Modify SegmentationMethod.from_dict to handle water/tissue (#290)

- Also update associated JSON files to include the `ref_material` for
  all `SegmentationMethod`s, even if it is not intended to change.

Author: arhowe00

src/openlifu/seg/seg_method.py

@@ -53,6 +53,9 @@ def from_dict(d: dict) -> SegmentationMethod:
                 for k, v in materials_dict.items()
             }
 
+        # Ignore ref_material if class is `UniformWater` or `UniformTissue`
+        if short_classname in ["UniformWater", "UniformTissue"]:
+            d.pop("ref_material")
         class_constructor = getattr(seg_methods, short_classname)
         return class_constructor(**d)
 

tests/resources/example_db/protocols/example_protocol/example_protocol.json

@@ -70,7 +70,8 @@
         "specific_heat": 1012,
         "thermal_conductivity": 0.025
       }
-    }
+    },
+    "ref_material": "water"
   },
   "sim_setup": {
     "dims": ["lat", "ele", "ax"],

tests/resources/example_db/subjects/example_subject/sessions/example_session/runs/example_run/example_run_protocol_snapshot.json

@@ -68,7 +68,8 @@
         "specific_heat": 1012,
         "thermal_conductivity": 0.025
       }
-    }
+    },
+    "ref_material": "water"
   },
   "sim_setup": {
     "dims": ["lat", "ele", "ax"],