Merge pull request #213 from computational-cell-analytics/fix-tuple-a…

…nnotation

Fix tuple annotations

micro_sam/instance_segmentation.py

@@ -52,7 +52,7 @@ def __getitem__(self, index):
 
 def mask_data_to_segmentation(
     masks: List[Dict[str, Any]],
-    shape: tuple[int, ...],
+    shape: Tuple[int, ...],
     with_background: bool,
     min_object_size: int = 0,
 ) -> np.ndarray:

micro_sam/prompt_based_segmentation.py

@@ -3,7 +3,7 @@
 """
 
 import warnings
-from typing import Optional
+from typing import Optional, Tuple
 
 import numpy as np
 from nifty.tools import blocking
@@ -308,7 +308,7 @@ def segment_from_mask(
     use_box: bool = True,
     use_mask: bool = True,
     use_points: bool = False,
-    original_size: Optional[tuple[int, ...]] = None,
+    original_size: Optional[Tuple[int, ...]] = None,
     multimask_output: bool = False,
     return_all: bool = False,
     return_logits: bool = False,
@@ -365,7 +365,7 @@ def segment_from_box(
     box: np.ndarray,
     image_embeddings: Optional[util.ImageEmbeddings] = None,
     i: Optional[int] = None,
-    original_size: Optional[tuple[int, ...]] = None,
+    original_size: Optional[Tuple[int, ...]] = None,
     multimask_output: bool = False,
     return_all: bool = False,
 ):
@@ -405,7 +405,7 @@ def segment_from_box_and_points(
     labels: np.ndarray,
     image_embeddings: Optional[util.ImageEmbeddings] = None,
     i: Optional[int] = None,
-    original_size: Optional[tuple[int, ...]] = None,
+    original_size: Optional[Tuple[int, ...]] = None,
     multimask_output: bool = False,
     return_all: bool = False,
 ):

micro_sam/prompt_generators.py

@@ -4,7 +4,7 @@
 """
 
 from collections.abc import Mapping
-from typing import Optional, Tuple
+from typing import List, Optional, Tuple
 
 import numpy as np
 from scipy.ndimage import binary_dilation
@@ -155,10 +155,10 @@ def __call__(
         self,
         segmentation: np.ndarray,
         segmentation_id: int,
-        bbox_coordinates: Mapping[int, tuple],
+        bbox_coordinates: Mapping[int, Tuple],
         center_coordinates: Optional[Mapping[int, np.ndarray]] = None
-    ) -> tuple[
-        Optional[list[tuple]], Optional[list[int]], Optional[list[tuple]], np.ndarray
+    ) -> Tuple[
+        Optional[List[Tuple]], Optional[List[int]], Optional[List[Tuple]], np.ndarray
     ]:
         """Generate the prompts for one object in the segmentation.
 

micro_sam/visualization.py

@@ -146,7 +146,7 @@ def _project_tiled_embeddings(image_embeddings):
 
 def project_embeddings_for_visualization(
     image_embeddings: ImageEmbeddings
-) -> tuple[np.ndarray, tuple[float, ...]]:
+) -> Tuple[np.ndarray, Tuple[float, ...]]:
     """Project image embeddings to pixel-wise PCA.
 
     Args: