From d502e860ffb13393a55c6596f8e48d1745d1ab89 Mon Sep 17 00:00:00 2001
From: mhoeijm <102799582+mhoeijm@users.noreply.github.com>
Date: Mon, 7 Apr 2025 15:50:49 +0200
Subject: [PATCH 01/12] fix: bring in fixes to mesh the cavities

---
 src/ansys/heart/core/models.py              |  59 +++++-----
 src/ansys/heart/core/pre/mesher.py          | 113 ++++++++++++--------
 src/ansys/heart/core/utils/fluent_reader.py |  15 ++-
 3 files changed, 111 insertions(+), 76 deletions(-)

diff --git a/src/ansys/heart/core/models.py b/src/ansys/heart/core/models.py
index 67d18add8..c3ea35efa 100644
--- a/src/ansys/heart/core/models.py
+++ b/src/ansys/heart/core/models.py
@@ -520,14 +520,8 @@ def mesh_volume(
 
         return self.mesh
 
-    def _mesh_fluid_volume(self, remesh_caps: bool = True):
-        """Generate a volume mesh of the cavities.
-
-        Parameters
-        ----------
-        remesh_caps : bool, optional
-            Flag indicating whether to remesh the caps of each cavity, by default True
-        """
+    def _mesh_fluid_volume(self):
+        """Generate a volume mesh of the cavities."""
         # get all relevant boundaries for the fluid cavities:
         substrings_include = ["endocardium", "valve-plane", "septum"]
         substrings_include_re = "|".join(substrings_include)
@@ -555,38 +549,45 @@ def _mesh_fluid_volume(self, remesh_caps: bool = True):
 
         LOGGER.info("Meshing fluid cavities...")
 
+        # get list of fluid cavities
         # mesh the fluid cavities
-        fluid_mesh = mesher._mesh_fluid_cavities(
-            boundaries_fluid, caps, self.workdir, remesh_caps=remesh_caps
-        )
+        cavity_surfaces = [
+            self.mesh.get_surface(part.cavity.surface.id) for part in self.parts if part.cavity
+        ]
+        # remove caps.
+        cavity_surfaces = [
+            SurfaceMesh(cs.threshold((0, 0), "_cap_id").extract_surface(), name=cs.name)
+            for cs in cavity_surfaces
+        ]
+        fluid_mesh = mesher._mesh_fluid_cavities(cavity_surfaces, self.workdir, mesh_size=1)
 
-        LOGGER.info(f"Meshed {len(fluid_mesh.cell_zones)} fluid regions...")
+        # LOGGER.info(f"Meshed {len(fluid_mesh.cell_zones)} fluid regions...")
 
         # add part-ids
-        cz_ids = np.sort([cz.id for cz in fluid_mesh.cell_zones])
+        # cz_ids = np.sort([cz.id for cz in fluid_mesh.cell_zones])
 
         # TODO: this offset is arbitrary.
-        offset = 10000
-        new_ids = np.arange(cz_ids.shape[0]) + offset
-        czid_to_pid = {cz_id: new_ids[ii] for ii, cz_id in enumerate(cz_ids)}
+        # offset = 10000
+        # new_ids = np.arange(cz_ids.shape[0]) + offset
+        # czid_to_pid = {cz_id: new_ids[ii] for ii, cz_id in enumerate(cz_ids)}
 
-        for cz in fluid_mesh.cell_zones:
-            cz.id = czid_to_pid[cz.id]
+        # for cz in fluid_mesh.cell_zones:
+        #     cz.id = czid_to_pid[cz.id]
 
-        fluid_mesh._fix_negative_cells()
-        fluid_mesh_vtk = fluid_mesh._to_vtk(add_cells=True, add_faces=False)
+        # fluid_mesh._fix_negative_cells()
+        # fluid_mesh_vtk = fluid_mesh._to_vtk(add_cells=True, add_faces=False)
 
-        fluid_mesh_vtk.cell_data["_volume-id"] = fluid_mesh_vtk.cell_data["cell-zone-ids"]
+        # fluid_mesh_vtk.cell_data["part-id"] = fluid_mesh_vtk.cell_data["cell-zone-ids"]
 
-        boundaries = [
-            SurfaceMesh(name=fz.name, triangles=fz.faces, nodes=fluid_mesh.nodes, id=fz.id)
-            for fz in fluid_mesh.face_zones
-            if "interior" not in fz.name
-        ]
+        # boundaries = [
+        #     SurfaceMesh(name=fz.name, triangles=fz.faces, nodes=fluid_mesh.nodes, id=fz.id)
+        #     for fz in fluid_mesh.face_zones
+        #     if "interior" not in fz.name
+        # ]
 
-        self.fluid_mesh = Mesh(fluid_mesh_vtk)
-        for boundary in boundaries:
-            self.fluid_mesh.add_surface(boundary, boundary.id, boundary.name)
+        self.fluid_mesh = Mesh(fluid_mesh)
+        # for boundary in boundaries:
+        #     self.fluid_mesh.add_surface(boundary, boundary.id, boundary.name)
 
         return
 
diff --git a/src/ansys/heart/core/pre/mesher.py b/src/ansys/heart/core/pre/mesher.py
index da1b856fc..cf6d39902 100644
--- a/src/ansys/heart/core/pre/mesher.py
+++ b/src/ansys/heart/core/pre/mesher.py
@@ -26,7 +26,7 @@
 import os
 from pathlib import Path
 import shutil
-from typing import List, Union
+from typing import Union
 
 import numpy as np
 import pyvista as pv
@@ -467,29 +467,28 @@ def _set_size_field_on_face_zones(
 
 # TODO: fix method.
 def _mesh_fluid_cavities(
-    fluid_boundaries: List[SurfaceMesh],
-    caps: List[SurfaceMesh],
-    workdir: str,
-    remesh_caps: bool = True,
-) -> _FluentMesh:
-    """Mesh the fluid cavities.
+    cavity_boundaries: list[SurfaceMesh], workdir: str, mesh_size: float = 1.0
+) -> pv.UnstructuredGrid:
+    """Mesh the caps of each fluid cavity with uniformly.
 
     Parameters
     ----------
-    fluid_boundaries : List[SurfaceMesh]
-        List of fluid boundaries used for meshing.
-    caps : List[SurfaceMesh]
-        List of caps that close each of the cavities.
+    cavity_boundaries : List[SurfaceMesh]
+        List of cavity boundaries used for meshing.
     workdir : str
         Working directory
-    remesh_caps : bool, optional
-        Flag indicating whether to remesh the caps, by default True
+    mesh_size : float
+        Mesh size
 
     Returns
     -------
-    Path
-        Path to the .msh.h5 volume mesh.
+    pv.UnstructuredGrid
+        Unstructured grid with fluid mesh.
     """
+    # Use the following tgrid api utility for each cavity:
+    # Consequently need to associate each "patch" with a cap. E.g. by centroid?
+    #
+    # (tgapi-util-fill-holes-in-face-zone-list '(face-zone-list) max-hole-edges)
     if _uses_container:
         mounted_volume = pyfluent.EXAMPLES_PATH
         work_dir_meshing = os.path.join(mounted_volume, "tmp_meshing-fluid")
@@ -504,16 +503,11 @@ def _mesh_fluid_cavities(
             os.remove(f)
 
     # write all boundaries
-    for b in fluid_boundaries:
+    for b in cavity_boundaries:
         filename = os.path.join(work_dir_meshing, b.name.lower() + ".stl")
         b.save(filename)
         add_solid_name_to_stl(filename, b.name.lower(), file_type="binary")
 
-    for c in caps:
-        filename = os.path.join(work_dir_meshing, c.name.lower() + ".stl")
-        c.save(filename)
-        add_solid_name_to_stl(filename, c.name.lower(), file_type="binary")
-
     session = _get_fluent_meshing_session(work_dir_meshing)
 
     # import all stls
@@ -522,43 +516,74 @@ def _mesh_fluid_cavities(
         # will be in /mnt/pyfluent. So need to use relative paths
         # or replace dirname by /mnt/pyfluent as prefix
         work_dir_meshing = "/mnt/pyfluent/meshing"
-    session.tui.file.import_.cad(f"no {work_dir_meshing} *.stl")
-
-    # merge objects
-    session.tui.objects.merge("'(*)", "model-fluid")
 
-    # fix duplicate nodes
-    session.tui.diagnostics.face_connectivity.fix_free_faces("objects '(*)")
+    session.tui.file.import_.cad(f"no {work_dir_meshing} *.stl")
 
     # set size field
-    session.tui.size_functions.set_global_controls(1, 1, 1.2)
+    session.tui.size_functions.set_global_controls(mesh_size, mesh_size, 1.2)
     session.tui.scoped_sizing.compute("yes")
 
-    # remesh all caps
-    if remesh_caps:
-        session.tui.boundary.remesh.remesh_constant_size("(cap_*)", "()", 40, 20, 1, "yes")
-
-    # convert to mesh object
-    session.tui.objects.change_object_type("(*)", "mesh", "yes")
-
-    # compute volumetric regions
-    session.tui.objects.volumetric_regions.compute("model-fluid")
+    # create caps
+    # (tgapi-util-fill-holes-in-face-zone-list '(face-zone-list) max-hole-edges)
+    # convert all to mesh object
+    session.tui.objects.change_object_type("'(*)", "mesh", "yes")
+    for cavity_boundary in cavity_boundaries:
+        cavity_name = "-".join(cavity_boundary.name.split()).lower()
+        session.scheme_eval.scheme_eval(
+            f"(tgapi-util-fill-holes-in-face-zone-list '({cavity_name}) 1000)"
+        )
+        # merge unreferenced with cavity
+        # (get-unreferenced-face-zones)
+        patch_ids = session.scheme_eval.scheme_eval("(get-unreferenced-face-zones)")
+        session.tui.objects.create(
+            f"{cavity_name}-patches",
+            "fluid",
+            3,
+            "({0})".format(" ".join([str(patch_id) for patch_id in patch_ids])),
+            "()",
+            "mesh",
+            "yes",
+        )
+        # merge objects
+        session.tui.objects.merge(f"'({cavity_name}*)")
+
+    # find overlapping pairs
+    # (tgapi-util-get-overlapping-face-zones "*patch*" 0.1 0.1 )
+    # try:
+    #     overlapping_pairs = session.scheme_eval.scheme_eval(
+    #         '(tgapi-util-get-overlapping-face-zones "*patch*" 0.1 0.1 )'
+    #     )
+    #     for pair in overlapping_pairs:
+    #         # remove first from pair
+    #         session.tui.boundary.manage.delete(f"'({pair[0]})", "yes")
+    # except:
+    #     LOGGER.debug("No overlapping face zones.")
+
+    # merge mesh objects
+    mesh_object_names = session.scheme_eval.scheme_eval("(get-objects-of-type 'mesh)")
+    if len(mesh_object_names) > 1:
+        session.tui.objects.merge("'(*)", "fluid-zones")
+    else:
+        session.tui.objects.rename_object(mesh_object_names[0].str, "fluid-zones")
 
-    # mesh volume
-    session.tui.mesh.auto_mesh("model-fluid")
+    # merge nodes
+    session.tui.boundary.merge_nodes("'(*)", "'(*)", "no", "no , ,")
+    # mesh volumes
+    session.tui.objects.volumetric_regions.compute("fluid-zones", "no")
+    session.tui.mesh.auto_mesh("fluid-zones", "yes", "pyr", "tet", "yes")
 
-    # clean up
     session.tui.objects.delete_all_geom()
-    session.tui.objects.delete_unreferenced_faces_and_edges()
 
-    # write
     file_path_mesh = os.path.join(workdir, "fluid-mesh.msh.h5")
     session.tui.file.write_mesh(file_path_mesh)
 
+    session.exit()
+
+    # # write
     mesh = _FluentMesh(file_path_mesh)
-    mesh.load_mesh()
+    mesh.load_mesh(reconstruct_tetrahedrons=True)
 
-    return mesh
+    return mesh._to_vtk(add_cells=True, add_faces=True, remove_interior_faces=True)
 
 
 def mesh_from_manifold_input_model(
diff --git a/src/ansys/heart/core/utils/fluent_reader.py b/src/ansys/heart/core/utils/fluent_reader.py
index 900677fbd..fdd868b7d 100644
--- a/src/ansys/heart/core/utils/fluent_reader.py
+++ b/src/ansys/heart/core/utils/fluent_reader.py
@@ -362,7 +362,9 @@ def _convert_interior_faces_to_tetrahedrons(self) -> Tuple[np.ndarray, np.ndarra
         return tetrahedrons, cell_ids
 
     # NOTE: no typehint due to lazy import of pyvista
-    def _to_vtk(self, add_cells: bool = True, add_faces: bool = False):
+    def _to_vtk(
+        self, add_cells: bool = True, add_faces: bool = False, remove_interior_faces: bool = False
+    ):
         """Convert mesh to vtk unstructured grid or polydata.
 
         Parameters
@@ -371,6 +373,8 @@ def _to_vtk(self, add_cells: bool = True, add_faces: bool = False):
             Whether to add cells to the vtk object, by default True
         add_faces : bool, optional
             Whether to add faces to the vtk object, by default False
+        remove_interior_faces : bool, optional
+            Remove interior faces, by default False
 
         Returns
         -------
@@ -407,11 +411,16 @@ def _to_vtk(self, add_cells: bool = True, add_faces: bool = False):
 
         if add_faces:
             # add faces.
+            face_zones = self.face_zones
+
+            if remove_interior_faces:
+                face_zones = [fz for fz in face_zones if "interior" not in fz.name]
+
             grid_faces = pv.UnstructuredGrid()
             grid_faces.nodes = self.nodes
 
-            face_zone_ids = np.concatenate([[fz.id] * fz.faces.shape[0] for fz in self.face_zones])
-            faces = np.array(np.concatenate([fz.faces for fz in self.face_zones]), dtype=int)
+            face_zone_ids = np.concatenate([[fz.id] * fz.faces.shape[0] for fz in face_zones])
+            faces = np.array(np.concatenate([fz.faces for fz in face_zones]), dtype=int)
             faces = np.hstack([np.ones((faces.shape[0], 1), dtype=int) * 3, faces])
 
             grid_faces = pv.UnstructuredGrid(

From c8fa17d6f8eab595a2df79700cb5142b8de278bb Mon Sep 17 00:00:00 2001
From: mhoeijm <102799582+mhoeijm@users.noreply.github.com>
Date: Mon, 7 Apr 2025 20:08:05 +0200
Subject: [PATCH 02/12] fix: fixes and cleanup

---
 src/ansys/heart/core/models.py     | 52 +++++++++---------------------
 src/ansys/heart/core/pre/mesher.py | 20 +-----------
 2 files changed, 16 insertions(+), 56 deletions(-)

diff --git a/src/ansys/heart/core/models.py b/src/ansys/heart/core/models.py
index c3ea35efa..96371a378 100644
--- a/src/ansys/heart/core/models.py
+++ b/src/ansys/heart/core/models.py
@@ -520,9 +520,12 @@ def mesh_volume(
 
         return self.mesh
 
+    # TODO: simplify
     def _mesh_fluid_volume(self):
         """Generate a volume mesh of the cavities."""
         # get all relevant boundaries for the fluid cavities:
+
+        # TODO: use naming convention caps.
         substrings_include = ["endocardium", "valve-plane", "septum"]
         substrings_include_re = "|".join(substrings_include)
 
@@ -537,14 +540,8 @@ def _mesh_fluid_volume(self):
         ]
         boundaries_fluid = [b for b in boundaries_fluid if b.name not in boundaries_exclude]
 
-        caps = [c._mesh for p in self.parts for c in p.caps]
-
         if len(boundaries_fluid) == 0:
-            LOGGER.debug("Meshing of fluid cavities not possible. No fluid surfaces detected.")
-            return
-
-        if len(caps) == 0:
-            LOGGER.debug("Meshing of fluid cavities not possible. No caps detected.")
+            LOGGER.error("Meshing of fluid cavities not possible. No fluid surfaces detected.")
             return
 
         LOGGER.info("Meshing fluid cavities...")
@@ -554,40 +551,21 @@ def _mesh_fluid_volume(self):
         cavity_surfaces = [
             self.mesh.get_surface(part.cavity.surface.id) for part in self.parts if part.cavity
         ]
-        # remove caps.
-        cavity_surfaces = [
-            SurfaceMesh(cs.threshold((0, 0), "_cap_id").extract_surface(), name=cs.name)
-            for cs in cavity_surfaces
-        ]
-        fluid_mesh = mesher._mesh_fluid_cavities(cavity_surfaces, self.workdir, mesh_size=1)
-
-        # LOGGER.info(f"Meshed {len(fluid_mesh.cell_zones)} fluid regions...")
 
-        # add part-ids
-        # cz_ids = np.sort([cz.id for cz in fluid_mesh.cell_zones])
-
-        # TODO: this offset is arbitrary.
-        # offset = 10000
-        # new_ids = np.arange(cz_ids.shape[0]) + offset
-        # czid_to_pid = {cz_id: new_ids[ii] for ii, cz_id in enumerate(cz_ids)}
-
-        # for cz in fluid_mesh.cell_zones:
-        #     cz.id = czid_to_pid[cz.id]
-
-        # fluid_mesh._fix_negative_cells()
-        # fluid_mesh_vtk = fluid_mesh._to_vtk(add_cells=True, add_faces=False)
-
-        # fluid_mesh_vtk.cell_data["part-id"] = fluid_mesh_vtk.cell_data["cell-zone-ids"]
+        # get cap meshes.
+        # TODO: for right ventricle add septal surface.
+        cavity_surfaces = []
+        for part in self.parts:
+            try:
+                cavity_surfaces += [self.mesh.get_surface(part.endocardium.id)]
+            except AttributeError:
+                pass
 
-        # boundaries = [
-        #     SurfaceMesh(name=fz.name, triangles=fz.faces, nodes=fluid_mesh.nodes, id=fz.id)
-        #     for fz in fluid_mesh.face_zones
-        #     if "interior" not in fz.name
-        # ]
+        fluid_mesh = mesher._mesh_fluid_cavities(cavity_surfaces, self.workdir, mesh_size=1)
 
+        # rename cell-zone-ids to part-ids
+        # TODO: check if all face zones properly exist.
         self.fluid_mesh = Mesh(fluid_mesh)
-        # for boundary in boundaries:
-        #     self.fluid_mesh.add_surface(boundary, boundary.id, boundary.name)
 
         return
 
diff --git a/src/ansys/heart/core/pre/mesher.py b/src/ansys/heart/core/pre/mesher.py
index cf6d39902..cd088816f 100644
--- a/src/ansys/heart/core/pre/mesher.py
+++ b/src/ansys/heart/core/pre/mesher.py
@@ -485,10 +485,6 @@ def _mesh_fluid_cavities(
     pv.UnstructuredGrid
         Unstructured grid with fluid mesh.
     """
-    # Use the following tgrid api utility for each cavity:
-    # Consequently need to associate each "patch" with a cap. E.g. by centroid?
-    #
-    # (tgapi-util-fill-holes-in-face-zone-list '(face-zone-list) max-hole-edges)
     if _uses_container:
         mounted_volume = pyfluent.EXAMPLES_PATH
         work_dir_meshing = os.path.join(mounted_volume, "tmp_meshing-fluid")
@@ -523,9 +519,7 @@ def _mesh_fluid_cavities(
     session.tui.size_functions.set_global_controls(mesh_size, mesh_size, 1.2)
     session.tui.scoped_sizing.compute("yes")
 
-    # create caps
-    # (tgapi-util-fill-holes-in-face-zone-list '(face-zone-list) max-hole-edges)
-    # convert all to mesh object
+    # create caps with uniform size.
     session.tui.objects.change_object_type("'(*)", "mesh", "yes")
     for cavity_boundary in cavity_boundaries:
         cavity_name = "-".join(cavity_boundary.name.split()).lower()
@@ -547,18 +541,6 @@ def _mesh_fluid_cavities(
         # merge objects
         session.tui.objects.merge(f"'({cavity_name}*)")
 
-    # find overlapping pairs
-    # (tgapi-util-get-overlapping-face-zones "*patch*" 0.1 0.1 )
-    # try:
-    #     overlapping_pairs = session.scheme_eval.scheme_eval(
-    #         '(tgapi-util-get-overlapping-face-zones "*patch*" 0.1 0.1 )'
-    #     )
-    #     for pair in overlapping_pairs:
-    #         # remove first from pair
-    #         session.tui.boundary.manage.delete(f"'({pair[0]})", "yes")
-    # except:
-    #     LOGGER.debug("No overlapping face zones.")
-
     # merge mesh objects
     mesh_object_names = session.scheme_eval.scheme_eval("(get-objects-of-type 'mesh)")
     if len(mesh_object_names) > 1:

From b2e182b13bab95ecde28f05c49508996836d7b25 Mon Sep 17 00:00:00 2001
From: pyansys-ci-bot <92810346+pyansys-ci-bot@users.noreply.github.com>
Date: Tue, 8 Apr 2025 08:38:16 +0000
Subject: [PATCH 03/12] chore: adding changelog file 1028.added.md
 [dependabot-skip]

---
 doc/source/changelog/1028.added.md | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 doc/source/changelog/1028.added.md

diff --git a/doc/source/changelog/1028.added.md b/doc/source/changelog/1028.added.md
new file mode 100644
index 000000000..71aa3b01d
--- /dev/null
+++ b/doc/source/changelog/1028.added.md
@@ -0,0 +1 @@
+mesh blood pools
\ No newline at end of file

From 720487c0d6c476c61af947612ccc26c79830ae73 Mon Sep 17 00:00:00 2001
From: mhoeijm <102799582+mhoeijm@users.noreply.github.com>
Date: Tue, 8 Apr 2025 13:11:53 +0200
Subject: [PATCH 04/12] feat: add method to mesh from fluid boundaries

---
 src/ansys/heart/core/pre/mesher.py | 97 ++++++++++++++++++++++++++++++
 1 file changed, 97 insertions(+)

diff --git a/src/ansys/heart/core/pre/mesher.py b/src/ansys/heart/core/pre/mesher.py
index cd088816f..96952c696 100644
--- a/src/ansys/heart/core/pre/mesher.py
+++ b/src/ansys/heart/core/pre/mesher.py
@@ -1048,3 +1048,100 @@ def mesh_from_non_manifold_input_model(
     vtk_mesh = _post_meshing_cleanup(new_mesh)
 
     return vtk_mesh
+
+
+def _mesh_fluid_from_boundaries(
+    fluid_boundaries: list[SurfaceMesh],
+    workdir: str,
+    mesh_size: float = 1.0,
+) -> pv.UnstructuredGrid:
+    """Mesh the fluid from the boundary surfaces.
+
+    Parameters
+    ----------
+    fluid_boundaries : List[SurfaceMesh]
+        List of fluid boundaries used for meshing.
+    workdir : str
+        Working directory
+    mesh_size : float
+        Mesh size of the patches that.
+
+    Returns
+    -------
+    pv.UnstructuredGrid
+        Unstructured grid with fluid mesh.
+    """
+    if _uses_container:
+        mounted_volume = pyfluent.EXAMPLES_PATH
+        work_dir_meshing = os.path.join(mounted_volume, "tmp_meshing-fluid")
+    else:
+        work_dir_meshing = os.path.join(workdir, "meshing-fluid")
+
+    if not os.path.isdir(work_dir_meshing):
+        os.makedirs(work_dir_meshing)
+    else:
+        files = glob.glob(os.path.join(work_dir_meshing, "*.stl"))
+        for f in files:
+            os.remove(f)
+
+    # write all boundaries
+    for b in fluid_boundaries:
+        filename = os.path.join(work_dir_meshing, b.name.lower() + ".stl")
+        b.save(filename)
+        add_solid_name_to_stl(filename, b.name.lower(), file_type="binary")
+
+    session = _get_fluent_meshing_session(work_dir_meshing)
+
+    # import all stls
+    if _uses_container:
+        # NOTE: when using a Fluent container visible files
+        # will be in /mnt/pyfluent. So need to use relative paths
+        # or replace dirname by /mnt/pyfluent as prefix
+        work_dir_meshing = "/mnt/pyfluent/meshing"
+
+    session.tui.file.import_.cad(f"no {work_dir_meshing} *.stl")
+
+    # set size field
+    session.tui.size_functions.set_global_controls(mesh_size, mesh_size, 1.2)
+    session.tui.scoped_sizing.compute("yes")
+
+    # create caps with uniform size.
+    session.tui.objects.merge("(*)", "fluid-mesh")
+    # object_names = list(session.scheme_eval.scheme_eval("(tgapi-util-get-all-object-name-list)"))
+    # session.tui.objects.rename_object(object_names[0], "fluid-mesh")
+    session.tui.diagnostics.face_connectivity.fix_free_faces(
+        "objects '(fluid-mesh) merge-nodes yes 1e-3"
+    )
+    session.tui.objects.change_object_type("'(fluid-mesh)", "mesh", "yes")
+
+    session.scheme_eval.scheme_eval("(tgapi-util-fill-holes-in-face-zone-list '(*) 1000)")
+
+    patch_ids = session.scheme_eval.scheme_eval("(get-unreferenced-face-zones)")
+
+    session.tui.objects.create(
+        "mesh-patches",
+        "fluid",
+        3,
+        "({0})".format(" ".join([str(patch_id) for patch_id in patch_ids])),
+        "()",
+        "mesh",
+        "yes",
+    )
+    session.tui.objects.merge("'(*)")
+
+    # compute volume and mesh
+    session.tui.objects.volumetric_regions.compute("fluid-mesh", "no")
+    session.tui.mesh.auto_mesh("fluid-mesh", "yes", "pyr", "tet", "yes")
+
+    session.tui.objects.delete_all_geom()
+
+    file_path_mesh = os.path.join(workdir, "fluid-mesh.msh.h5")
+    session.tui.file.write_mesh(file_path_mesh)
+
+    session.exit()
+
+    # write to file.
+    mesh = _FluentMesh(file_path_mesh)
+    mesh.load_mesh(reconstruct_tetrahedrons=True)
+
+    return mesh._to_vtk(add_cells=True, add_faces=True, remove_interior_faces=True)

From a4c614d734b9ba976917ff6e8bda8f024ab2e052 Mon Sep 17 00:00:00 2001
From: mhoeijm <102799582+mhoeijm@users.noreply.github.com>
Date: Tue, 8 Apr 2025 13:12:32 +0200
Subject: [PATCH 05/12] feat: cleanup

---
 src/ansys/heart/core/models.py | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/src/ansys/heart/core/models.py b/src/ansys/heart/core/models.py
index 96371a378..89a093121 100644
--- a/src/ansys/heart/core/models.py
+++ b/src/ansys/heart/core/models.py
@@ -527,16 +527,16 @@ def _mesh_fluid_volume(self):
 
         # TODO: use naming convention caps.
         substrings_include = ["endocardium", "valve-plane", "septum"]
-        substrings_include_re = "|".join(substrings_include)
+        substrings_include_regex = "|".join(substrings_include)
 
-        substrings_exlude = ["pulmonary-valve", "aortic-valve"]
-        substrings_exlude_re = "|".join(substrings_exlude)
+        substrings_exlude = [CapType.PULMONARY_VALVE.value, CapType.AORTIC_VALVE.value]
+        substrings_exlude_regex = "|".join(substrings_exlude)
 
         boundaries_fluid = [
-            b for b in self.mesh._surfaces if re.search(substrings_include_re, b.name)
+            b for b in self.mesh._surfaces if re.search(substrings_include_regex, b.name)
         ]
         boundaries_exclude = [
-            b.name for b in boundaries_fluid if re.search(substrings_exlude_re, b.name)
+            b.name for b in boundaries_fluid if re.search(substrings_exlude_regex, b.name)
         ]
         boundaries_fluid = [b for b in boundaries_fluid if b.name not in boundaries_exclude]
 
@@ -561,7 +561,11 @@ def _mesh_fluid_volume(self):
             except AttributeError:
                 pass
 
-        fluid_mesh = mesher._mesh_fluid_cavities(cavity_surfaces, self.workdir, mesh_size=1)
+        fluid_mesh = mesher._mesh_fluid_from_boundaries(
+            cavity_surfaces, boundaries_fluid, self.workdir, mesh_size=1
+        )
+
+        # TODO: rename caps accordingly
 
         # rename cell-zone-ids to part-ids
         # TODO: check if all face zones properly exist.

From dba3a9b2677d50e6e214f52b52be821dabee8076 Mon Sep 17 00:00:00 2001
From: mhoeijm <102799582+mhoeijm@users.noreply.github.com>
Date: Tue, 8 Apr 2025 13:13:49 +0200
Subject: [PATCH 06/12] feat: cleanup

---
 src/ansys/heart/core/models.py | 23 +++--------------------
 1 file changed, 3 insertions(+), 20 deletions(-)

diff --git a/src/ansys/heart/core/models.py b/src/ansys/heart/core/models.py
index 89a093121..6ace727da 100644
--- a/src/ansys/heart/core/models.py
+++ b/src/ansys/heart/core/models.py
@@ -541,29 +541,12 @@ def _mesh_fluid_volume(self):
         boundaries_fluid = [b for b in boundaries_fluid if b.name not in boundaries_exclude]
 
         if len(boundaries_fluid) == 0:
-            LOGGER.error("Meshing of fluid cavities not possible. No fluid surfaces detected.")
+            LOGGER.error("Meshing of blood pool not possible. No fluid surfaces detected.")
             return
 
-        LOGGER.info("Meshing fluid cavities...")
+        LOGGER.info("Meshing blood pool...")
 
-        # get list of fluid cavities
-        # mesh the fluid cavities
-        cavity_surfaces = [
-            self.mesh.get_surface(part.cavity.surface.id) for part in self.parts if part.cavity
-        ]
-
-        # get cap meshes.
-        # TODO: for right ventricle add septal surface.
-        cavity_surfaces = []
-        for part in self.parts:
-            try:
-                cavity_surfaces += [self.mesh.get_surface(part.endocardium.id)]
-            except AttributeError:
-                pass
-
-        fluid_mesh = mesher._mesh_fluid_from_boundaries(
-            cavity_surfaces, boundaries_fluid, self.workdir, mesh_size=1
-        )
+        fluid_mesh = mesher._mesh_fluid_from_boundaries(boundaries_fluid, self.workdir, mesh_size=1)
 
         # TODO: rename caps accordingly
 

From e25b61235e566a1c725a25cf8aeb4e44cf1dc24d Mon Sep 17 00:00:00 2001
From: mhoeijm <102799582+mhoeijm@users.noreply.github.com>
Date: Tue, 8 Apr 2025 13:14:05 +0200
Subject: [PATCH 07/12] feat: to non public method

---
 src/ansys/heart/core/models.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/ansys/heart/core/models.py b/src/ansys/heart/core/models.py
index 6ace727da..9d2b18d46 100644
--- a/src/ansys/heart/core/models.py
+++ b/src/ansys/heart/core/models.py
@@ -291,7 +291,7 @@ def __init__(self, working_directory: pathlib.Path | str = None) -> None:
         self.mesh = Mesh()
         """Computational mesh."""
 
-        self.fluid_mesh = Mesh()
+        self._fluid_mesh = Mesh()
         """Generated fluid mesh."""
 
         #! TODO: non-functional flag. Remove or replace.
@@ -552,7 +552,7 @@ def _mesh_fluid_volume(self):
 
         # rename cell-zone-ids to part-ids
         # TODO: check if all face zones properly exist.
-        self.fluid_mesh = Mesh(fluid_mesh)
+        self._fluid_mesh = Mesh(fluid_mesh)
 
         return
 

From b34df3d3861861d691800e0da484b90c8c931ce1 Mon Sep 17 00:00:00 2001
From: mhoeijm <102799582+mhoeijm@users.noreply.github.com>
Date: Tue, 8 Apr 2025 13:16:23 +0200
Subject: [PATCH 08/12] feat: cleanup old method

---
 src/ansys/heart/core/pre/mesher.py | 103 -----------------------------
 1 file changed, 103 deletions(-)

diff --git a/src/ansys/heart/core/pre/mesher.py b/src/ansys/heart/core/pre/mesher.py
index 96952c696..bb725566a 100644
--- a/src/ansys/heart/core/pre/mesher.py
+++ b/src/ansys/heart/core/pre/mesher.py
@@ -465,109 +465,6 @@ def _set_size_field_on_face_zones(
     return session
 
 
-# TODO: fix method.
-def _mesh_fluid_cavities(
-    cavity_boundaries: list[SurfaceMesh], workdir: str, mesh_size: float = 1.0
-) -> pv.UnstructuredGrid:
-    """Mesh the caps of each fluid cavity with uniformly.
-
-    Parameters
-    ----------
-    cavity_boundaries : List[SurfaceMesh]
-        List of cavity boundaries used for meshing.
-    workdir : str
-        Working directory
-    mesh_size : float
-        Mesh size
-
-    Returns
-    -------
-    pv.UnstructuredGrid
-        Unstructured grid with fluid mesh.
-    """
-    if _uses_container:
-        mounted_volume = pyfluent.EXAMPLES_PATH
-        work_dir_meshing = os.path.join(mounted_volume, "tmp_meshing-fluid")
-    else:
-        work_dir_meshing = os.path.join(workdir, "meshing-fluid")
-
-    if not os.path.isdir(work_dir_meshing):
-        os.makedirs(work_dir_meshing)
-    else:
-        files = glob.glob(os.path.join(work_dir_meshing, "*.stl"))
-        for f in files:
-            os.remove(f)
-
-    # write all boundaries
-    for b in cavity_boundaries:
-        filename = os.path.join(work_dir_meshing, b.name.lower() + ".stl")
-        b.save(filename)
-        add_solid_name_to_stl(filename, b.name.lower(), file_type="binary")
-
-    session = _get_fluent_meshing_session(work_dir_meshing)
-
-    # import all stls
-    if _uses_container:
-        # NOTE: when using a Fluent container visible files
-        # will be in /mnt/pyfluent. So need to use relative paths
-        # or replace dirname by /mnt/pyfluent as prefix
-        work_dir_meshing = "/mnt/pyfluent/meshing"
-
-    session.tui.file.import_.cad(f"no {work_dir_meshing} *.stl")
-
-    # set size field
-    session.tui.size_functions.set_global_controls(mesh_size, mesh_size, 1.2)
-    session.tui.scoped_sizing.compute("yes")
-
-    # create caps with uniform size.
-    session.tui.objects.change_object_type("'(*)", "mesh", "yes")
-    for cavity_boundary in cavity_boundaries:
-        cavity_name = "-".join(cavity_boundary.name.split()).lower()
-        session.scheme_eval.scheme_eval(
-            f"(tgapi-util-fill-holes-in-face-zone-list '({cavity_name}) 1000)"
-        )
-        # merge unreferenced with cavity
-        # (get-unreferenced-face-zones)
-        patch_ids = session.scheme_eval.scheme_eval("(get-unreferenced-face-zones)")
-        session.tui.objects.create(
-            f"{cavity_name}-patches",
-            "fluid",
-            3,
-            "({0})".format(" ".join([str(patch_id) for patch_id in patch_ids])),
-            "()",
-            "mesh",
-            "yes",
-        )
-        # merge objects
-        session.tui.objects.merge(f"'({cavity_name}*)")
-
-    # merge mesh objects
-    mesh_object_names = session.scheme_eval.scheme_eval("(get-objects-of-type 'mesh)")
-    if len(mesh_object_names) > 1:
-        session.tui.objects.merge("'(*)", "fluid-zones")
-    else:
-        session.tui.objects.rename_object(mesh_object_names[0].str, "fluid-zones")
-
-    # merge nodes
-    session.tui.boundary.merge_nodes("'(*)", "'(*)", "no", "no , ,")
-    # mesh volumes
-    session.tui.objects.volumetric_regions.compute("fluid-zones", "no")
-    session.tui.mesh.auto_mesh("fluid-zones", "yes", "pyr", "tet", "yes")
-
-    session.tui.objects.delete_all_geom()
-
-    file_path_mesh = os.path.join(workdir, "fluid-mesh.msh.h5")
-    session.tui.file.write_mesh(file_path_mesh)
-
-    session.exit()
-
-    # # write
-    mesh = _FluentMesh(file_path_mesh)
-    mesh.load_mesh(reconstruct_tetrahedrons=True)
-
-    return mesh._to_vtk(add_cells=True, add_faces=True, remove_interior_faces=True)
-
-
 def mesh_from_manifold_input_model(
     model: _InputModel,
     workdir: Union[str, Path],

From d4962cd61e2149db8737b503342c9717d7f01cec Mon Sep 17 00:00:00 2001
From: mhoeijm <102799582+mhoeijm@users.noreply.github.com>
Date: Tue, 8 Apr 2025 15:34:40 +0200
Subject: [PATCH 09/12] feat: return Mesh and update cap names

---
 src/ansys/heart/core/models.py     | 25 +++++++++++++++----------
 src/ansys/heart/core/pre/mesher.py | 19 ++++++++++++++++---
 2 files changed, 31 insertions(+), 13 deletions(-)

diff --git a/src/ansys/heart/core/models.py b/src/ansys/heart/core/models.py
index 9d2b18d46..7c9d923f3 100644
--- a/src/ansys/heart/core/models.py
+++ b/src/ansys/heart/core/models.py
@@ -520,12 +520,10 @@ def mesh_volume(
 
         return self.mesh
 
-    # TODO: simplify
-    def _mesh_fluid_volume(self):
+    def _mesh_fluid_volume(self) -> Mesh:
         """Generate a volume mesh of the cavities."""
-        # get all relevant boundaries for the fluid cavities:
-
-        # TODO: use naming convention caps.
+        # get all relevant boundaries for the fluid:
+        # NOTE: relies on substrings to select the right surfaces/boundaries.
         substrings_include = ["endocardium", "valve-plane", "septum"]
         substrings_include_regex = "|".join(substrings_include)
 
@@ -548,13 +546,20 @@ def _mesh_fluid_volume(self):
 
         fluid_mesh = mesher._mesh_fluid_from_boundaries(boundaries_fluid, self.workdir, mesh_size=1)
 
-        # TODO: rename caps accordingly
+        # update patches with appropriate cap name, based on centroid location.
+        model_caps = [c for part in self.parts for c in part.caps]
+        cap_centroids = np.array([cap.centroid for cap in model_caps])
+        cap_names = [cap.name for cap in model_caps]
 
-        # rename cell-zone-ids to part-ids
-        # TODO: check if all face zones properly exist.
-        self._fluid_mesh = Mesh(fluid_mesh)
+        patches = {sid: sn for sid, sn in fluid_mesh._surface_id_to_name.items() if "patch" in sn}
+        for patch_id in patches.keys():
+            patch_mesh = fluid_mesh.get_surface(patch_id)
+            cap_index = np.argmin(np.linalg.norm(cap_centroids - patch_mesh.center, axis=1))
+            fluid_mesh._surface_id_to_name[patch_id] = cap_names[cap_index]
 
-        return
+        self._fluid_mesh = fluid_mesh
+
+        return fluid_mesh
 
     def get_part(self, name: str, by_substring: bool = False) -> Union[Part, None]:
         """Get specific part based on part name."""
diff --git a/src/ansys/heart/core/pre/mesher.py b/src/ansys/heart/core/pre/mesher.py
index bb725566a..6929291d2 100644
--- a/src/ansys/heart/core/pre/mesher.py
+++ b/src/ansys/heart/core/pre/mesher.py
@@ -951,7 +951,7 @@ def _mesh_fluid_from_boundaries(
     fluid_boundaries: list[SurfaceMesh],
     workdir: str,
     mesh_size: float = 1.0,
-) -> pv.UnstructuredGrid:
+) -> Mesh:
     """Mesh the fluid from the boundary surfaces.
 
     Parameters
@@ -1033,7 +1033,9 @@ def _mesh_fluid_from_boundaries(
     session.tui.objects.delete_all_geom()
 
     file_path_mesh = os.path.join(workdir, "fluid-mesh.msh.h5")
-    session.tui.file.write_mesh(file_path_mesh)
+    if os.path.isfile(file_path_mesh):
+        os.remove(file_path_mesh)
+    session.tui.file.write_mesh(file_path_mesh, "ok")
 
     session.exit()
 
@@ -1041,4 +1043,15 @@ def _mesh_fluid_from_boundaries(
     mesh = _FluentMesh(file_path_mesh)
     mesh.load_mesh(reconstruct_tetrahedrons=True)
 
-    return mesh._to_vtk(add_cells=True, add_faces=True, remove_interior_faces=True)
+    vtk_mesh = Mesh(mesh._to_vtk(add_cells=True, add_faces=True, remove_interior_faces=True))
+    vtk_mesh.rename_array("face-zone-ids", "_surface-id")
+    vtk_mesh.rename_array("cell-zone-ids", "_volume-id")
+
+    vtk_mesh._surface_id_to_name = {
+        int(fz.id): fz.name for fz in mesh.face_zones if fz.id in vtk_mesh.surface_ids
+    }
+    vtk_mesh._volume_id_to_name = {
+        int(cz.id): cz.name for cz in mesh.cell_zones if cz.id in vtk_mesh.volume_ids
+    }
+
+    return vtk_mesh

From 450cbd3026ca8060acce30b2c792131681d80798 Mon Sep 17 00:00:00 2001
From: pyansys-ci-bot <92810346+pyansys-ci-bot@users.noreply.github.com>
Date: Thu, 19 Jun 2025 11:02:59 +0000
Subject: [PATCH 10/12] chore: adding changelog file 1028.added.md
 [dependabot-skip]

---
 doc/source/changelog/1028.added.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/source/changelog/1028.added.md b/doc/source/changelog/1028.added.md
index 71aa3b01d..25d7c395f 100644
--- a/doc/source/changelog/1028.added.md
+++ b/doc/source/changelog/1028.added.md
@@ -1 +1 @@
-mesh blood pools
\ No newline at end of file
+Mesh blood pools
\ No newline at end of file

From f6d5c73b9eefda4533afd7d059351ac41bb56f1f Mon Sep 17 00:00:00 2001
From: mhoeijm <102799582+mhoeijm@users.noreply.github.com>
Date: Mon, 11 Aug 2025 13:01:08 +0200
Subject: [PATCH 11/12] do not allow CONTAINER and PIM modes

---
 src/ansys/health/heart/pre/mesher.py | 23 +++++++++++++++++++----
 1 file changed, 19 insertions(+), 4 deletions(-)

diff --git a/src/ansys/health/heart/pre/mesher.py b/src/ansys/health/heart/pre/mesher.py
index 892ef5237..86e24b9f4 100644
--- a/src/ansys/health/heart/pre/mesher.py
+++ b/src/ansys/health/heart/pre/mesher.py
@@ -1042,6 +1042,12 @@ def _mesh_fluid_from_boundaries(
     pv.UnstructuredGrid
         Unstructured grid with fluid mesh.
     """
+    if _launch_mode in [LaunchMode.CONTAINER, LaunchMode.PIM]:
+        raise NotImplementedError(
+            "Meshing of fluid boundaries is not yet supported in PIM mode. "
+            "Please use the containerized or standalone mode."
+        )
+
     if _uses_container:
         mounted_volume = pyfluent.EXAMPLES_PATH
         work_dir_meshing = os.path.join(mounted_volume, "tmp_meshing-fluid")
@@ -1063,11 +1069,20 @@ def _mesh_fluid_from_boundaries(
 
     session = _get_fluent_meshing_session(work_dir_meshing)
 
-    # import all stls
-    if _uses_container:
+    LOGGER.info(f"Starting Fluent Meshing in mode: {_launch_mode}")
+
+    if _launch_mode == LaunchMode.PIM:
+        # Upload files to session if in PIM or Container modes.
+        LOGGER.info(f"Uploading files to session with working directory {work_dir_meshing}...")
+        files = glob.glob(os.path.join(work_dir_meshing, "*.stl"))
+        for file in files:
+            session.upload(file)
+        # In PIM mode files are uploaded to the Fluents working directory.
+        work_dir_meshing = "."
+
+    elif _launch_mode == LaunchMode.CONTAINER:
         # NOTE: when using a Fluent container visible files
-        # will be in /mnt/pyfluent. So need to use relative paths
-        # or replace dirname by /mnt/pyfluent as prefix
+        # will be in /mnt/pyfluent. (equal to mount target)
         work_dir_meshing = "/mnt/pyfluent/meshing"
 
     session.tui.file.import_.cad(f"no {work_dir_meshing} *.stl")

From be01d28761d9e475f916225bf9deb2f2f0351154 Mon Sep 17 00:00:00 2001
From: pyansys-ci-bot <92810346+pyansys-ci-bot@users.noreply.github.com>
Date: Tue, 19 Aug 2025 08:16:16 +0000
Subject: [PATCH 12/12] chore: adding changelog file 1028.added.md
 [dependabot-skip]

---
 doc/source/changelog/1028.added.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/source/changelog/1028.added.md b/doc/source/changelog/1028.added.md
index 25d7c395f..8d63d46e9 100644
--- a/doc/source/changelog/1028.added.md
+++ b/doc/source/changelog/1028.added.md
@@ -1 +1 @@
-Mesh blood pools
\ No newline at end of file
+Mesh blood pools