Refactor gui for wrong embedding files

Author: constantinpape

micro_sam/sam_annotator/annotator_2d.py

@@ -9,6 +9,7 @@
 from .. import util
 from .. import instance_segmentation
 from ..visualization import project_embeddings_for_visualization
+from .gui_utils import show_wrong_file_warning
 from .util import (
     clear_all_prompts, commit_segmentation_widget, create_prompt_menu,
     prompt_layer_to_boxes, prompt_layer_to_points, prompt_segmentation, toggle_label, LABEL_COLOR_CYCLE,
@@ -215,7 +216,8 @@ def annotator_2d(
     else:
         PREDICTOR = predictor
     IMAGE_EMBEDDINGS = util.precompute_image_embeddings(
-        PREDICTOR, raw, save_path=embedding_path, ndim=2, tile_shape=tile_shape, halo=halo
+        PREDICTOR, raw, save_path=embedding_path, ndim=2, tile_shape=tile_shape, halo=halo,
+        wrong_file_callback=show_wrong_file_warning
     )
 
     # we set the pre-computed image embeddings if we don't use tiling

micro_sam/sam_annotator/annotator_3d.py

@@ -8,6 +8,7 @@
 from .. import util
 from ..prompt_based_segmentation import segment_from_mask
 from ..visualization import project_embeddings_for_visualization
+from .gui_utils import show_wrong_file_warning
 from .util import (
     clear_all_prompts, commit_segmentation_widget, create_prompt_menu,
     prompt_layer_to_boxes, prompt_layer_to_points, prompt_segmentation,
@@ -195,7 +196,8 @@ def annotator_3d(
     global PREDICTOR, IMAGE_EMBEDDINGS
     PREDICTOR = util.get_sam_model(model_type=model_type)
     IMAGE_EMBEDDINGS = util.precompute_image_embeddings(
-        PREDICTOR, raw, save_path=embedding_path, tile_shape=tile_shape, halo=halo
+        PREDICTOR, raw, save_path=embedding_path, tile_shape=tile_shape, halo=halo,
+        wrong_file_callback=show_wrong_file_warning,
     )
 
     #

micro_sam/sam_annotator/annotator_tracking.py

@@ -12,6 +12,7 @@
 
 from .. import util
 from ..prompt_based_segmentation import segment_from_mask
+from .gui_utils import show_wrong_file_warning
 from .util import (
     create_prompt_menu, clear_all_prompts,
     prompt_layer_to_boxes, prompt_layer_to_points,
@@ -358,7 +359,8 @@ def annotator_tracking(
 
     PREDICTOR = util.get_sam_model(model_type=model_type)
     IMAGE_EMBEDDINGS = util.precompute_image_embeddings(
-        PREDICTOR, raw, save_path=embedding_path, tile_shape=tile_shape, halo=halo
+        PREDICTOR, raw, save_path=embedding_path, tile_shape=tile_shape, halo=halo,
+        wrong_file_callback=show_wrong_file_warning,
     )
 
     CURRENT_TRACK_ID = 1

micro_sam/util.py

@@ -354,7 +354,7 @@ def precompute_image_embeddings(
 
             # data signature does not match or is not in the file
             if "data_signature" not in f.attrs or f.attrs["data_signature"] != data_signature:
-                warnings.warn("Embeddings file is invalid. Please recompute embeddings to new file.")
+                warnings.warn("Embeddings file is invalid. Please recompute embeddings in a new file.")
                 if wrong_file_callback is not None:
                     save_path = wrong_file_callback(save_path)
                 f = zarr.open(save_path, "a")