Implement CLI for interactive instance segmentation

Author: constantinpape

micro_sam/sam_annotator/interactive_instance_segmentation.py

@@ -4,6 +4,7 @@
 from magicgui import magicgui
 
 from .annotator_2d import _get_shape
+from .util import _initialize_parser
 from ..import util
 from ..import segment_instances
 from ..visualization import project_embeddings_for_visualization
@@ -71,3 +72,20 @@ def interactive_instance_segmentation(
     v.window.add_dock_widget(autosegment_widget)
 
     napari.run()
+
+
+def main():
+    parser = _initialize_parser(
+        description="Run the automatic instance segmentation in interactive mode"
+        "to determine the optimal segmentation parameters.",
+        with_segmentation_result=False, with_show_embeddings=False,
+    )
+    parser.add_argument(
+        "-c", "--checkpoint", default=None,
+        help="Path to alternative checkpoint instead of the standard model."
+    )
+    args = parser.parse_args()
+    raw = util.load_image_data(args.input, ndim=2, key=args.key)
+    interactive_instance_segmentation(
+        raw, args.embedding_path, args.model_type, args.tile_shape, args.halo, args.checkpoint
+    )

micro_sam/sam_annotator/util.py

@@ -323,7 +323,7 @@ def toggle_label(prompts):
     prompts.refresh_colors()
 
 
-def _initialize_parser(description, with_segmentation_result=True):
+def _initialize_parser(description, with_segmentation_result=True, with_show_embeddings=True):
     parser = argparse.ArgumentParser(description=description)
 
     parser.add_argument(
@@ -336,6 +336,7 @@ def _initialize_parser(description, with_segmentation_result=True):
         help="The key for opening data with elf.io.open_file. This is the internal path for a hdf5 or zarr container, "
         "for a image series it is a wild-card, e.g. '*.png' and for mrc it is 'data'."
     )
+
     parser.add_argument(
         "-e", "--embedding_path",
         help="The filepath for saving/loading the pre-computed image embeddings. "
@@ -356,10 +357,11 @@ def _initialize_parser(description, with_segmentation_result=True):
             help="The key for opening the segmentation data. Same rules as for 'key' apply."
         )
 
-    parser.add_argument(
-        "--show_embeddings", action="store_true",
-        help="Visualize the embeddings computed by SegmentAnything. This can be helpful for debugging."
-    )
+    if with_show_embeddings:
+        parser.add_argument(
+            "--show_embeddings", action="store_true",
+            help="Visualize the embeddings computed by SegmentAnything. This can be helpful for debugging."
+        )
     parser.add_argument(
         "--model_type", default="vit_h", help="The segment anything model that will be used, one of vit_h,l,b."
     )

setup.py

@@ -17,6 +17,7 @@
             "micro_sam.annotator_3d = micro_sam.sam_annotator.annotator_3d:main",
             "micro_sam.annotator_tracking = micro_sam.sam_annotator.annotator_tracking:main",
             "micro_sam.image_series_annotator = micro_sam.sam_annotator.image_series_annotator:main",
+            "micro_sam.interactive_instance_segmentation = micro_sam.sam_annotator.interactive_instance_segmentation:main",
             "micro_sam.precompute_embeddings = micro_sam.util:main",
         ]
     }