cardiac-geometriesx 0.4.7__tar.gz → 0.10.5__tar.gz

{cardiac_geometriesx-0.4.7/src/cardiac_geometriesx.egg-info → cardiac_geometriesx-0.10.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cardiac-geometriesx
-Version: 0.4.7
+Version: 0.10.5
 Summary: A python library for cardiac geometries
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License: MIT
@@ -9,12 +9,12 @@ Keywords: cardiac,geometry
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3 :: Only
-Requires-Python: >=3.8
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: fenics-dolfinx>=0.8.0
+Requires-Dist: fenics-dolfinx>=0.9.0
 Requires-Dist: structlog
-Requires-Dist: cardiac-geometries-core
+Requires-Dist: cardiac-geometries-core>=0.4
 Requires-Dist: rich-click
 Requires-Dist: adios4dolfinx
 Requires-Dist: scifem
@@ -26,14 +26,17 @@ Requires-Dist: pre-commit; extra == "dev"
 Requires-Dist: twine; extra == "dev"
 Requires-Dist: wheel; extra == "dev"
 Provides-Extra: docs
-Requires-Dist: jupyter-book; extra == "docs"
+Requires-Dist: jupyter-book<2.0; 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"
@@ -77,7 +80,11 @@ To install the package you can use `pip`
 ```
 python3 -m pip install cardiac-geometriesx
 ```
-however, this assumes that you already have `dolfinx` pre-installed. You can also use the provided docker image e.g
+however, this assumes that you already have `dolfinx` pre-installed. You can also use `conda`
+```
+conda install -c conda-forge cardiac-geometriesx
+```
+or the provided docker image
 ```
 docker pull ghcr.io/computationalphysiology/cardiac-geometriesx:latest
 ```

{cardiac_geometriesx-0.4.7 → cardiac_geometriesx-0.10.5}/README.md

@@ -26,7 +26,11 @@ To install the package you can use `pip`
 ```
 python3 -m pip install cardiac-geometriesx
 ```
-however, this assumes that you already have `dolfinx` pre-installed. You can also use the provided docker image e.g
+however, this assumes that you already have `dolfinx` pre-installed. You can also use `conda`
+```
+conda install -c conda-forge cardiac-geometriesx
+```
+or the provided docker image
 ```
 docker pull ghcr.io/computationalphysiology/cardiac-geometriesx:latest
 ```

{cardiac_geometriesx-0.4.7 → cardiac_geometriesx-0.10.5}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cardiac-geometriesx"
-version = "0.4.7"
+version = "0.10.5"
 description = "A python library for cardiac geometries"
 authors = [{name = "Henrik Finsberg", email = "henriknf@simula.no"}]
 license = {text = "MIT"}
@@ -15,11 +15,11 @@ classifiers = [
 ]
 keywords = ["cardiac", "geometry"]
 urls = {Homepage = "https://github.com/finsberg/cardiac-geometriesx" }
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 dependencies = [
-    "fenics-dolfinx>=0.8.0",
+    "fenics-dolfinx>=0.9.0",
     "structlog",
-    "cardiac-geometries-core",
+    "cardiac-geometries-core>=0.4",
     "rich-click",
     "adios4dolfinx",
     "scifem",
@@ -39,14 +39,17 @@ dev = [
     "wheel",
 ]
 docs = [
-    "jupyter-book",
+    "jupyter-book<2.0",
     "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 = "0.4.7"
+current_version = "0.10.5"
 
 
 [[tool.bumpversion.files]]

{cardiac_geometriesx-0.4.7 → cardiac_geometriesx-0.10.5}/src/cardiac_geometries/__init__.py

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

cardiac_geometriesx-0.10.5/src/cardiac_geometries/aha.py

@@ -0,0 +1,240 @@
+import dolfinx
+import numpy as np
+
+
+def focal(r_long_endo: float | np.ndarray, r_short_endo: float | np.ndarray) -> float | np.ndarray:
+    """Calculate the focal distance for a prolate ellipsoid
+
+    Parameters
+    ----------
+    r_long_endo : float | np.ndarray
+        Radius of the long axis of the endocardium
+    r_short_endo : float | np.ndarray
+        Radius of the short axis of the endocardium"
+
+    Returns
+    -------
+    float | np.ndarray
+        The focal distance for the prolate ellipsoid
+    """
+    return np.sqrt(r_long_endo**2 - r_short_endo**2)
+
+
+def full_arctangent(x, y) -> float | np.ndarray:
+    """Compute the full arctangent in [0, 2pi]
+
+    Parameters
+    ----------
+    x : float | np.ndarray
+    y : float | np.ndarray
+
+    Returns
+    -------
+    float | np.ndarray
+        The angle in [0, 2pi]
+    """
+    t = np.arctan2(x, y)
+    return np.where(t < 0, t + 2 * np.pi, t)
+
+
+def cartesian_to_prolate_ellipsoidal(
+    x: float | np.ndarray,
+    y: float | np.ndarray,
+    z: float | np.ndarray,
+    a: float | np.ndarray,
+) -> tuple[float | np.ndarray, float | np.ndarray, float | np.ndarray]:
+    """Convert Cartesian coordinates to prolate ellipsoidal coordinates
+
+    Parameters
+    ----------
+    x : float | np.ndarray
+    y : float | np.ndarray
+    z : float | np.ndarray
+    a : float | np.ndarray
+
+    Returns
+    -------
+    tuple[float | np.ndarray, float | np.ndarray, float | np.ndarray]
+        The prolate ellipsoidal coordinates (nu, mu, phi)
+    """
+    b1 = np.sqrt((x + a) ** 2 + y**2 + z**2)
+    b2 = np.sqrt((x - a) ** 2 + y**2 + z**2)
+
+    sigma = 1 / (2.0 * a) * (b1 + b2)
+    tau = 1 / (2.0 * a) * (b1 - b2)
+    phi = full_arctangent(z, y)
+    nu = np.arccosh(sigma)
+    mu = np.arccos(tau)
+    return nu, mu, phi
+
+
+def get_level(region: int, mu: np.ndarray | float, mu_base: float, dmu: float) -> np.ndarray | bool:
+    """Get the level set for a given AHA region.
+
+    Notes
+    -----
+    The regions are defined as follows:
+    - Regions 1-6: Basal (mu_base <= mu <= mu_base + dmu)
+    - Regions 7-12: Midventricular (mu_base + dmu < mu <= mu_base + 2 * dmu)
+    - Regions 13-16: Apical (mu_base + 2 * dmu < mu <= mu_base + 3 * dmu)
+    - Region 17: Apex (mu > mu_base + 3 * dmu)
+    This function returns a boolean array indicating whether
+    each mu value belongs to the specified region.
+
+    Parameters
+    ----------
+    region : int
+        The AHA region (1-17)
+    mu : np.ndarray | float
+        The mu coordinate(s)
+    mu_base : float
+        The base value of mu for segmentation
+    dmu : float
+        The segmentation width
+    Returns
+    -------
+    np.ndarray | bool
+        The level set for the given AHA region
+    """
+    if 1 <= region <= 6:
+        return np.logical_and(mu_base <= mu, mu <= mu_base + dmu)
+    elif 7 <= region <= 12:
+        return np.logical_and(mu_base + dmu < mu, mu <= mu_base + 2 * dmu)
+    elif 13 <= region <= 16:
+        return np.logical_and(mu_base + 2 * dmu < mu, mu <= mu_base + 3 * dmu)
+    else:
+        return mu > mu_base + 3 * dmu
+
+
+def get_sector(region: int, phi: np.ndarray | float) -> np.ndarray | bool:
+    if region in (1, 7):
+        return np.logical_and(0 < phi, phi <= np.pi / 3)
+    elif region in (2, 8):
+        return np.logical_and(np.pi / 3 < phi, phi <= 2 * np.pi / 3)
+    elif region in (3, 9):
+        return np.logical_and(2 * np.pi / 3 < phi, phi <= np.pi)
+    elif region in (4, 10):
+        return np.logical_and(np.pi < phi, phi <= 4 * np.pi / 3)
+    elif region in (5, 11):
+        return np.logical_and(4 * np.pi / 3 < phi, phi <= 5 * np.pi / 3)
+    elif region in (6, 12):
+        return np.logical_and(5 * np.pi / 3 < phi, phi <= 2 * np.pi)
+    elif region == 13:
+        return np.logical_and(0 < phi, phi <= np.pi / 2)
+    elif region == 14:
+        return np.logical_and(np.pi / 2 < phi, phi <= np.pi)
+    elif region == 15:
+        return np.logical_and(np.pi < phi, phi <= 3 * np.pi / 2)
+    elif region == 16:
+        return np.logical_and(3 * np.pi / 2 < phi, phi <= 2 * np.pi)
+    else:
+        # 17 APEX
+        return np.ones_like(phi, dtype=bool)
+
+
+def find_region_entities(
+    mu: np.ndarray, phi: np.ndarray, mu_base: float, region: int, dmu: float
+) -> np.ndarray:
+    """Find the entities belonging to a given AHA region.
+
+    Parameters
+    ----------
+    mu : np.ndarray
+        The mu coordinate(s)
+    phi : np.ndarray
+        The phi coordinate(s)
+    mu_base : float
+        The base value of mu for segmentation
+    region : int
+        The AHA region (1-17)
+    dmu : float
+        The segmentation width
+
+    Returns
+    -------
+    np.ndarray
+        The indices of entities belonging to the specified AHA region
+    """
+    level = get_level(region=region, mu=mu, mu_base=mu_base, dmu=dmu)
+    sector = get_sector(region=region, phi=phi)
+    return np.where(np.logical_and(level, sector))[0]
+
+
+def lv_aha(
+    mesh: dolfinx.mesh.Mesh,
+    r_long_endo: float,
+    r_short_endo: float,
+    mu_base: float,
+    dmu_factor: float = 1 / 4,
+) -> tuple[dolfinx.mesh.MeshTags, dict[str, tuple[int, int]]]:
+    """Generate AHA segments for idealized LV ellipsoid
+
+    Parameters
+    ----------
+    mesh : dolfinx.mesh.Mesh
+        The LV ellipsoidal mesh
+    r_long_endo : float
+        Radius of the long axis of the endocardium
+    r_short_endo : float
+        Radius of the short axis of the endocardium
+    mu_base : float
+        Base value of mu for segmentation
+    dmu_factor : float, optional
+        Factor to determine the segmentation width, by default 1/4
+
+    Returns
+    -------
+    tuple[dolfinx.mesh.MeshTags, dict[str, tuple[int, int]]]
+        A tuple with the MeshTags object containing the cell tags
+        for the AHA segments and a dictionary with the marker
+        names and corresponding (tag, dim) values
+    """
+    assert mesh.topology.dim == 3, "AHA segmentation only implemented for 3D geometries"
+    foc = focal(r_long_endo=r_long_endo, r_short_endo=r_short_endo)
+    mu_base = abs(mu_base)
+    x, y, z = dolfinx.mesh.compute_midpoints(
+        mesh,
+        3,
+        entities=np.arange(mesh.topology.index_map(mesh.topology.dim).size_local, dtype=np.int32),
+    ).T
+
+    dmu = (np.pi - mu_base) * dmu_factor
+    _, mu, phi = cartesian_to_prolate_ellipsoidal(x, y, z, a=foc)
+    entities = [
+        find_region_entities(mu=mu, phi=phi, mu_base=mu_base, region=region, dmu=dmu)
+        for region in range(1, 18)
+    ]
+
+    values = [np.full(len(e), i + 1, dtype=np.int32) for i, e in enumerate(entities)]
+
+    cell_tags = dolfinx.mesh.meshtags(
+        mesh,
+        3,
+        np.hstack(entities),
+        np.hstack(values),
+    )
+
+    markers = {}
+    i = 1
+
+    for level in ["BASAL", "MID", "APICAL"]:
+        for sector in [
+            "ANTERIOR",
+            "ANTEROSEPTAL",
+            "SEPTAL",
+            "INFERIOR",
+            "POSTERIOR",
+            "LATERAL",
+        ]:
+            if level == "APICAL" and sector in ("ANTEROSEPTAL", "POSTERIOR"):
+                continue
+
+            markers["-".join((level, sector))] = (i, 3)
+            i += 1
+
+    markers["APEX"] = (17, 3)
+
+    return cell_tags, markers
+
+
+def biv_aha(): ...