refactor: remove material settings from settings class (#1257)

Co-authored-by: pyansys-ci-bot <[email protected]>

Author: mhoeijm

doc/source/changelog/1257.miscellaneous.md

@@ -0,0 +1 @@
+Remove material settings from settings class

src/ansys/health/heart/settings/defaults/electrophysiology.py

@@ -51,17 +51,12 @@
         "sigma_passive": Quantity(1.0, "mS/mm"),  # mS/mm: use for passive conduction (e.g. blood)
         "beta": Quantity(140, "1/mm"),
         "cm": Quantity(0.01, "uF/mm^2"),  # uF/mm^2
-        # These are not really material properties?
-        "lambda": Quantity(0.2, "dimensionless"),  # activate extracellular potential solve
-        "percent_endo": Quantity(0.17, "dimensionless"),  # thickness of endocardial layer
-        "percent_mid": Quantity(0.41, "dimensionless"),  # thickness of midmyocardial layer
     },
     "beam": {
         "velocity": Quantity(1, "mm/ms"),  # mm/ms in case of eikonal model
         "sigma": Quantity(1, "mS/mm"),  # mS/mm
         "beta": Quantity(140, "1/mm"),
         "cm": Quantity(0.001, "uF/mm^2"),  # uF/mm^2
-        "lambda": Quantity(0.2, "dimensionless"),
     },
 }
 
@@ -72,15 +67,11 @@
     "sigma_sheet_normal": Quantity(0.2, "mm/ms"),  # mm/ms in case of eikonal model
     "beta": Quantity(140, "1/mm"),
     "cm": Quantity(0.01, "uF/mm^2"),  # uF/mm^2
-    "lambda": Quantity(0.2, "dimensionless"),
-    "percent_endo": Quantity(0.17, "dimensionless"),
-    "percent_mid": Quantity(0.41, "dimensionless"),
 }
 default_beam_material_eikonal = {
     "sigma_fiber": Quantity(1, "mm/ms"),  # mm/ms in case of eikonal model
     "beta": Quantity(140, "1/mm"),
     "cm": Quantity(0.001, "uF/mm^2"),  # uF/mm^2
-    "lambda": Quantity(0.2, "dimensionless"),
 }
 
 # Create monodomain defaults by copying eikonal and changing relevant fields

src/ansys/health/heart/settings/settings.py

@@ -168,33 +168,6 @@ class EPAnalysis(Analysis):
     solvertype: Literal["Monodomain", "Eikonal", "ReactionEikonal"] = "Monodomain"
 
 
-@dataclass(repr=False)
-class Material(Settings):
-    """Class for storing material settings."""
-
-    myocardium: AttrDict = None
-    """Myocardium material."""
-    passive: AttrDict = None
-    """Passive material. For example, the vessel wall."""
-    cap: AttrDict = None
-    """Cap material."""
-
-
-@dataclass(repr=False)
-class EpMaterial(Settings):
-    """Class for storing EP material settings."""
-
-    myocardium: AttrDict = None
-    """Myocardium material."""
-    atrium: AttrDict = None
-    """Atrial material."""
-    cap: AttrDict = None
-    """Cap material."""
-    beam: AttrDict = None
-    """Beam material."""
-    # TODO: consider 'other', e.g passive conductor, soft tissue...?
-
-
 @dataclass(repr=False)
 class BoundaryConditions(Settings):
     """Stores settings/parameters for boundary conditions."""
@@ -226,8 +199,6 @@ class Mechanics(Settings):
 
     analysis: Analysis = field(default_factory=lambda: Analysis())
     """Generic analysis settings."""
-    material: Material = field(default_factory=lambda: Material())
-    """Material settings/configuration."""
     boundary_conditions: BoundaryConditions = field(default_factory=lambda: BoundaryConditions())
     """Boundary condition specifications."""
     system: SystemModel = field(default_factory=lambda: SystemModel())
@@ -297,13 +268,22 @@ def __setattr__(self, __name: str, __value) -> None:
 class Electrophysiology(Settings):
     """Class for keeping track of EP settings."""
 
-    material: EpMaterial = field(default_factory=lambda: EpMaterial())
-    """Material settings/configuration."""
     analysis: EPAnalysis = field(default_factory=lambda: EPAnalysis())
     """Generic analysis settings."""
     stimulation: AttrDict[str, Stimulation] = None
     """Stimulation settings."""
 
+    _layers: dict = field(
+        default_factory=lambda: {
+            "percent_endo": Quantity(0.17, "dimensionless"),  # thickness of endocardial layer
+            "percent_mid": Quantity(0.41, "dimensionless"),  # thickness of midmyocardial layer
+        }
+    )
+    """Layers for material assignment of the myocardium."""
+
+    _lambda: Quantity = Quantity(0.2, "dimensionless")  # activate extracellular potential solve
+    """Intra to extracellular conductivity ratio."""
+
 
 @dataclass(repr=False)
 class Fibers(Settings):
@@ -544,14 +524,11 @@ def load(self, filename: pathlib.Path):
             # assign values to each respective attribute
             analysis = Analysis()
             analysis.set_values(settings[attribute_name]["analysis"])
-            material = Material()
-            material.set_values(settings[attribute_name]["material"])
             boundary_conditions = BoundaryConditions()
             boundary_conditions.set_values(settings[attribute_name]["boundary_conditions"])
             system_model = SystemModel()
             system_model.set_values(settings[attribute_name]["system"])
             self.mechanics.analysis = analysis
-            self.mechanics.material = material
             self.mechanics.boundary_conditions = boundary_conditions
             self.mechanics.system = system_model
 
@@ -593,15 +570,12 @@ def load_defaults(self):
             if isinstance(getattr(self, attr), Mechanics):
                 analysis = Analysis()
                 analysis.set_values(mech_defaults.analysis)
-                material = Material()
-                material.set_values(mech_defaults.material)
                 boundary_conditions = BoundaryConditions()
                 boundary_conditions.set_values(mech_defaults.boundary_conditions)
                 system_model = SystemModel()
                 system_model.set_values(mech_defaults.system_model)
 
                 self.mechanics.analysis = analysis
-                self.mechanics.material = material
                 self.mechanics.boundary_conditions = boundary_conditions
                 self.mechanics.system = system_model
 
@@ -613,12 +587,7 @@ def load_defaults(self):
             if isinstance(getattr(self, attr), Electrophysiology):
                 analysis = EPAnalysis()
                 analysis.set_values(ep_defaults.analysis)
-                # TODO: Deprecate this way of handling default materials
-                material = EpMaterial()
-                material.set_values(ep_defaults.material)
-
                 self.electrophysiology.analysis = analysis
-                self.electrophysiology.material = material
                 self.electrophysiology.stimulation: AttrDict[str, Stimulation] = AttrDict()
                 for key in ep_defaults.stimulation.keys():
                     system_model = Stimulation()

src/ansys/health/heart/writer/ep_writer.py

@@ -425,8 +425,8 @@ def _update_parts_cellmodels(self) -> None:
 
     def _create_myocardial_nodeset_layers(self) -> tuple[int, int, int]:
         """Create myocardial node set layers."""
-        percent_endo = self.settings.electrophysiology.material.myocardium["percent_endo"]
-        percent_mid = self.settings.electrophysiology.material.myocardium["percent_mid"]
+        percent_endo = self.settings.electrophysiology._layers["percent_endo"].m
+        percent_mid = self.settings.electrophysiology._layers["percent_mid"].m
         values = self.model.mesh.point_data["transmural"]
         # Values from experimental data. See:
         # https://www.frontiersin.org/articles/10.3389/fphys.2019.00580/full
@@ -699,7 +699,7 @@ def _update_blood_settings(self) -> None:
                 for kw in deck.keywords:
                     # activate extracellular potential solve
                     if "EM_MAT" in kw.get_title():
-                        kw.lambda_ = self.settings.electrophysiology.material.myocardium["lambda"].m
+                        kw.lambda_ = self.settings.electrophysiology._lambda.m
 
     def _update_ECG_coordinates(self) -> None:  # noqa N802
         """Add ECG computation content."""

src/ansys/health/heart/writer/mechanics_writer.py

@@ -38,7 +38,6 @@
     Mat295,
     NeoHookean,
 )
-import ansys.health.heart.settings.settings as sett
 from ansys.health.heart.settings.settings import SimulationSettings
 from ansys.health.heart.utils.vtk_utils import compute_surface_nodal_area_pyvista
 from ansys.health.heart.writer import custom_keywords as custom_keywords
@@ -81,8 +80,6 @@ def __init__(
         self.set_flow_area: bool = True
         """Flag indicating if the flow area is set for control volume."""
 
-        if sett.Mechanics not in self._get_subsettings():
-            raise ValueError("Expecting mechanics settings.")
         return
 
     def update(self, dynain_name: Optional[str] = None, robin_bcs: list[Callable] = None) -> None:

tests/heart/settings/test_settings.py

@@ -51,10 +51,6 @@
     "      dt_icvout: 5 millisecond\n"
     "      global_damping: 0.33 / second\n"
     "      stiffness_damping: 0.1 second\n"
-    "    material:\n"
-    "      myocardium: null\n"
-    "      passive: null\n"
-    "      cap: null\n"
     "    boundary_conditions:\n"
     "      robin: null\n"
     "      valve: null\n"
@@ -68,11 +64,6 @@
 REF_STRING_SETTINGS_YML_EP = (
     "Simulation Settings:\n"
     "  electrophysiology:\n"
-    "    material:\n"
-    "      myocardium: null\n"
-    "      atrium: null\n"
-    "      cap: null\n"
-    "      beam: null\n"
     "    analysis:\n"
     "      end_time: 1 second\n"
     "      dtmin: 2 second\n"
@@ -89,6 +80,10 @@
     "        period: 800 millisecond\n"
     "        duration: 20 millisecond\n"
     "        amplitude: 50 microfarad / millimeter ** 3\n"
+    "    _layers:\n"
+    "      percent_endo: 0.17 dimensionless\n"
+    "      percent_mid: 0.41 dimensionless\n"
+    "    _lambda: 0.2 dimensionless\n"
 )
 
 
@@ -279,9 +274,7 @@ def default_allsettings():
 def test_load_defaults(default_settings):
     default_settings.to_consistent_unit_system()
 
-    assert default_settings.mechanics.material.myocardium["isotropic"]["rho"].m == pytest.approx(
-        0.001, 1e-9
-    )
+    assert default_settings.mechanics.analysis.end_time.m == 800.0
 
 
 def test_purkinje_settings(default_allsettings: SimulationSettings):