feat(Zettaset): allow sharing of a user-specified mask volume across …

…different annotations

deepem/data/dataset/multi_zettaset.py

@@ -132,6 +132,7 @@ def load_sample(
     zettaset_lookup: dict[str, str] | None = None,
     zettaset_resolution: tuple[int, int, int] | None = None,
     requires_binarize: list[str] = [],
+    zettaset_share_mask: str | None = None,
     **kwargs
 ) -> dict[str, np.ndarray]:
     """Load image and labels from a Sample."""
@@ -164,6 +165,16 @@ def convert_array(arr: ArrayLike) -> np.ndarray:
     # Assumes that zettaset's annotation names follow DeepEM's convention.
     zettaset_lookup = zettaset_lookup or {x: x for x in sample.annotation_names}
 
+    # Shared mask
+    shared_mask = None
+    if (not no_mask) and zettaset_share_mask:
+        key = zettaset_share_mask
+        mask_key = f"{zettaset_share_mask}_mask"
+        if key not in sample.masks:
+            raise KeyError(f"Mask '{mask_key}' not found.")
+        mask_vol = sample.read_mask(key)[key]
+        shared_mask = convert_array(mask_vol).astype("uint8")
+
     # Process annotations
     for name, key in zettaset_lookup.items():
 
@@ -178,7 +189,9 @@ def convert_array(arr: ArrayLike) -> np.ndarray:
 
         # Mask
         mask_key = f"{name}_mask"
-        if (not no_mask) and (key in sample.masks):
+        if shared_mask is not None:
+            dset[mask_key] = shared_mask
+        elif (not no_mask) and (key in sample.masks):
             mask_vol = sample.read_mask(key)[key]
             dset[mask_key] = convert_array(mask_vol).astype("uint8")
         else:

deepem/train/option.py

@@ -32,6 +32,7 @@ def initialize(self):
         self.parser.add_argument('--zettaset_padding_spec', type=json.loads, default={})
         self.parser.add_argument('--zettaset_resolution', type=vec3f, default=None)
         self.parser.add_argument('--zettaset_no_mask', action='store_true')
+        self.parser.add_argument('--zettaset_share_mask', type=str, default=None)
 
         # file synchronization for spot/preemptible training
         self.parser.add_argument('--samwise_map', nargs='*', default=None)
@@ -319,6 +320,7 @@ def parse(self):
             zettaset_resolution=opt.zettaset_resolution,
             zettaset_mask=not opt.zettaset_no_mask,
             requires_binarize=requires_binarize,
+            zettaset_share_mask=opt.zettaset_share_mask,
         )
 
         # ONNX