👽 scikit-image>0.26.0 API uses max_image for remove_small_objects

Author: shaneahmed

requirements/requirements.txt

@@ -24,7 +24,7 @@ pillow>=9.3.0
 pydicom>=2.3.1 # Used by wsidicom
 pyyaml>=6.0
 requests>=2.28.1
-scikit-image>=0.20
+scikit-image>=0.26.0
 scikit-learn>=1.2.0
 scipy>=1.8
 shapely>=2.0.0

tiatoolbox/models/architecture/hovernet.py

@@ -541,7 +541,7 @@ def _proc_np_hv(
         blb = np.array(blb_raw >= 0.5, dtype=np.int32)  # noqa: PLR2004
 
         blb = ndimage.label(blb)[0]
-        blb = remove_small_objects(blb, min_size=10)
+        blb = remove_small_objects(blb, max_size=9)
         blb[blb > 0] = 1  # background is 0 already
 
         h_dir = cv2.normalize(
@@ -610,7 +610,8 @@ def _proc_np_hv(
                 "ignore",
                 message="Only one label was provided to `remove_small_objects`",
             )
-            marker = remove_small_objects(marker, min_size=obj_size)
+            # scikit-image changed API in 0.26.0 from min_size to max_size.
+            marker = remove_small_objects(marker, max_size=obj_size - 1)
 
         return watershed(dist, markers=marker, mask=blb)
 

tiatoolbox/models/architecture/hovernetplus.py

@@ -158,7 +158,7 @@ def _proc_ls(ls_map: np.ndarray) -> np.ndarray:
         epith_all = epith_all > 0
         epith_mask = morphology.remove_small_objects(
             epith_all,
-            min_size=min_size,
+            max_size=min_size - 1,  # scikit-image >0.26.0
         ).astype("uint8")
         epith_edited = epith_mask * ls_map
         epith_edited = epith_edited.astype("uint8")

tiatoolbox/models/architecture/micronet.py

@@ -603,7 +603,7 @@ def postproc(
         pred_map = raw_maps[0].compute() if is_dask else raw_maps[0]
         pred_bin = np.argmax(pred_map, axis=2)
         pred_inst = ndimage.label(pred_bin)[0]
-        pred_inst = morphology.remove_small_objects(pred_inst, min_size=50)
+        pred_inst = morphology.remove_small_objects(pred_inst, max_size=49)
         canvas = np.zeros(pred_inst.shape[:2], dtype=np.int32)
         # if margin is zero, there could be arrays of size zero.
         max_value = 0 if not np.any(pred_inst) else np.max(pred_inst)

tiatoolbox/models/architecture/nuclick.py

@@ -619,7 +619,7 @@ def postproc(
 
         """
         masks = preds > thresh
-        masks = remove_small_objects(masks, min_size=min_size)
+        masks = remove_small_objects(masks, max_size=min_size - 1)
         masks = remove_small_holes(masks, area_threshold=min_hole_size)
         if do_reconstruction:
             for i in range(len(masks)):