Change logic for converting mesh from wildmeshing to dolfinx

examples/cli.ipynb

@@ -283,7 +283,7 @@
    "id": "27",
    "metadata": {},
    "source": [
-    "Let us have a look at the mesh"
+    "Now lets convert the mesh to dolfinx"
    ]
   },
   {
@@ -292,6 +292,34 @@
    "id": "28",
    "metadata": {},
    "outputs": [],
+   "source": [
+    "!mri2mesh mesh convert idealized-brain"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "29",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!ls idealized-brain/"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "30",
+   "metadata": {},
+   "source": [
+    "Let us have a look at the mesh"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "31",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "from mpi4py import MPI\n",
     "import dolfinx\n",
@@ -304,7 +332,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "29",
+   "id": "32",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -326,7 +354,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "30",
+   "id": "33",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -348,7 +376,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.9"
+   "version": "3.12.11"
   }
  },
  "nbformat": 4,

src/mri2mesh/mesh/__init__.py

@@ -27,6 +27,10 @@ def add_mesh_parser(parser: argparse.ArgumentParser) -> None:
 
     convert_parser = subparsers.add_parser("convert", help="Convert mesh to dolfinx")
     convert_parser.add_argument("mesh_dir", type=Path, help="Directory containing mesh files")
+    convert_parser.add_argument(
+        "--extract-facet-tags", action="store_true", help="Extract facet tags"
+    )
+    convert_parser.add_argument("--extract-submesh", action="store_true", help="Extract submesh")
 
     idealized_parser = subparsers.add_parser(
         "idealized",
@@ -41,12 +45,7 @@ def dispatch(command, args: dict[str, typing.Any]) -> int:
         basic.generate_sameple_config(**args)
 
     elif command == "create":
-        mesh_dir = basic.create_mesh_from_config(**args)
-        try:
-            basic.convert_mesh_dolfinx(mesh_dir=mesh_dir)
-        except ImportError:
-            logger.debug("dolfinx not installed, skipping conversion to dolfinx")
-
+        basic.create_mesh_from_config(**args)
     elif command == "convert":
         basic.convert_mesh_dolfinx(**args)
 

src/mri2mesh/mesh/basic.py

@@ -156,83 +156,149 @@ def create_mesh(
         manifold_surface=manifold_surface,
         correct_surface_orientation=True,
     )
-    coords, connections = tetra.get_tracked_surfaces()
 
     tetra_mesh = meshio.Mesh(
         point_array, [("tetra", cell_array)], cell_data={"cell_tags": [marker.ravel()]}
     )
-    tetra_mesh_pv = pv.from_meshio(tetra_mesh).clean()
+
+    tetra_mesh_pv = pv.from_meshio(tetra_mesh)
     pv.save_meshio(outdir / "tetra_mesh.xdmf", tetra_mesh_pv)
 
-    for i, coord in enumerate(coords):
-        np.save(outdir / f"coords_{i}.npy", coord)
+    np.save(outdir / "point_array.npy", point_array)
+    np.save(outdir / "cell_array.npy", cell_array)
+    np.save(outdir / "marker.npy", marker)
+
+    # coords, connections = tetra.get_tracked_surfaces()
+    # for i, coord in enumerate(coords):
+    #     np.save(outdir / f"coords_{i}.npy", coord)
 
-    for i, conn in enumerate(connections):
-        np.save(outdir / f"connections_{i}.npy", conn)
+    # for i, conn in enumerate(connections):
+    #     np.save(outdir / f"connections_{i}.npy", conn)
 
+    # cell_tags.find
+    # Compute incident with facets
+    # Intersection exterior facets
 
-def convert_mesh_dolfinx(mesh_dir: Path):
+
+def convert_mesh_dolfinx(
+    mesh_dir: Path, extract_facet_tags: bool = False, extract_submesh: bool = False
+):
     logger.info("Converting mesh to dolfinx in %s", mesh_dir)
     from mpi4py import MPI
-    from scipy.spatial.distance import cdist
     import dolfinx
+    import basix
+    import ufl
 
-    threshold = 1.0
-    fdim = 2
+    point_array = np.load(mesh_dir / "point_array.npy")
+    cell_array = np.load(mesh_dir / "cell_array.npy")
+    marker = np.load(mesh_dir / "marker.npy")
 
-    coords = []
-    for path in sorted(mesh_dir.glob("coords_*.npy"), key=lambda x: int(x.stem.split("_")[-1])):
-        coords.append(np.load(path))
-    logger.debug(f"Found {len(coords)} coordinates")
-
-    connections = []
-    for path in sorted(
-        mesh_dir.glob("connections_*.npy"), key=lambda x: int(x.stem.split("_")[-1])
-    ):
-        connections.append(np.load(path))
-    logger.debug(f"Found {len(connections)} connections")
+    comm = MPI.COMM_WORLD
+    mesh = dolfinx.mesh.create_mesh(
+        comm,
+        cell_array.astype(np.int64),
+        point_array,
+        ufl.Mesh(basix.ufl.element("Lagrange", "tetrahedron", 1, shape=(3,))),
+    )
+    tdim = mesh.topology.dim
+    fdim = tdim - 1
+    local_entities, local_values = dolfinx.io.gmshio.distribute_entity_data(
+        mesh,
+        tdim,
+        cell_array.astype(np.int64),
+        marker.flatten().astype(np.int32),
+    )
+    adj = dolfinx.graph.adjacencylist(local_entities)
+    cell_tags = dolfinx.mesh.meshtags_from_entities(
+        mesh,
+        tdim,
+        adj,
+        local_values.astype(np.int32, copy=False),
+    )
+    cell_tags.name = "cell_tags"
+    if not extract_facet_tags:
+        logger.debug("Save files")
+        with dolfinx.io.XDMFFile(comm, mesh_dir / "mesh.xdmf", "w") as xdmf:
+            xdmf.write_mesh(mesh)
+            xdmf.write_meshtags(cell_tags, mesh.geometry)
 
-    assert len(connections) == len(coords)
+        return
 
-    logger.debug("Loading mesh")
-    comm = MPI.COMM_WORLD
-    with dolfinx.io.XDMFFile(comm, mesh_dir / "tetra_mesh.xdmf", "r") as xdmf:
-        mesh = xdmf.read_mesh(name="Grid")
-        cell_tags = xdmf.read_meshtags(mesh, name="Grid")
+    mesh.topology.create_connectivity(tdim - 1, tdim)
 
-    logger.debug("Mesh loaded")
+    # FIXME: Here we just add hard coded values for now. This should be fixed in the future.
 
-    facets = []
+    entities = []
     values = []
-    for i, coord in enumerate(coords, start=1):
-        logger.debug(f"Processing coord {i}")
+    # 1 = Parenchyma
+    PARENCHYMA = 1
+
+    cells = cell_tags.find(PARENCHYMA)
+    exterior_facets = dolfinx.mesh.exterior_facet_indices(mesh.topology)
+    incident_facets = dolfinx.mesh.compute_incident_entities(mesh.topology, cells, tdim, tdim - 1)
+    exterior_facets_marker = np.intersect1d(incident_facets, exterior_facets)
+    values.append(np.full(exterior_facets_marker.shape[0], PARENCHYMA, dtype=np.int32))
+    entities.append(exterior_facets_marker)
 
-        def locator(x):
-            # Find the distance to all coordinates
-            distances = cdist(x.T, coord)
-            # And return True is they are close
-            return np.any(distances < threshold, axis=1)
+    VENTRICLES = 3
+    all_cell_tags = np.unique(cell_tags.values)
+    cell_not_ventricles = np.setdiff1d(all_cell_tags, [VENTRICLES])
+    import scifem
 
-        f = dolfinx.mesh.locate_entities_boundary(mesh, dim=fdim, marker=locator)
-        v = np.full(f.shape[0], i, dtype=np.int32)
-        facets.append(f)
-        values.append(v)
+    interface_entities = scifem.mesh.find_interface(cell_tags, [VENTRICLES], cell_not_ventricles)
+    entities.append(interface_entities)
+    values.append(np.full(interface_entities.shape[0], VENTRICLES, dtype=np.int32))
 
-    logger.debug("Create meshtags")
     facet_tags = dolfinx.mesh.meshtags(
         mesh,
         fdim,
-        np.hstack(facets),
+        np.hstack(entities),
         np.hstack(values),
     )
     facet_tags.name = "facet_tags"
-    cell_tags.name = "cell_tags"
+
     mesh.name = "mesh"
 
     logger.debug("Save files")
-    with dolfinx.io.XDMFFile(comm, mesh_dir / "mesh.xdmf", "w") as xdmf:
+    meshname = "mesh_full.xdmf" if extract_submesh else "mesh.xdmf"
+    with dolfinx.io.XDMFFile(comm, mesh_dir / meshname, "w") as xdmf:
         xdmf.write_mesh(mesh)
         xdmf.write_meshtags(facet_tags, mesh.geometry)
         xdmf.write_meshtags(cell_tags, mesh.geometry)
 
-    logger.info("Mesh saved to %s", mesh_dir / "mesh.xdmf")
+    logger.info("Mesh saved to %s", mesh_dir / meshname)
+
+    if not extract_submesh:
+        return
+    submesh_data = scifem.mesh.extract_submesh(mesh, cell_tags, cell_not_ventricles)
+
+    # Transfer the facet tags to the submesh
+    submesh_data.domain.topology.create_connectivity(2, 3)
+    facet_tags_submesh, sub_to_parent_entity_map = scifem.mesh.transfer_meshtags_to_submesh(
+        facet_tags,
+        # geo.facet_tags,   # If available
+        submesh_data.domain,
+        vertex_to_parent=submesh_data.vertex_map,
+        cell_to_parent=submesh_data.cell_map,
+    )
+
+    np.save(mesh_dir / "sub_to_parent_entity_map.npy", sub_to_parent_entity_map)
+    np.save(mesh_dir / "vertex_map.npy", submesh_data.vertex_map)
+    np.save(mesh_dir / "cell_map.npy", submesh_data.cell_map)
+
+    # Remove overflow values
+    keep_indices = facet_tags_submesh.values > 0
+    facet_tags_new = dolfinx.mesh.meshtags(
+        submesh_data.domain,
+        fdim,
+        facet_tags_submesh.indices[keep_indices],
+        facet_tags_submesh.values[keep_indices],
+    )
+
+    facet_tags_new.name = "facet_tags"
+    submesh_data.cell_tag.name = "cell_tags"
+
+    with dolfinx.io.XDMFFile(comm, mesh_dir / "mesh.xdmf", "w") as xdmf:
+        xdmf.write_mesh(submesh_data.domain)
+        xdmf.write_meshtags(submesh_data.cell_tag, submesh_data.domain.geometry)
+        xdmf.write_meshtags(facet_tags_new, submesh_data.domain.geometry)

tests/test_cli.py

@@ -14,14 +14,9 @@ def test_labels_cli(name, capsys):
 def test_mesh_idealized_cli(tmp_path):
     cli.main(["mesh", "idealized", "-o", str(tmp_path)])
     for name in [
-        "connections_3.npy",
-        "coords_0.npy",
-        "coords_1.npy",
-        "connections_2.npy",
-        "connections_0.npy",
-        "coords_3.npy",
-        "coords_2.npy",
-        "connections_1.npy",
+        "point_array.npy",
+        "cell_array.npy",
+        "marker.npy",
         "mesh.h5",
         "ventricles.ply",
         "skull.ply",
@@ -34,4 +29,4 @@ def test_mesh_idealized_cli(tmp_path):
         "V34.ply",
         "mesh_params.json",
     ]:
-        assert (tmp_path / name).exists()
+        assert (tmp_path / name).exists(), name