cardiac-geometriesx 0.4.1__py3-none-any.whl → 0.4.3__py3-none-any.whl

cardiac_geometries/fibers/lv_ellipsoid.py

@@ -8,7 +8,12 @@ from . import utils
 
 
 def mu_theta(
-    x: np.ndarray, y: np.ndarray, z: np.ndarray, long_axis: int = 0
+    x: np.ndarray,
+    y: np.ndarray,
+    z: np.ndarray,
+    rs: np.ndarray,
+    rl: np.ndarray,
+    long_axis: int = 0,
 ) -> tuple[np.ndarray, np.ndarray, list[int]]:
     """Get the angles mu and theta from the coordinates x, y, z
     given the long axis.
@@ -21,6 +26,10 @@ def mu_theta(
         The y-coordinates
     z : np.ndarray
         The z-coordinates
+    rs : np.ndarray
+        The short radius
+    rl : np.ndarray
+        The long radius
     long_axis : int, optional
         The long axis, by default 0 (x-axis)
 
@@ -35,18 +44,18 @@ def mu_theta(
         If the long axis is not 0, 1 or 2
     """
     if long_axis == 0:
-        a = np.sqrt(y**2 + z**2)
-        b = x
+        a = np.sqrt(y**2 + z**2) / rs
+        b = x / rl
         theta = np.pi - np.arctan2(z, -y)
         perm = [0, 1, 2]
     elif long_axis == 1:
-        a = np.sqrt(x**2 + z**2)
-        b = y
+        a = np.sqrt(x**2 + z**2) / rs
+        b = y / rl
         theta = np.pi - np.arctan2(z, -x)
         perm = [1, 0, 2]
     elif long_axis == 2:
-        a = np.sqrt(x**2 + y**2)
-        b = z
+        a = np.sqrt(x**2 + y**2) / rs
+        b = z / rl
         theta = np.pi - np.arctan2(x, -y)
         perm = [2, 1, 0]
     else:
@@ -120,7 +129,7 @@ def compute_system(
     y = dof_coordinates[:, 1]
     z = dof_coordinates[:, 2]
 
-    mu, theta, perm = mu_theta(x, y, z, long_axis=long_axis)
+    mu, theta, perm = mu_theta(x, y, z, rs, rl, long_axis=long_axis)
 
     e_t = np.array(
         [

cardiac_geometries/fibers/utils.py

@@ -25,6 +25,7 @@ def save_microstructure(
     if len(functions) == 0:
         return
     # Save for paraview visualization
+
     if functions[0].function_space.ufl_element().family_name == "quadrature":
         from scifem.xdmf import create_pointcloud
 
@@ -35,8 +36,8 @@ def save_microstructure(
                 mesh.comm, Path(outdir) / "microstructure-viz.bp", functions, engine="BP4"
             ) as file:
                 file.write(0.0)
-        except RuntimeError:
-            pass
+        except RuntimeError as ex:
+            print(f"Failed to write microstructure: {ex}")
 
     # Save with proper function space
     filename = Path(outdir) / "microstructure.bp"

cardiac_geometries/geometry.py

@@ -5,9 +5,11 @@ from pathlib import Path
 
 from mpi4py import MPI
 
+import adios2
 import adios4dolfinx
 import dolfinx
 import numpy as np
+from packaging.version import Version
 
 from . import utils
 
@@ -31,12 +33,16 @@ class Geometry:
         self.mesh.comm.barrier()
         adios4dolfinx.write_mesh(mesh=self.mesh, filename=path)
 
-        adios4dolfinx.write_attributes(
-            comm=self.mesh.comm,
-            filename=path,
-            name="markers",
-            attributes={k: np.array(v, dtype=np.uint8) for k, v in self.markers.items()},
-        )
+        if Version(np.__version__) <= Version("2.11") or Version(adios2.__version__) >= Version(
+            "2.10.2"
+        ):
+            # This is broken in adios < 2.10.2 and numpy >= 2.11
+            adios4dolfinx.write_attributes(
+                comm=self.mesh.comm,
+                filename=path,
+                name="markers",
+                attributes={k: np.array(v, dtype=np.uint8) for k, v in self.markers.items()},
+            )
 
         if self.cfun is not None:
             adios4dolfinx.write_meshtags(
@@ -52,31 +58,34 @@ class Geometry:
                 filename=path,
                 meshtag_name="Facet tags",
             )
-        if self.efun is not None:
-            adios4dolfinx.write_meshtags(
-                meshtags=self.efun,
-                mesh=self.mesh,
-                filename=path,
-                meshtag_name="Edge tags",
-            )
-        if self.vfun is not None:
-            adios4dolfinx.write_meshtags(
-                meshtags=self.vfun,
-                mesh=self.mesh,
-                filename=path,
-                meshtag_name="Vertex tags",
-            )
+        # if self.efun is not None:
+        #     adios4dolfinx.write_meshtags(
+        #         meshtags=self.efun,
+        #         mesh=self.mesh,
+        #         filename=path,
+        #         meshtag_name="Edge tags",
+        #     )
+        # if self.vfun is not None:
+        #     adios4dolfinx.write_meshtags(
+        #         meshtags=self.vfun,
+        #         mesh=self.mesh,
+        #         filename=path,
+        #         meshtag_name="Vertex tags",
+        #     )
 
         if self.f0 is not None:
             el = self.f0.ufl_element()
             arr = utils.element2array(el)
-
-            adios4dolfinx.write_attributes(
-                comm=self.mesh.comm,
-                filename=path,
-                name="function_space",
-                attributes={k: arr for k in ("f0", "s0", "n0")},
-            )
+            if Version(np.__version__) <= Version("2.11") or Version(adios2.__version__) >= Version(
+                "2.10.2"
+            ):
+                # This is broken in adios for numpy >= 2.11
+                adios4dolfinx.write_attributes(
+                    comm=self.mesh.comm,
+                    filename=path,
+                    name="function_space",
+                    attributes={k: arr for k in ("f0", "s0", "n0")},
+                )
             adios4dolfinx.write_function(u=self.f0, filename=path, name="f0")
         if self.s0 is not None:
             adios4dolfinx.write_function(u=self.s0, filename=path, name="s0")

cardiac_geometries/mesh.py

@@ -682,7 +682,6 @@ def slab(
         )
 
     geo = Geometry.from_folder(comm=comm, folder=outdir)
-
     return geo
 
 

cardiac_geometries/utils.py

@@ -10,6 +10,7 @@ from mpi4py import MPI
 import basix
 import dolfinx
 import numpy as np
+from packaging.version import Version
 from structlog import get_logger
 
 logger = get_logger()
@@ -32,7 +33,7 @@ def distribute_entity_data(
     marked_entities: np.ndarray,
     entity_values: np.ndarray,
 ) -> tuple[np.ndarray, np.ndarray]:
-    if dolfinx.__version__ >= "0.9.0":
+    if Version(dolfinx.__version__) >= Version("0.9.0"):
         local_entities, local_values = dolfinx.io.utils.distribute_entity_data(
             mesh, tdim, marked_entities, entity_values
         )

{cardiac_geometriesx-0.4.1.dist-info → cardiac_geometriesx-0.4.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cardiac-geometriesx
-Version: 0.4.1
+Version: 0.4.3
 Summary: A python library for cardiac geometries
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License: MIT

cardiac_geometriesx-0.4.3.dist-info/RECORD

@@ -0,0 +1,16 @@
+cardiac_geometries/__init__.py,sha256=2W_ywAeLjyRk5MqSPAodHa4UN2lOnW1h8tmGLQ3gaJ0,150
+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=hR-uV9lzmfM_kQkqHY9MmJ_b3-Lv5oTsNOKCb-0nn_U,20616
+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=bEz2MMSRhzYhiRSFahdqQRsOWzCCauERKU2V6tdgSkQ,3239
+cardiac_geometriesx-0.4.3.dist-info/LICENSE,sha256=lo5K2rJPZOSv6luutGHbzzi3IpXNaB9E2UWq60qvNx0,1111
+cardiac_geometriesx-0.4.3.dist-info/METADATA,sha256=mpSvjuPehah4Z-XxkLrZkcq7U-HUxg66uPFpAFD2BTM,4185
+cardiac_geometriesx-0.4.3.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
+cardiac_geometriesx-0.4.3.dist-info/entry_points.txt,sha256=xOBnlc6W-H9oCDYLNz3kpki26OmpfYSoFSrmi_4V-Ec,52
+cardiac_geometriesx-0.4.3.dist-info/top_level.txt,sha256=J0gQxkWR2my5Vf7Qt8buDY8ZOjYdVfIweVunCGXWKNE,19
+cardiac_geometriesx-0.4.3.dist-info/RECORD,,

{cardiac_geometriesx-0.4.1.dist-info → cardiac_geometriesx-0.4.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.1.0)
+Generator: setuptools (75.3.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

cardiac_geometriesx-0.4.1.dist-info/RECORD

@@ -1,16 +0,0 @@
-cardiac_geometries/__init__.py,sha256=2W_ywAeLjyRk5MqSPAodHa4UN2lOnW1h8tmGLQ3gaJ0,150
-cardiac_geometries/cli.py,sha256=GKcsMNhVFoxWDr-o3jiDCXmTvPgCSEB9Kws8AvYIK4Q,19678
-cardiac_geometries/geometry.py,sha256=s-1BIDKvP9M3uu3Sl8JpGRnTnXZAa9Aq3FfpIIEAxhY,5982
-cardiac_geometries/gui.py,sha256=9WYR850wLrqsUrVUC37E2SaO0OWA_oagSe-YNrsxz3k,8376
-cardiac_geometries/mesh.py,sha256=Ejciny48mnKKN20RrY9DwLY7_Lh1jb6Kldj4CW1wr1o,26909
-cardiac_geometries/utils.py,sha256=8QKkdK3JFZMH3qF4PzvEVfk7vMB5Ciui-KFIct2Kd2g,20560
-cardiac_geometries/fibers/__init__.py,sha256=WpRrn9Iakl-3m8IGtFkqP0LXGjw5EZHZ8Eg9JCnCdrg,137
-cardiac_geometries/fibers/lv_ellipsoid.py,sha256=nJYkwvacH1xMhuWAV06NRR4fFzyprowfWv4UIQkCPQM,5830
-cardiac_geometries/fibers/slab.py,sha256=TYQhckJ8mwXz_08Cx3QsPQMtemkaxZ955SnSMrDfBPE,3898
-cardiac_geometries/fibers/utils.py,sha256=rOGWyJTRQ7M1W5_JBOIuVPw5LGBVB0u_LGxBicfc--w,3190
-cardiac_geometriesx-0.4.1.dist-info/LICENSE,sha256=lo5K2rJPZOSv6luutGHbzzi3IpXNaB9E2UWq60qvNx0,1111
-cardiac_geometriesx-0.4.1.dist-info/METADATA,sha256=zbG7thVfZ1t_0dusLr0y8-YhOfo4pUNBD9POw9Ge2Q0,4185
-cardiac_geometriesx-0.4.1.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
-cardiac_geometriesx-0.4.1.dist-info/entry_points.txt,sha256=xOBnlc6W-H9oCDYLNz3kpki26OmpfYSoFSrmi_4V-Ec,52
-cardiac_geometriesx-0.4.1.dist-info/top_level.txt,sha256=J0gQxkWR2my5Vf7Qt8buDY8ZOjYdVfIweVunCGXWKNE,19
-cardiac_geometriesx-0.4.1.dist-info/RECORD,,