implement set_hp_flag function

examples/MeshAPI/BrainVerciseMesh_AdaptiveMeshRefinement.py

@@ -57,7 +57,11 @@
     ],
     "MaterialDistribution": {"MRIPath": "../../input_files/Butenko_segmask.nii.gz"},
     "Mesh": {
-        "AdaptiveMeshRefinement": {"Active": True, "MaxIterations": 2},
+        "AdaptiveMeshRefinement": {
+            "Active": True,
+            "MaxIterations": 2,
+            "ErrorTolerance": 0.1,
+        },
         "HPRefinement": {"Active": False, "Order": 1},
     },
     "StimulationSignal": {

ossdbs/api.py

@@ -15,7 +15,6 @@
     dielectric_models,
 )
 from ossdbs.electrodes import ELECTRODE_MODELS, ELECTRODE_PARAMETERS, ELECTRODES
-from ossdbs.electrodes.electrode_model_template import ElectrodeModel
 from ossdbs.fem import (
     PRECONDITIONERS,
     SOLVERS,
@@ -60,6 +59,10 @@ def create_bounding_box(box_parameters: dict) -> BoundingBox:
 def generate_electrodes(settings: dict):
     """Generate an OCC electrode model from the settings dict."""
     _logger.info("Generate electrode geometries")
+
+    hp_refinement = False
+    if "HPRefinement" in settings["Mesh"]:
+        hp_refinement = settings["Mesh"]["HPRefinement"]["Active"]
     electrodes = []
     for electrode_parameters in settings["Electrodes"]:
         name = electrode_parameters["Name"]
@@ -95,18 +98,11 @@ def generate_electrodes(settings: dict):
                 rotation=rotation,
             )
 
-        # Apply hp-refinement only on active contacts
-        if "HPRefinement" in settings["Mesh"]:
-            hp_settings = settings["Mesh"]["HPRefinement"]
-            if hp_settings["Active"] and "Contacts" in electrode_parameters:
-                for contact_info in electrode_parameters["Contacts"]:
-                    if contact_info["Active"]:
-                        contact_idx = contact_info["Contact_ID"]
-                        order = hp_settings["Order"]
-                        _set_edge_hp_flag(electrode, {f"Contact_{contact_idx}": order})
-                        _set_vertex_hp_flag(
-                            electrode, {f"Contact_{contact_idx}": order}
-                        )
+        if hp_refinement:
+            electrode.set_hp_flag(
+                electrode_parameters=electrode_parameters,
+                hp_parameters=settings["Mesh"]["HPRefinement"],
+            )
 
         if "EncapsulationLayer" in electrode_parameters:
             electrode.encapsulation_thickness = electrode_parameters[
@@ -631,17 +627,3 @@ def run_PAM(settings):
             scaling=settings["Scaling"],
             scaling_index=settings["ScalingIndex"],
         )
-
-
-def _set_edge_hp_flag(electrode: ElectrodeModel, edge_sizes: dict) -> None:
-    """Set flag on edges."""
-    for edge in electrode.geometry.edges:
-        if edge.name in edge_sizes:
-            edge.hpref = edge_sizes[edge.name]
-
-
-def _set_vertex_hp_flag(electrode: ElectrodeModel, vertex_sizes) -> None:
-    """Set flag on vertices."""
-    for vertex in electrode.geometry.vertices:
-        if vertex.name in vertex_sizes:
-            vertex.hpref = vertex_sizes[vertex.name]

ossdbs/electrodes/electrode_model_template.py

@@ -225,3 +225,25 @@ def export_electrode(self, output_path, brain_dict, n_electrode) -> None:
             filename=f"{output_path}/electrode_{n_electrode}",
             subdivision=0,
         ).Do(vb=BND)
+
+    def set_hp_flag(self, electrode_parameters: dict, hp_parameters: dict):
+        """Set hp-flags only on active contacts."""
+        if "Contacts" in electrode_parameters:
+            for contact_info in electrode_parameters["Contacts"]:
+                if contact_info["Active"]:
+                    contact_idx = contact_info["Contact_ID"]
+                    order = hp_parameters["Order"]
+                    self._set_edge_hp_flag({f"Contact_{contact_idx}": order})
+                    self._set_vertex_hp_flag({f"Contact_{contact_idx}": order})
+
+    def _set_edge_hp_flag(self, edge_sizes: dict) -> None:
+        """Set flags on edges."""
+        for edge in self.geometry.edges:
+            if edge.name in edge_sizes:
+                edge.hpref = edge_sizes[edge.name]
+
+    def _set_vertex_hp_flag(self, vertex_sizes) -> None:
+        """Set flags on vertices."""
+        for vertex in self.geometry.vertices:
+            if vertex.name in vertex_sizes:
+                vertex.hpref = vertex_sizes[vertex.name]

ossdbs/fem/volume_conductor/volume_conductor_model.py

@@ -260,11 +260,10 @@ def run_full_analysis(
                     # currently: refine until impedance doesn't change by more than 0.1%
                     error = 100
                     refinements = 0
+                    tolerance = adaptive_mesh_refinement["ErrorTolerance"]
+                    max_iterations = adaptive_mesh_refinement["MaxIterations"]
                     # TODO write a meaningful algo
-                    while (
-                        error > 0.1
-                        and refinements < adaptive_mesh_refinement["MaxIterations"]
-                    ):
+                    while error > tolerance and refinements < max_iterations:
                         self.adaptive_mesh_refinement()
                         # solve on refined mesh
                         self.compute_solution(frequency)

ossdbs/utils/settings.py

@@ -65,7 +65,11 @@ class Settings:
                 "MaxMeshSize": 1e6,
             },
             "HPRefinement": {"Active": False, "Order": 1},
-            "AdaptiveMeshRefinement": {"Active": False, "MaxIterations": 10},
+            "AdaptiveMeshRefinement": {
+                "Active": False,
+                "MaxIterations": 10,
+                "ErrorTolerance": 0.1,
+            },
             "MeshSize": {"Edges": {}, "Faces": {}, "Volumes": {}},
             "SaveMesh": False,
             "SavePath": "mesh",