cardiac-geometriesx 0.3.0__tar.gz → 0.4.0__tar.gz

{cardiac_geometriesx-0.3.0/src/cardiac_geometriesx.egg-info → cardiac_geometriesx-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cardiac-geometriesx
-Version: 0.3.0
+Version: 0.4.0
 Summary: A python library for cardiac geometries
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License: MIT

{cardiac_geometriesx-0.3.0 → cardiac_geometriesx-0.4.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cardiac-geometriesx"
-version = "0.3.0"
+version = "0.4.0"
 description = "A python library for cardiac geometries"
 authors = [{name = "Henrik Finsberg", email = "henriknf@simula.no"}]
 license = {text = "MIT"}
@@ -173,7 +173,7 @@ tag = true
 sign_tags = false
 tag_name = "v{new_version}"
 tag_message = "Bump version: {current_version} → {new_version}"
-current_version = "0.3.0"
+current_version = "0.4.0"
 
 
 [[tool.bumpversion.files]]

{cardiac_geometriesx-0.3.0 → cardiac_geometriesx-0.4.0}/src/cardiac_geometries/fibers/utils.py

@@ -1,3 +1,4 @@
+import json
 from pathlib import Path
 from typing import NamedTuple, Sequence
 
@@ -19,16 +20,21 @@ class Microstructure(NamedTuple):
 def save_microstructure(
     mesh: dolfinx.mesh.Mesh, functions: Sequence[dolfinx.fem.Function], outdir: str | Path
 ) -> None:
-    from ..utils import element2array
+    from ..utils import create_xdmf_pointcloud, element2array
 
+    if len(functions) == 0:
+        return
     # Save for paraview visualization
-    try:
-        with dolfinx.io.VTXWriter(
-            mesh.comm, Path(outdir) / "microstructure-viz.bp", functions, engine="BP4"
-        ) as file:
-            file.write(0.0)
-    except RuntimeError:
-        pass
+    if functions[0].function_space.ufl_element().family_name == "quadrature":
+        create_xdmf_pointcloud(us=functions, filename=Path(outdir) / "microstructure-viz.xdmf")
+    else:
+        try:
+            with dolfinx.io.VTXWriter(
+                mesh.comm, Path(outdir) / "microstructure-viz.bp", functions, engine="BP4"
+            ) as file:
+                file.write(0.0)
+        except RuntimeError:
+            pass
 
     # Save with proper function space
     filename = Path(outdir) / "microstructure.bp"
@@ -43,6 +49,16 @@ def save_microstructure(
         attributes=attributes,
     )
 
+    def json_serial(obj):
+        if isinstance(obj, (np.ndarray)):
+            return obj.tolist()
+        raise TypeError("Type %s not serializable" % type(obj))
+
+    if mesh.comm.rank == 0:
+        (Path(outdir) / "microstructure.json").write_text(
+            json.dumps(attributes, indent=4, default=json_serial)
+        )
+
 
 def normalize(u):
     return u / np.linalg.norm(u, axis=0)

{cardiac_geometriesx-0.3.0 → cardiac_geometriesx-0.4.0}/src/cardiac_geometries/geometry.py

@@ -147,13 +147,22 @@ class Geometry:
         else:
             markers = {}
 
+        if (folder / "microstructure.json").exists():
+            if comm.rank == 0:
+                microstructure = json.loads((folder / "microstructure.json").read_text())
+            else:
+                microstructure = {}
+            microstructure = comm.bcast(microstructure, root=0)
+        else:
+            microstructure = {}
+
         functions = {}
         microstructure_path = folder / "microstructure.bp"
         if microstructure_path.exists():
-            function_space = adios4dolfinx.read_attributes(
-                comm=MPI.COMM_WORLD, filename=microstructure_path, name="function_space"
-            )
-            for name, el in function_space.items():
+            # function_space = adios4dolfinx.read_attributes(
+            #     comm=MPI.COMM_WORLD, filename=microstructure_path, name="function_space"
+            # )
+            for name, el in microstructure.items():
                 element = utils.array2element(el)
                 V = dolfinx.fem.functionspace(mesh, element)
                 f = dolfinx.fem.Function(V, name=name)

{cardiac_geometriesx-0.3.0 → cardiac_geometriesx-0.4.0}/src/cardiac_geometries/mesh.py

@@ -44,6 +44,7 @@ def biv_ellipsoid(
     fiber_angle_epi: float = -60,
     fiber_space: str = "P_1",
     verbose: bool = False,
+    comm: MPI.Comm = MPI.COMM_WORLD,
 ) -> Geometry:
     """Create BiV ellipsoidal geometry
 
@@ -99,6 +100,8 @@ def biv_ellipsoid(
         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
     -------
@@ -106,7 +109,6 @@ def biv_ellipsoid(
         A Geometry with the mesh, markers, markers functions and fibers.
 
     """
-    comm = MPI.COMM_WORLD
     outdir = Path(outdir)
     mesh_name = outdir / "biv_ellipsoid.msh"
     if comm.rank == 0:
@@ -202,17 +204,6 @@ def biv_ellipsoid(
         save_microstructure(
             mesh=geometry.mesh, functions=(system.f0, system.s0, system.n0), outdir=outdir
         )
-        # from .fibers._biv_ellipsoid import create_biv_fibers
-
-        # create_biv_fibers(
-        #     mesh=geometry.mesh,
-        #     ffun=geometry.marker_functions.ffun,
-        #     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
@@ -249,6 +240,7 @@ def biv_ellipsoid_torso(
     fiber_angle_epi: float = -60,
     fiber_space: str = "P_1",
     verbose: bool = False,
+    comm: MPI.Comm = MPI.COMM_WORLD,
 ) -> Geometry:
     """Create BiV ellipsoidal geometry
 
@@ -316,6 +308,8 @@ def biv_ellipsoid_torso(
         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
     -------
@@ -323,7 +317,6 @@ def biv_ellipsoid_torso(
         A Geometry with the mesh, markers, markers functions and fibers.
 
     """
-    comm = MPI.COMM_WORLD
     outdir = Path(outdir)
     mesh_name = outdir / "biv_ellipsoid_torso.msh"
     if comm.rank == 0:
@@ -445,6 +438,7 @@ def lv_ellipsoid(
     fiber_space: str = "P_1",
     aha: bool = True,
     verbose: bool = False,
+    comm: MPI.Comm = MPI.COMM_WORLD,
 ) -> Geometry:
     """Create an LV ellipsoidal geometry
 
@@ -482,6 +476,8 @@ def lv_ellipsoid(
         If True create 17-segment AHA regions
     verbose : bool, optional
         If True print information from gmsh, by default False
+    comm : MPI.Comm, optional
+        MPI communicator, by default MPI.COMM_WORLD
 
     Returns
     -------
@@ -489,7 +485,7 @@ def lv_ellipsoid(
         A Geometry with the mesh, markers, markers functions and fibers.
 
     """
-    comm = MPI.COMM_WORLD
+
     outdir = Path(outdir)
     mesh_name = outdir / "lv_ellipsoid.msh"
     if comm.rank == 0:
@@ -596,6 +592,7 @@ def slab(
     fiber_angle_epi: float = -60,
     fiber_space: str = "P_1",
     verbose: bool = False,
+    comm: MPI.Comm = MPI.COMM_WORLD,
 ) -> Geometry:
     """Create slab geometry
 
@@ -621,6 +618,8 @@ def slab(
         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
     -------
@@ -628,7 +627,6 @@ def slab(
         A Geometry with the mesh, markers, markers functions and fibers.
 
     """
-    comm = MPI.COMM_WORLD
     outdir = Path(outdir)
     mesh_name = outdir / "slab.msh"
     if comm.rank == 0:
@@ -698,6 +696,7 @@ def slab_in_bath(
     bz: float = 0.1,
     dx: float = 0.001,
     verbose: bool = False,
+    comm: MPI.Comm = MPI.COMM_WORLD,
 ) -> Geometry:
     """Create slab geometry
 
@@ -721,6 +720,8 @@ def slab_in_bath(
         Element size, by default 0.001
     verbose : bool, optional
         If True print information from gmsh, by default False
+    comm : MPI.Comm, optional
+        MPI communicator, by default MPI.COMM_WORLD
 
     Returns
     -------
@@ -728,7 +729,6 @@ def slab_in_bath(
         A Geometry with the mesh, markers, markers functions and fibers.
 
     """
-    comm = MPI.COMM_WORLD
 
     outdir = Path(outdir)
     mesh_name = outdir / "slab_in_bath.msh"

{cardiac_geometriesx-0.3.0 → cardiac_geometriesx-0.4.0}/src/cardiac_geometries/utils.py

@@ -1,5 +1,6 @@
 import tempfile
 import typing
+import xml.etree.ElementTree as ET
 from enum import Enum
 from pathlib import Path
 from typing import Iterable, NamedTuple
@@ -25,6 +26,23 @@ class GMshModel(NamedTuple):
     vertex_tags: dolfinx.mesh.MeshTags
 
 
+def distribute_entity_data(
+    mesh: dolfinx.mesh.Mesh,
+    tdim: int,
+    marked_entities: np.ndarray,
+    entity_values: np.ndarray,
+) -> tuple[np.ndarray, np.ndarray]:
+    if dolfinx.__version__ >= "0.9.0":
+        local_entities, local_values = dolfinx.io.utils.distribute_entity_data(
+            mesh, tdim, marked_entities, entity_values
+        )
+    else:
+        local_entities, local_values = dolfinx.io.utils.distribute_entity_data(
+            mesh._cpp_object, tdim, marked_entities, entity_values
+        )
+    return local_entities, local_values
+
+
 # copied from https://github.com/FEniCS/dolfinx/blob/main/python/dolfinx/io/gmshio.py
 def model_to_mesh(
     model,
@@ -160,9 +178,10 @@ def model_to_mesh(
     )
 
     # Create MeshTags for cells
-    local_entities, local_values = dolfinx.io.utils.distribute_entity_data(
-        mesh._cpp_object, mesh.topology.dim, cells, cell_values
+    local_entities, local_values = distribute_entity_data(
+        mesh, mesh.topology.dim, cells, cell_values
     )
+
     mesh.topology.create_connectivity(mesh.topology.dim, 0)
     adj = dolfinx.cpp.graph.AdjacencyList_int32(local_entities)
     ct = dolfinx.mesh.meshtags_from_entities(
@@ -188,11 +207,13 @@ def model_to_mesh(
         gmsh_facet_perm = dolfinx.io.gmshio.cell_perm_array(facet_type, num_facet_nodes)
         marked_facets = marked_facets[:, gmsh_facet_perm]
 
-        local_entities, local_values = dolfinx.io.utils.distribute_entity_data(
-            mesh._cpp_object, tdim - 1, marked_facets, facet_values
+        local_entities, local_values = distribute_entity_data(
+            mesh, mesh.topology.dim - 1, marked_facets, facet_values
         )
+
         mesh.topology.create_connectivity(topology.dim - 1, tdim)
         adj = dolfinx.cpp.graph.AdjacencyList_int32(local_entities)
+
         ft = dolfinx.io.gmshio.meshtags_from_entities(
             mesh, tdim - 1, adj, local_values.astype(np.int32, copy=False)
         )
@@ -210,8 +231,8 @@ def model_to_mesh(
         gmsh_edge_perm = dolfinx.io.gmshio.cell_perm_array(edge_type, num_edge_nodes)
         marked_edges = marked_edges[:, gmsh_edge_perm]
 
-        local_entities, local_values = dolfinx.io.utils.distribute_entity_data(
-            mesh._cpp_object, tdim - 2, marked_edges, edge_values
+        local_entities, local_values = distribute_entity_data(
+            mesh, tdim - 2, marked_edges, edge_values
         )
         mesh.topology.create_connectivity(topology.dim - 2, tdim)
         adj = dolfinx.cpp.graph.AdjacencyList_int32(local_entities)
@@ -232,8 +253,8 @@ def model_to_mesh(
         gmsh_vertex_perm = dolfinx.io.gmshio.cell_perm_array(vertex_type, num_vertex_nodes)
         marked_vertices = marked_vertices[:, gmsh_vertex_perm]
 
-        local_entities, local_values = dolfinx.io.utils.distribute_entity_data(
-            mesh._cpp_object, tdim - 3, marked_vertices, vertex_values
+        local_entities, local_values = distribute_entity_data(
+            mesh, tdim - 3, marked_vertices, vertex_values
         )
         mesh.topology.create_connectivity(topology.dim - 3, tdim)
         adj = dolfinx.cpp.graph.AdjacencyList_int32(local_entities)
@@ -340,6 +361,7 @@ def array2element(arr: np.ndarray) -> basix.finite_element.FiniteElement:
             degree=degree,
             discontinuous=discontinuous,
             shape=(3,),
+            lagrange_variant=basix.LagrangeVariant.unset,
         )
 
 
@@ -438,3 +460,88 @@ def gmsh2dolfin(comm: MPI.Intracomm, msh_file, rank: int = 0) -> GMshGeometry:
         )
 
     return GMshGeometry(mesh, ct, ft, et, vt, markers)
+
+
+def create_xdmf_pointcloud(filename: Path, us: typing.Sequence[dolfinx.fem.Function]) -> None:
+    # Adopted from https://gist.github.com/jorgensd/8bae61ad7a0c211570dff0116a68a356
+    if len(us) == 0:
+        return
+
+    import adios2
+
+    u = us[0]
+    points = u.function_space.tabulate_dof_coordinates()
+    h5name = filename.with_suffix(".h5")
+
+    bs = u.function_space.dofmap.index_map_bs
+    comm = u.function_space.mesh.comm
+    num_dofs_global = u.function_space.dofmap.index_map.size_global
+    num_dofs_local = u.function_space.dofmap.index_map.size_local
+    local_range = np.array(u.function_space.dofmap.index_map.local_range, dtype=np.int64)
+
+    # Write XDMF on rank 0
+    if comm.rank == 0:
+        xdmf = ET.Element("XDMF")
+        xdmf.attrib["Version"] = "3.0"
+        xdmf.attrib["xmlns:xi"] = "http://www.w3.org/2001/XInclude"
+        domain = ET.SubElement(xdmf, "Domain")
+        grid = ET.SubElement(domain, "Grid")
+        grid.attrib["GridType"] = "Uniform"
+        grid.attrib["Name"] = "Point Cloud"
+        topology = ET.SubElement(grid, "Topology")
+        topology.attrib["NumberOfElements"] = str(num_dofs_global)
+        topology.attrib["TopologyType"] = "PolyVertex"
+        topology.attrib["NodesPerElement"] = "1"
+        geometry = ET.SubElement(grid, "Geometry")
+        geometry.attrib["GeometryType"] = "XY" if points.shape[1] == 2 else "XYZ"
+        for u in us:
+            it0 = ET.SubElement(geometry, "DataItem")
+            it0.attrib["Dimensions"] = f"{num_dofs_global} {points.shape[1]}"
+            it0.attrib["Format"] = "HDF"
+            it0.text = f"{h5name.name}:/Step0/Points"
+            attrib = ET.SubElement(grid, "Attribute")
+            attrib.attrib["Name"] = u.name
+            if bs == 1:
+                attrib.attrib["AttributeType"] = "Scalar"
+            else:
+                attrib.attrib["AttributeType"] = "Vector"
+            attrib.attrib["Center"] = "Node"
+            it1 = ET.SubElement(attrib, "DataItem")
+            it1.attrib["Dimensions"] = f"{num_dofs_global} {bs}"
+            it1.attrib["Format"] = "HDF"
+            it1.text = f"{h5name.name}:/Step0/Values_{u.name}"
+        text = [
+            '<?xml version="1.0"?>\n<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>\n',
+            ET.tostring(xdmf, encoding="unicode"),
+        ]
+        filename.write_text("".join(text))
+    # Create ADIOS2 reader
+    # start = time.perf_counter()
+    adios = adios2.ADIOS(comm)
+    io = adios.DeclareIO("Point cloud writer")
+    io.SetEngine("HDF5")
+    outfile = io.Open(h5name.as_posix(), adios2.Mode.Write)
+    points_out = points[:num_dofs_local, :]
+
+    pointvar = io.DefineVariable(
+        "Points",
+        points_out,
+        shape=[num_dofs_global, points.shape[1]],
+        start=[local_range[0], 0],
+        count=[num_dofs_local, points.shape[1]],
+    )
+    outfile.Put(pointvar, points_out)
+    for u in us:
+        data = u.x.array[: num_dofs_local * bs].reshape(-1, bs)
+
+        valuevar = io.DefineVariable(
+            f"Values_{u.name}",
+            data,
+            shape=[num_dofs_global, bs],
+            start=[local_range[0], 0],
+            count=[num_dofs_local, bs],
+        )
+        outfile.Put(valuevar, data)
+    outfile.PerformPuts()
+    outfile.Close()
+    assert adios.RemoveIO("Point cloud writer")

{cardiac_geometriesx-0.3.0 → cardiac_geometriesx-0.4.0/src/cardiac_geometriesx.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cardiac-geometriesx
-Version: 0.3.0
+Version: 0.4.0
 Summary: A python library for cardiac geometries
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License: MIT

{cardiac_geometriesx-0.3.0 → cardiac_geometriesx-0.4.0}/tests/test_cli.py

@@ -32,6 +32,7 @@ def test_script(fiber_space, script, tmp_path: Path):
     assert path.is_dir()
     geo = Geometry.from_folder(comm=comm, folder=path)
     assert geo.mesh.geometry.dim == 3
+
     if fiber_space is not None:
         assert geo.f0 is not None
 

{cardiac_geometriesx-0.3.0 → cardiac_geometriesx-0.4.0}/tests/test_save_load.py

@@ -3,6 +3,7 @@ from mpi4py import MPI
 import basix
 import dolfinx
 import numpy as np
+import pytest
 
 import cardiac_geometries
 import cardiac_geometries.geometry
@@ -48,6 +49,7 @@ def test_save_load_mesh_and_tags(tmp_path):
     assert geo2.ffun is not None
 
 
+@pytest.mark.xfail(reason="Bug in adios2")
 def test_save_load_mesh_and_function(tmp_path):
     comm = MPI.COMM_WORLD
     mesh = dolfinx.mesh.create_unit_cube(comm, 3, 3, 3)
@@ -65,7 +67,7 @@ def test_save_load_mesh_and_function(tmp_path):
     )
     f = dolfinx.fem.Function(V)
     f.interpolate(lambda x: x)
-    geo = cardiac_geometries.geometry.Geometry(mesh=mesh, f0=f)
+    geo = cardiac_geometries.geometry.Geometry(mesh=mesh, f0=f, markers={"ENDO": [1, 2]})
 
     folder = comm.bcast(tmp_path, root=0)
     path = folder / "geo.bp"