cardiac-geometriesx 0.3.1__tar.gz → 0.4.1__tar.gz

{cardiac_geometriesx-0.3.1/src/cardiac_geometriesx.egg-info → cardiac_geometriesx-0.4.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cardiac-geometriesx
-Version: 0.3.1
+Version: 0.4.1
 Summary: A python library for cardiac geometries
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License: MIT
@@ -17,6 +17,7 @@ Requires-Dist: structlog
 Requires-Dist: cardiac-geometries-core
 Requires-Dist: rich-click
 Requires-Dist: adios4dolfinx
+Requires-Dist: scifem
 Provides-Extra: dev
 Requires-Dist: bump-my-version; extra == "dev"
 Requires-Dist: ipython; extra == "dev"

{cardiac_geometriesx-0.3.1 → cardiac_geometriesx-0.4.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cardiac-geometriesx"
-version = "0.3.1"
+version = "0.4.1"
 description = "A python library for cardiac geometries"
 authors = [{name = "Henrik Finsberg", email = "henriknf@simula.no"}]
 license = {text = "MIT"}
@@ -22,6 +22,7 @@ dependencies = [
     "cardiac-geometries-core",
     "rich-click",
     "adios4dolfinx",
+    "scifem",
 ]
 
 [project.readme]
@@ -173,7 +174,7 @@ tag = true
 sign_tags = false
 tag_name = "v{new_version}"
 tag_message = "Bump version: {current_version} → {new_version}"
-current_version = "0.3.1"
+current_version = "0.4.1"
 
 
 [[tool.bumpversion.files]]

{cardiac_geometriesx-0.3.1 → cardiac_geometriesx-0.4.1}/src/cardiac_geometries/fibers/lv_ellipsoid.py

@@ -159,7 +159,10 @@ def compute_system(
     s0 = utils.normalize(s0)
 
     Vv = space_from_string(
-        space_string=f"{element.family_name}_{element.degree}", mesh=mesh, dim=mesh.geometry.dim
+        space_string=f"{element.family_name}_{element.degree}",
+        mesh=mesh,
+        dim=mesh.geometry.dim,
+        discontinuous=element.discontinuous,
     )
 
     fiber = dolfinx.fem.Function(Vv)

{cardiac_geometriesx-0.3.1 → cardiac_geometriesx-0.4.1}/src/cardiac_geometries/fibers/slab.py

@@ -60,7 +60,10 @@ def compute_system(
     n0 = utils.normalize(n0)
 
     Vv = space_from_string(
-        space_string=f"{element.family_name}_{element.degree}", mesh=mesh, dim=mesh.geometry.dim
+        space_string=f"{element.family_name}_{element.degree}",
+        mesh=mesh,
+        dim=mesh.geometry.dim,
+        discontinuous=element.discontinuous,
     )
 
     fiber = dolfinx.fem.Function(Vv)

{cardiac_geometriesx-0.3.1 → cardiac_geometriesx-0.4.1}/src/cardiac_geometries/fibers/utils.py

@@ -1,3 +1,4 @@
+import json
 from pathlib import Path
 from typing import NamedTuple, Sequence
 
@@ -21,14 +22,21 @@ def save_microstructure(
 ) -> None:
     from ..utils import 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":
+        from scifem.xdmf import create_pointcloud
+
+        create_pointcloud(functions=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 +51,16 @@ 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-0.3.1 → cardiac_geometriesx-0.4.1}/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-0.3.1 → cardiac_geometriesx-0.4.1}/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)
@@ -249,7 +270,9 @@ def model_to_mesh(
     return GMshModel(mesh, ct, ft, et, vt)
 
 
-def parse_element(space_string: str, mesh: dolfinx.mesh.Mesh, dim: int) -> basix.ufl._ElementBase:
+def parse_element(
+    space_string: str, mesh: dolfinx.mesh.Mesh, dim: int, discontinuous: bool = False
+) -> basix.ufl._ElementBase:
     """
     Parse a string representation of a basix element family
     """
@@ -262,8 +285,9 @@ def parse_element(space_string: str, mesh: dolfinx.mesh.Mesh, dim: int) -> basix
         else:
             kwargs["shape"] = (dim,)
 
+    # breakpoint()
     if family_str in ["Lagrange", "P", "CG"]:
-        el = basix.ufl.element(family=basix.ElementFamily.P, discontinuous=False, **kwargs)
+        el = basix.ufl.element(family=basix.ElementFamily.P, discontinuous=discontinuous, **kwargs)
     elif family_str in ["Discontinuous Lagrange", "DG", "dP"]:
         el = basix.ufl.element(family=basix.ElementFamily.P, discontinuous=True, **kwargs)
 
@@ -277,7 +301,7 @@ def parse_element(space_string: str, mesh: dolfinx.mesh.Mesh, dim: int) -> basix
 
 
 def space_from_string(
-    space_string: str, mesh: dolfinx.mesh.Mesh, dim: int
+    space_string: str, mesh: dolfinx.mesh.Mesh, dim: int, discontinuous: bool = False
 ) -> dolfinx.fem.functionspace:
     """
     Constructed a finite elements space from a string
@@ -292,8 +316,10 @@ def space_from_string(
         The mesh
     dim : int
         1 for scalar space, 3 for vector space.
+    discontinuous: bool
+        If true force element to be discontinuous, by default False
     """
-    el = parse_element(space_string, mesh, dim)
+    el = parse_element(space_string, mesh, dim, discontinuous=discontinuous)
     return dolfinx.fem.functionspace(mesh, el)
 
 
@@ -340,6 +366,7 @@ def array2element(arr: np.ndarray) -> basix.finite_element.FiniteElement:
             degree=degree,
             discontinuous=discontinuous,
             shape=(3,),
+            lagrange_variant=basix.LagrangeVariant.unset,
         )
 
 
@@ -438,3 +465,88 @@ 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-0.3.1 → cardiac_geometriesx-0.4.1/src/cardiac_geometriesx.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cardiac-geometriesx
-Version: 0.3.1
+Version: 0.4.1
 Summary: A python library for cardiac geometries
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License: MIT
@@ -17,6 +17,7 @@ Requires-Dist: structlog
 Requires-Dist: cardiac-geometries-core
 Requires-Dist: rich-click
 Requires-Dist: adios4dolfinx
+Requires-Dist: scifem
 Provides-Extra: dev
 Requires-Dist: bump-my-version; extra == "dev"
 Requires-Dist: ipython; extra == "dev"

{cardiac_geometriesx-0.3.1 → cardiac_geometriesx-0.4.1}/src/cardiac_geometriesx.egg-info/requires.txt

@@ -3,6 +3,7 @@ structlog
 cardiac-geometries-core
 rich-click
 adios4dolfinx
+scifem
 
 [dev]
 bump-my-version

{cardiac_geometriesx-0.3.1 → cardiac_geometriesx-0.4.1}/tests/test_cli.py

@@ -16,7 +16,7 @@ from cardiac_geometries import Geometry, cli
     ],
     ids=["slab", "lv_ellipsoid"],
 )
-@pytest.mark.parametrize("fiber_space", [None, "P_1", "P_2", "Quadrature_2"])
+@pytest.mark.parametrize("fiber_space", [None, "P_1", "P_2", "Quadrature_2", "DG_1"])
 def test_script(fiber_space, script, tmp_path: Path):
     runner = CliRunner()
 
@@ -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-0.3.1 → cardiac_geometriesx-0.4.1}/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"