fibers",
-    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",
+    help="Enable verbose output",
     show_default=True,
 )
-def biv_ellipsoid_torso(
+def biv_ellipsoid(
     outdir: Path,
-    char_length: float = 0.5,
-    heart_as_surface: bool = True,
-    torso_length: float = 20.0,
-    torso_width: float = 20.0,
-    torso_height: float = 20.0,
-    rotation_angle: float = math.pi / 6,
-    center_lv_x: float = 0.0,
-    center_lv_y: float = 0.0,
-    center_lv_z: float = 0.0,
-    a_endo_lv: float = 2.5,
-    b_endo_lv: float = 1.0,
-    c_endo_lv: float = 1.0,
-    a_epi_lv: float = 3.0,
-    b_epi_lv: float = 1.5,
-    c_epi_lv: float = 1.5,
-    center_rv_x: float = 0.0,
-    center_rv_y: float = 0.5,
-    center_rv_z: float = 0.0,
-    a_endo_rv: float = 3.0,
-    b_endo_rv: float = 1.5,
-    c_endo_rv: float = 1.5,
-    a_epi_rv: float = 4.0,
-    b_epi_rv: float = 2.5,
-    c_epi_rv: float = 2.0,
+    char_length: float = 0.4,  # cm
+    base_cut_z: float = 2.5,
+    box_size: float = 15.0,  # Size of the cutting box
+    rv_wall_thickness: float = 0.4,  # cm
+    lv_wall_thickness: float = 0.5,  # cm
+    rv_offset_x: float = 3.0,
+    lv_radius_x: float = 2.0,
+    lv_radius_y: float = 1.8,
+    lv_radius_z: float = 3.25,
+    rv_radius_x: float = 1.9,
+    rv_radius_y: float = 2.5,
+    rv_radius_z: float = 3.0,
     create_fibers: bool = False,
     fiber_angle_endo: float = -60,
     fiber_angle_epi: float = +60,
     fiber_space: str = "P_1",
+    verbose: bool = False,
 ):
+    init_logging(verbose=verbose)
     outdir = Path(outdir)
     outdir.mkdir(exist_ok=True)
 
-    geo = mesh.biv_ellipsoid_torso(
+    geo = mesh.biv_ellipsoid(
         outdir=outdir,
         char_length=char_length,
-        heart_as_surface=heart_as_surface,
-        torso_length=torso_length,
-        torso_height=torso_height,
-        torso_width=torso_width,
-        rotation_angle=rotation_angle,
-        center_lv_x=center_lv_x,
-        center_lv_y=center_lv_y,
-        center_lv_z=center_lv_z,
-        a_endo_lv=a_endo_lv,
-        b_endo_lv=b_endo_lv,
-        c_endo_lv=c_endo_lv,
-        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,
-        b_endo_rv=b_endo_rv,
-        c_endo_rv=c_endo_rv,
-        a_epi_rv=a_epi_rv,
-        b_epi_rv=b_epi_rv,
-        c_epi_rv=c_epi_rv,
+        base_cut_z=base_cut_z,
+        box_size=box_size,
+        rv_wall_thickness=rv_wall_thickness,
+        lv_wall_thickness=lv_wall_thickness,
+        rv_offset_x=rv_offset_x,
+        lv_radius_x=lv_radius_x,
+        lv_radius_y=lv_radius_y,
+        lv_radius_z=lv_radius_z,
+        rv_radius_x=rv_radius_x,
+        rv_radius_y=rv_radius_y,
+        rv_radius_z=rv_radius_z,
         create_fibers=create_fibers,
         fiber_angle_endo=fiber_angle_endo,
         fiber_angle_epi=fiber_angle_epi,
         fiber_space=fiber_space,
+        verbose=verbose,
     )
-
-    geo.save(outdir / "biv_ellipsoid_torso.bp")
+    geo.save(outdir / "biv_ellipsoid.bp")
 
 
 @click.command(help="Create slab geometry")
@@ -1310,7 +989,6 @@ def gui():
 
 app.add_command(lv_ellipsoid)
 app.add_command(biv_ellipsoid)
-app.add_command(biv_ellipsoid_torso)
 app.add_command(slab)
 app.add_command(slab_in_bath)
 app.add_command(gui)

{cardiac_geometriesx-0.6.1 → cardiac_geometriesx-0.7.0}/src/cardiac_geometries/gui.py

@@ -51,8 +51,6 @@ def load_geometry(folder: str):
 def plot_geometry(geo):
     V = dolfinx.fem.functionspace(geo.mesh, ("Lagrange", 1))
 
-    pv.start_xvfb()
-
     # Plot the mesh with cell tags
     mesh_plotter = pv.Plotter()
     mesh_plotter.background_color = "white"

{cardiac_geometriesx-0.6.1 → cardiac_geometriesx-0.7.0}/src/cardiac_geometries/mesh.py

@@ -211,27 +211,29 @@ def ukb(
     return geo
 
 
+def transform_biv_markers(markers: dict[str, tuple[int, int]]) -> dict[str, list[int]]:
+    return {
+        "base": [markers["BASE"][0]],
+        "lv": [markers["LV_ENDO_FW"][0], markers["LV_SEPTUM"][0]],
+        "rv": [markers["RV_ENDO_FW"][0], markers["RV_SEPTUM"][0]],
+        "epi": [markers["LV_EPI_FW"][0], markers["RV_EPI_FW"][0]],
+    }
+
+
 def biv_ellipsoid(
     outdir: str | Path,
     char_length: float = 0.5,
-    center_lv_x: float = 0.0,
-    center_lv_y: float = 0.0,
-    center_lv_z: float = 0.0,
-    a_endo_lv: float = 2.5,
-    b_endo_lv: float = 1.0,
-    c_endo_lv: float = 1.0,
-    a_epi_lv: float = 3.0,
-    b_epi_lv: float = 1.5,
-    c_epi_lv: float = 1.5,
-    center_rv_x: float = 0.0,
-    center_rv_y: float = 0.5,
-    center_rv_z: float = 0.0,
-    a_endo_rv: float = 3.0,
-    b_endo_rv: float = 1.5,
-    c_endo_rv: float = 1.5,
-    a_epi_rv: float = 4.0,
-    b_epi_rv: float = 2.5,
-    c_epi_rv: float = 2.0,
+    base_cut_z: float = 2.5,
+    box_size: float = 15.0,  # Size of the cutting box
+    rv_wall_thickness: float = 0.4,  # cm
+    lv_wall_thickness: float = 0.5,  # cm
+    rv_offset_x: float = 2.5,
+    lv_radius_x: float = 2.0,
+    lv_radius_y: float = 1.8,
+    lv_radius_z: float = 3.25,
+    rv_radius_x: float = 1.9,
+    rv_radius_y: float = 2.5,
+    rv_radius_z: float = 3.0,
     create_fibers: bool = False,
     fiber_angle_endo: float = 60,
     fiber_angle_epi: float = -60,
@@ -247,42 +249,20 @@ def biv_ellipsoid(
         Directory where to save the results.
     char_length : float, optional
         Characteristic length of mesh, by default 0.5
-    center_lv_y : float, optional
-        X-coordinate for the center of the lv, by default 0.0
-    center_lv_y : float, optional
-        Y-coordinate for the center of the lv, by default 0.0
-    center_lv_z : float, optional
-        Z-coordinate for the center of the lv, by default 0.0
-    a_endo_lv : float, optional
-        Dilation of lv endo ellipsoid in the x-direction, by default 2.5
-    b_endo_lv : float, optional
-       Dilation of lv endo ellipsoid in the y-direction, by default 1.0
-    c_endo_lv : float, optional
-       Dilation of lv endo ellipsoid in the z-direction, by default 1.0
-    a_epi_lv : float, optional
-        Dilation of lv epi ellipsoid in the x-direction, by default 3.0
-    b_epi_lv : float, optional
-        Dilation of lv epi ellipsoid in the y-direction, by default 1.5
-    c_epi_lv : float, optional
-        Dilation of lv epi ellipsoid in the z-direction, by default 1.5
-    center_rv_x : float, optional
-        X-coordinate for the center of the rv, by default 0.0
-    center_rv_y : float, optional
-        Y-coordinate for the center of the rv, by default 0.5
-    center_rv_z : float, optional
-        Z-coordinate for the center of the rv, by default 0.0
-    a_endo_rv : float, optional
-       Dilation of rv endo ellipsoid in the x-direction, by default 3.0
-    b_endo_rv : float, optional
-       Dilation of rv endo ellipsoid in the y-direction, by default 1.5
-    c_endo_rv : float, optional
-       Dilation of rv endo ellipsoid in the z-direction, by default 1.5
-    a_epi_rv : float, optional
-        Dilation of rv epi ellipsoid in the x-direction, by default 4.0
-    b_epi_rv : float, optional
-        Dilation of rv epi ellipsoid in the y-direction, by default 2.5
-    c_epi_rv : float, optional
-        Dilation of rv epi ellipsoid in the z-direction, by default 2.0
+    box_size : float, optional
+        Size of the cutting box, by default 15.0
+    lv_radius_x : float, optional
+        Radius of the left ventricle in the x-direction, by default 2.0
+    lv_radius_y : float, optional
+        Radius of the left ventricle in the y-direction, by default 1.8
+    lv_radius_z : float, optional
+        Radius of the left ventricle in the z-direction, by default 3.25
+    rv_radius_x : float, optional
+        Radius of the right ventricle in the x-direction, by default 1.9
+    rv_radius_y : float, optional
+        Radius of the right ventricle in the y-direction, by default 2.5
+    rv_radius_z : float, optional
+        Radius of the right ventricle in the z-direction, by default 3.0
     create_fibers : bool, optional
         If True create analytic fibers, by default False
     fiber_angle_endo : float, optional
@@ -311,24 +291,17 @@ def biv_ellipsoid(
             json.dump(
                 {
                     "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,
-                    "b_endo_lv": b_endo_lv,
-                    "c_endo_lv": c_endo_lv,
-                    "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,
-                    "b_endo_rv": b_endo_rv,
-                    "c_endo_rv": c_endo_rv,
-                    "a_epi_rv": a_epi_rv,
-                    "b_epi_rv": b_epi_rv,
-                    "c_epi_rv": c_epi_rv,
+                    "base_cut_z": base_cut_z,
+                    "box_size": box_size,
+                    "rv_wall_thickness": rv_wall_thickness,
+                    "lv_wall_thickness": lv_wall_thickness,
+                    "rv_offset_x": rv_offset_x,
+                    "lv_radius_x": lv_radius_x,
+                    "lv_radius_y": lv_radius_y,
+                    "lv_radius_z": lv_radius_z,
+                    "rv_radius_x": rv_radius_x,
+                    "rv_radius_y": rv_radius_y,
+                    "rv_radius_z": rv_radius_z,
                     "create_fibers": create_fibers,
                     "fiber_angle_endo": fiber_angle_endo,
                     "fiber_angle_epi": fiber_angle_epi,
@@ -345,24 +318,17 @@ def biv_ellipsoid(
         cgc.biv_ellipsoid(
             mesh_name=mesh_name.as_posix(),
             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,
-            b_endo_lv=b_endo_lv,
-            c_endo_lv=c_endo_lv,
-            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,
-            b_endo_rv=b_endo_rv,
-            c_endo_rv=c_endo_rv,
-            a_epi_rv=a_epi_rv,
-            b_epi_rv=b_epi_rv,
-            c_epi_rv=c_epi_rv,
+            base_cut_z=base_cut_z,
+            box_size=box_size,
+            rv_wall_thickness=rv_wall_thickness,
+            lv_wall_thickness=lv_wall_thickness,
+            rv_offset_x=rv_offset_x,
+            lv_radius_x=lv_radius_x,
+            lv_radius_y=lv_radius_y,
+            lv_radius_z=lv_radius_z,
+            rv_radius_x=rv_radius_x,
+            rv_radius_y=rv_radius_y,
+            rv_radius_z=rv_radius_z,
             verbose=verbose,
         )
     comm.barrier()
@@ -382,10 +348,12 @@ def biv_ellipsoid(
             )
             raise ImportError(msg)
 
+        ldrb_markers = transform_biv_markers(geometry.markers)
+
         system = ldrb.dolfinx_ldrb(
             mesh=geometry.mesh,
             ffun=geometry.ffun,
-            markers=geometry.markers,
+            markers=ldrb_markers,
             alpha_endo_lv=fiber_angle_endo,
             alpha_epi_lv=fiber_angle_epi,
             beta_endo_lv=0,
@@ -403,218 +371,6 @@ def biv_ellipsoid(
     return geo
 
 
-def biv_ellipsoid_torso(
-    outdir: str | Path,
-    char_length: float = 0.5,
-    heart_as_surface: bool = False,
-    torso_length: float = 20.0,
-    torso_width: float = 20.0,
-    torso_height: float = 20.0,
-    rotation_angle: float = math.pi / 6,
-    center_lv_x: float = 0.0,
-    center_lv_y: float = 0.0,
-    center_lv_z: float = 0.0,
-    a_endo_lv: float = 2.5,
-    b_endo_lv: float = 1.0,
-    c_endo_lv: float = 1.0,
-    a_epi_lv: float = 3.0,
-    b_epi_lv: float = 1.5,
-    c_epi_lv: float = 1.5,
-    center_rv_x: float = 0.0,
-    center_rv_y: float = 0.5,
-    center_rv_z: float = 0.0,
-    a_endo_rv: float = 3.0,
-    b_endo_rv: float = 1.5,
-    c_endo_rv: float = 1.5,
-    a_epi_rv: float = 4.0,
-    b_epi_rv: float = 2.5,
-    c_epi_rv: float = 2.0,
-    create_fibers: bool = False,
-    fiber_angle_endo: float = 60,
-    fiber_angle_epi: float = -60,
-    fiber_space: str = "P_1",
-    verbose: bool = False,
-    comm: MPI.Comm = MPI.COMM_WORLD,
-) -> Geometry:
-    """Create BiV ellipsoidal geometry
-
-    Parameters
-    ----------
-    outdir : str | Path
-        Directory where to save the results.
-    char_length : float, optional
-        Characteristic length of mesh, by default 0.5
-    heart_as_surface: bool
-        If true, create the heart as a a surface inside the torso,
-        otherwise let the heart be a volume, by default True.
-    torso_length : float, optional
-        Length of torso in the x-direction, by default 20.0
-    torso_width : float, optional
-        Length of torso in the y-direction, by default 20.0
-    torso_height : float, optional
-        Length of torso in the z-direction, by default 20.0
-    rotation_angle: float, optional
-        Angle to rotate the torso in order to object realistic position of
-        the heart in a torso, by default pi / 6
-    center_lv_x : float, optional
-        X-coordinate for the center of the lv, by default 0.0
-    center_lv_y : float, optional
-        Y-coordinate for the center of the lv, by default 0.0
-    center_lv_z : float, optional
-        Z-coordinate for the center of the lv, by default 0.0
-    a_endo_lv : float, optional
-        Dilation of lv endo ellipsoid in the x-direction, by default 2.5
-    b_endo_lv : float, optional
-       Dilation of lv endo ellipsoid in the y-direction, by default 1.0
-    c_endo_lv : float, optional
-       Dilation of lv endo ellipsoid in the z-direction, by default 1.0
-    a_epi_lv : float, optional
-        Dilation of lv epi ellipsoid in the x-direction, by default 3.0
-    b_epi_lv : float, optional
-        Dilation of lv epi ellipsoid in the y-direction, by default 1.5
-    c_epi_lv : float, optional
-        Dilation of lv epi ellipsoid in the z-direction, by default 1.5
-    center_rv_x : float, optional
-        X-coordinate for the center of the rv, by default 0.0
-    center_rv_y : float, optional
-        Y-coordinate for the center of the rv, by default 0.5
-    center_rv_z : float, optional
-        Z-coordinate for the center of the rv, by default 0.0
-    a_endo_rv : float, optional
-       Dilation of rv endo ellipsoid in the x-direction, by default 3.0
-    b_endo_rv : float, optional
-       Dilation of rv endo ellipsoid in the y-direction, by default 1.5
-    c_endo_rv : float, optional
-       Dilation of rv endo ellipsoid in the z-direction, by default 1.5
-    a_epi_rv : float, optional
-        Dilation of rv epi ellipsoid in the x-direction, by default 4.0
-    b_epi_rv : float, optional
-        Dilation of rv epi ellipsoid in the y-direction, by default 2.5
-    c_epi_rv : float, optional
-        Dilation of rv epi ellipsoid in the z-direction, by default 2.0
-    create_fibers : bool, optional
-        If True create analytic fibers, by default False
-    fiber_angle_endo : float, optional
-        Angle for the endocardium, by default 60
-    fiber_angle_epi : float, optional
-        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
-    comm : MPI.Comm, optional
-        MPI communicator, by default MPI.COMM_WORLD
-
-    Returns
-    -------
-    cardiac_geometries.geometry.Geometry
-        A Geometry with the mesh, markers, markers functions and fibers.
-
-    """
-    outdir = Path(outdir)
-    mesh_name = outdir / "biv_ellipsoid_torso.msh"
-    if comm.rank == 0:
-        outdir.mkdir(exist_ok=True, parents=True)
-
-        with open(outdir / "info.json", "w") as f:
-            json.dump(
-                {
-                    "char_length": char_length,
-                    "heart_as_surface": heart_as_surface,
-                    "torso_length": torso_length,
-                    "torso_width": torso_width,
-                    "torso_height": torso_height,
-                    "rotation_angle": rotation_angle,
-                    "center_lv_x": center_lv_x,
-                    "center_lv_y": center_lv_y,
-                    "center_lv_z": center_lv_z,
-                    "a_endo_lv": a_endo_lv,
-                    "b_endo_lv": b_endo_lv,
-                    "c_endo_lv": c_endo_lv,
-                    "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,
-                    "b_endo_rv": b_endo_rv,
-                    "c_endo_rv": c_endo_rv,
-                    "a_epi_rv": a_epi_rv,
-                    "b_epi_rv": b_epi_rv,
-                    "c_epi_rv": c_epi_rv,
-                    "create_fibers": create_fibers,
-                    "fiber_angle_endo": fiber_angle_endo,
-                    "fiber_angle_epi": fiber_angle_epi,
-                    "fiber_space": fiber_space,
-                    "mesh_type": "biv",
-                    "cardiac_geometry_version": __version__,
-                    "timestamp": datetime.datetime.now().isoformat(),
-                },
-                f,
-                indent=2,
-                default=utils.json_serial,
-            )
-
-        cgc.biv_ellipsoid_torso(
-            mesh_name=mesh_name.as_posix(),
-            char_length=char_length,
-            heart_as_surface=heart_as_surface,
-            torso_length=torso_length,
-            torso_height=torso_height,
-            torso_width=torso_width,
-            rotation_angle=rotation_angle,
-            center_lv_x=center_lv_x,
-            center_lv_y=center_lv_y,
-            center_lv_z=center_lv_z,
-            a_endo_lv=a_endo_lv,
-            b_endo_lv=b_endo_lv,
-            c_endo_lv=c_endo_lv,
-            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,
-            b_endo_rv=b_endo_rv,
-            c_endo_rv=c_endo_rv,
-            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)
-
-    if comm.rank == 0:
-        with open(outdir / "markers.json", "w") as f:
-            json.dump(geometry.markers, f, default=utils.json_serial)
-    comm.barrier()
-
-    if create_fibers:
-        if heart_as_surface:
-            logger.warning("Can only create fibers when heart is a volume.")
-        else:
-            raise NotImplementedError("Fibers not implemented yet for biv ellipsoid.")
-            # from .fibers._biv_ellipsoid import create_biv_in_torso_fibers
-
-            # create_biv_in_torso_fibers(
-            #     mesh=geometry.mesh,
-            #     ffun=geometry.marker_functions.ffun,
-            #     cfun=geometry.marker_functions.cfun,
-            #     markers=geometry.markers,
-            #     fiber_space=fiber_space,
-            #     alpha_endo=fiber_angle_endo,
-            #     alpha_epi=fiber_angle_epi,
-            #     outdir=outdir,
-            # )
-
-    geo = Geometry.from_folder(comm=comm, folder=outdir)
-    return geo
-
-
 def lv_ellipsoid(
     outdir: Path | str,
     r_short_endo: float = 7.0,

{cardiac_geometriesx-0.6.1 → cardiac_geometriesx-0.7.0}/src/cardiac_geometries/utils.py

@@ -14,6 +14,11 @@ from dolfinx.graph import adjacencylist
 from packaging.version import Version
 from structlog import get_logger
 
+try:
+    import dolfinx.io.gmsh as gmshio
+except ImportError:
+    import dolfinx.io.gmshio as gmshio  # type: ignore[import]
+
 logger = get_logger()
 
 quads = ("Quadrature", "Q", "Quad", "quadrature", "q", "quad")
@@ -90,8 +95,8 @@ def model_to_mesh(
     if comm.rank == rank:
         assert model is not None, "Gmsh model is None on rank responsible for mesh creation."
         # Get mesh geometry and mesh topology for each element
-        x = dolfinx.io.gmshio.extract_geometry(model)
-        topologies = dolfinx.io.gmshio.extract_topology_and_markers(model)
+        x = gmshio.extract_geometry(model)
+        topologies = gmshio.extract_topology_and_markers(model)
 
         # Extract Gmsh cell id, dimension of cell and number of nodes to
         # cell for each
@@ -170,8 +175,8 @@ def model_to_mesh(
             vertex_values = np.empty((0,), dtype=np.int32)
 
     # Create distributed mesh
-    ufl_domain = dolfinx.io.gmshio.ufl_mesh(cell_id, gdim, dtype=dtype)
-    gmsh_cell_perm = dolfinx.io.gmshio.cell_perm_array(
+    ufl_domain = gmshio.ufl_mesh(cell_id, gdim, dtype=dtype)
+    gmsh_cell_perm = gmshio.cell_perm_array(
         dolfinx.cpp.mesh.to_type(str(ufl_domain.ufl_cell())), num_nodes
     )
     cells = cells[:, gmsh_cell_perm].copy()
@@ -207,7 +212,7 @@ def model_to_mesh(
         facet_type = dolfinx.cpp.mesh.cell_entity_type(
             dolfinx.cpp.mesh.to_type(str(ufl_domain.ufl_cell())), tdim - 1, 0
         )
-        gmsh_facet_perm = dolfinx.io.gmshio.cell_perm_array(facet_type, num_facet_nodes)
+        gmsh_facet_perm = gmshio.cell_perm_array(facet_type, num_facet_nodes)
         marked_facets = marked_facets[:, gmsh_facet_perm]
 
         local_entities, local_values = distribute_entity_data(
@@ -217,7 +222,7 @@ def model_to_mesh(
         mesh.topology.create_connectivity(topology.dim - 1, tdim)
         adj = adjacencylist(local_entities)
 
-        ft = dolfinx.io.gmshio.meshtags_from_entities(
+        ft = gmshio.meshtags_from_entities(
             mesh, tdim - 1, adj, local_values.astype(np.int32, copy=False)
         )
         ft.name = "Facet tags"
@@ -231,7 +236,7 @@ def model_to_mesh(
         edge_type = dolfinx.cpp.mesh.cell_entity_type(
             dolfinx.cpp.mesh.to_type(str(ufl_domain.ufl_cell())), tdim - 2, 0
         )
-        gmsh_edge_perm = dolfinx.io.gmshio.cell_perm_array(edge_type, num_edge_nodes)
+        gmsh_edge_perm = gmshio.cell_perm_array(edge_type, num_edge_nodes)
         marked_edges = marked_edges[:, gmsh_edge_perm]
 
         local_entities, local_values = distribute_entity_data(
@@ -239,7 +244,7 @@ def model_to_mesh(
         )
         mesh.topology.create_connectivity(topology.dim - 2, tdim)
         adj = adjacencylist(local_entities)
-        et = dolfinx.io.gmshio.meshtags_from_entities(
+        et = gmshio.meshtags_from_entities(
             mesh, tdim - 2, adj, local_values.astype(np.int32, copy=False)
         )
         et.name = "Edge tags"
@@ -253,7 +258,7 @@ def model_to_mesh(
         vertex_type = dolfinx.cpp.mesh.cell_entity_type(
             dolfinx.cpp.mesh.to_type(str(ufl_domain.ufl_cell())), tdim - 3, 0
         )
-        gmsh_vertex_perm = dolfinx.io.gmshio.cell_perm_array(vertex_type, num_vertex_nodes)
+        gmsh_vertex_perm = gmshio.cell_perm_array(vertex_type, num_vertex_nodes)
         marked_vertices = marked_vertices[:, gmsh_vertex_perm]
 
         local_entities, local_values = distribute_entity_data(
@@ -261,7 +266,7 @@ def model_to_mesh(
         )
         mesh.topology.create_connectivity(topology.dim - 3, tdim)
         adj = adjacencylist(local_entities)
-        vt = dolfinx.io.gmshio.meshtags_from_entities(
+        vt = gmshio.meshtags_from_entities(
             mesh, tdim - 3, adj, local_values.astype(np.int32, copy=False)
         )
         vt.name = "Vertex tags"
@@ -281,7 +286,7 @@ def parse_element(
     """
 
     family_str, degree_str = space_string.split("_")
-    kwargs = {"degree": int(degree_str), "cell": mesh.ufl_cell().cellname()}
+    kwargs = {"degree": int(degree_str), "cell": mesh.basix_cell()}
     if dim > 1:
         if family_str in quads:
             kwargs["value_shape"] = (dim,)
@@ -425,7 +430,7 @@ def gmsh2dolfin(comm: MPI.Intracomm, msh_file, rank: int = 0) -> GMshGeometry:
     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)
+        mesh_data = gmshio.read_from_msh(comm=comm, filename=msh_file)
         mesh = mesh_data.mesh
         markers_ = mesh_data.physical_groups
         ct = mesh_data.cell_tags

{cardiac_geometriesx-0.6.1 → cardiac_geometriesx-0.7.0/src/cardiac_geometriesx.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cardiac-geometriesx
-Version: 0.6.1
+Version: 0.7.0
 Summary: A python library for cardiac geometries
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License: MIT
@@ -29,11 +29,14 @@ Provides-Extra: docs
 Requires-Dist: jupyter-book; extra == "docs"
 Requires-Dist: jupytext; extra == "docs"
 Requires-Dist: jupyter; extra == "docs"
-Requires-Dist: pyvista[all]>=0.43.0; extra == "docs"
+Requires-Dist: pyvista[all]>=0.45.0; extra == "docs"
+Requires-Dist: vtk>=9.5.0; extra == "docs"
 Requires-Dist: trame-vuetify; extra == "docs"
 Requires-Dist: ipywidgets; extra == "docs"
 Requires-Dist: fenicsx-ldrb; extra == "docs"
 Requires-Dist: ukb-atlas; extra == "docs"
+Requires-Dist: sphinx-codeautolink; extra == "docs"
+Requires-Dist: sphinx-copybutton; extra == "docs"
 Provides-Extra: test
 Requires-Dist: pre-commit; extra == "test"
 Requires-Dist: pytest; extra == "test"

{cardiac_geometriesx-0.6.1 → cardiac_geometriesx-0.7.0}/src/cardiac_geometriesx.egg-info/requires.txt

@@ -17,11 +17,14 @@ wheel
 jupyter-book
 jupytext
 jupyter
-pyvista[all]>=0.43.0
+pyvista[all]>=0.45.0
+vtk>=9.5.0
 trame-vuetify
 ipywidgets
 fenicsx-ldrb
 ukb-atlas
+sphinx-codeautolink
+sphinx-copybutton
 
 [gui]
 streamlit

{cardiac_geometriesx-0.6.1 → cardiac_geometriesx-0.7.0}/tests/test_cli.py

@@ -81,9 +81,8 @@ def test_biv_fibers(tmp_path: Path):
     [
         cli.slab_in_bath,
         cli.biv_ellipsoid,
-        cli.biv_ellipsoid_torso,
     ],
-    ids=["slab_in_bath", "biv_ellipsoid", "biv_ellipsoid_torso"],
+    ids=["slab_in_bath", "biv_ellipsoid"],
 )
 @pytest.mark.skipif(gmsh.__version__ == "4.14.0", reason="GMSH 4.14.0 has a bug with fuse")
 def test_script_no_fibers(script, tmp_path: Path):

{cardiac_geometriesx-0.6.1 → cardiac_geometriesx-0.7.0}/tests/test_save_load.py

@@ -132,7 +132,7 @@ def test_load_from_folder_mesh_and_function(tmp_path):
         mesh,
         basix.ufl.element(
             family="Lagrange",
-            cell=mesh.ufl_cell().cellname(),
+            cell=mesh.basix_cell(),
             degree=1,
             discontinuous=False,
             shape=(3,),