cardiac-geometriesx 0.5.2__py3-none-any.whl → 0.5.3__py3-none-any.whl

cardiac_geometries/mesh.py

@@ -59,6 +59,8 @@ def ukb(
     create_fibers: bool = True,
     fiber_space: str = "P_1",
     clipped: bool = False,
+    use_burns: bool = False,
+    burns_path: Path | None = None,
     comm: MPI.Comm = MPI.COMM_WORLD,
 ) -> Geometry:
     """Create a mesh from the UK-Biobank atlas using
@@ -88,6 +90,12 @@ def ukb(
         Function space for fibers of the form family_degree, by default "P_1"
     clipped : bool, optional
         If True create a clipped mesh, by default False
+    use_burns : bool
+        If true, use the atlas from Richard Burns to generate the surfaces.
+        This will override the `all` parameter and use the burns atlas instead.
+    burns_path : Path | None
+        Path to the burns atlas file. This will be a .mat file which will be loaded
+        using scipy.io.loadmat. This needs to be specified if `use_burns`.
     comm : MPI.Comm, optional
         MPI communicator, by default MPI.COMM_WORLD
 
@@ -107,7 +115,11 @@ 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])
+        surf_args = ["surf", str(outdir), "--mode", str(mode), "--std", str(std), "--case", case]
+        if use_burns:
+            surf_args.extend(["--use_burns", "--burns_path", str(burns_path)])
+
+        ukb.cli.main(surf_args)
         mesh_args = [
             "mesh",
             str(outdir),

{cardiac_geometriesx-0.5.2.dist-info → cardiac_geometriesx-0.5.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cardiac-geometriesx
-Version: 0.5.2
+Version: 0.5.3
 Summary: A python library for cardiac geometries
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License: MIT

{cardiac_geometriesx-0.5.2.dist-info → cardiac_geometriesx-0.5.3.dist-info}/RECORD

@@ -2,16 +2,16 @@ cardiac_geometries/__init__.py,sha256=2W_ywAeLjyRk5MqSPAodHa4UN2lOnW1h8tmGLQ3gaJ
 cardiac_geometries/cli.py,sha256=bJ0ICY2KRCVBYxhTrMg66PbqSXrThMWwzQ61dJQgJo0,24018
 cardiac_geometries/geometry.py,sha256=b-JbxV1wTgrjgQaNNG4NiGmXLs3nqRabsUUtYDnyKKA,13616
 cardiac_geometries/gui.py,sha256=9WYR850wLrqsUrVUC37E2SaO0OWA_oagSe-YNrsxz3k,8376
-cardiac_geometries/mesh.py,sha256=nmabevdnhTC3FXWFWyIOuw-hCBOrRZBPXOXSGFp_hS4,38637
+cardiac_geometries/mesh.py,sha256=YLSlT1lJSw8ySNSyKr8vdbMArwON_uymer53lybF4j4,39199
 cardiac_geometries/utils.py,sha256=6H0tZif7GPINdrxfPm3HQH1T4_DfDvWMejjpXPb8mLY,22206
 cardiac_geometries/fibers/__init__.py,sha256=iggELqJBQySc6ihph1-yaweOfxNvvTE2670RnUnOgDw,2229
 cardiac_geometries/fibers/cylinder.py,sha256=Q1GIuVvntPQ7pW6Z4UYSC8-8WfkClbakiW81Fl9dvk0,3345
 cardiac_geometries/fibers/lv_ellipsoid.py,sha256=KMVOHg2VPg1tF2R9TKIX-vQr6dDM4HThh12WW_diNfU,6024
 cardiac_geometries/fibers/slab.py,sha256=IbyWyB4sFSa8Yo0gc4eiC9AXZtB5QB2Tm_IvdRZKg0o,3904
 cardiac_geometries/fibers/utils.py,sha256=v4vmB-2FM0JU-7Oy7Q3FRSuvDEXPCm5mWHi8CRxfxn8,3696
-cardiac_geometriesx-0.5.2.dist-info/licenses/LICENSE,sha256=lo5K2rJPZOSv6luutGHbzzi3IpXNaB9E2UWq60qvNx0,1111
-cardiac_geometriesx-0.5.2.dist-info/METADATA,sha256=ybcIww5jdSy9wraYoqA9lv2DeTOHYWEisur8A6pc5Ro,4384
-cardiac_geometriesx-0.5.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-cardiac_geometriesx-0.5.2.dist-info/entry_points.txt,sha256=xOBnlc6W-H9oCDYLNz3kpki26OmpfYSoFSrmi_4V-Ec,52
-cardiac_geometriesx-0.5.2.dist-info/top_level.txt,sha256=J0gQxkWR2my5Vf7Qt8buDY8ZOjYdVfIweVunCGXWKNE,19
-cardiac_geometriesx-0.5.2.dist-info/RECORD,,
+cardiac_geometriesx-0.5.3.dist-info/licenses/LICENSE,sha256=lo5K2rJPZOSv6luutGHbzzi3IpXNaB9E2UWq60qvNx0,1111
+cardiac_geometriesx-0.5.3.dist-info/METADATA,sha256=AYgpMoysb5JDcotfHSeFAbiufEvr51FcmQ6i6TfDF3s,4384
+cardiac_geometriesx-0.5.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+cardiac_geometriesx-0.5.3.dist-info/entry_points.txt,sha256=xOBnlc6W-H9oCDYLNz3kpki26OmpfYSoFSrmi_4V-Ec,52
+cardiac_geometriesx-0.5.3.dist-info/top_level.txt,sha256=J0gQxkWR2my5Vf7Qt8buDY8ZOjYdVfIweVunCGXWKNE,19
+cardiac_geometriesx-0.5.3.dist-info/RECORD,,