feat: first round of annotation cli

src/cryo_et_neuroglancer/cli.py

@@ -4,6 +4,7 @@
 from typing import Optional
 
 from .write_segmentation import main as segmentation_encode
+from .write_annotations import main as annotations_encode
 
 
 def encode_segmentation(
@@ -75,6 +76,24 @@ def parse_args(args):
     )
     subcommand.set_defaults(func=encode_segmentation)
 
+    # annotations
+    subcommand = subparsers.add_parser(
+        "encode-annotations", help="Encode annotations file"
+    )
+    subcommand.add_argument(
+        "zarr_paths",
+        help="Path towards your segmentation ZARR folders",
+        nargs="+",
+        type=Path,
+    )
+    subcommand.add_argument(
+        "-o", "--output", required=False, help="Output folder to produce", type=Path
+    )
+    subcommand.add_argument(
+        "-r", "--resolution", required=False, help="Resolution", type=float
+    )
+    subcommand.set_defaults(func=annotations_encode)
+
     return parser.parse_args(args)
 
 

src/cryo_et_neuroglancer/write_annotations.py

@@ -96,32 +96,20 @@ def view_data(coordinate_space: neuroglancer.CoordinateSpace, output_dir: Path)
     print(viewer)
 
 
-def main(paths: list[tuple[Path, Path]], output_dir: Path, should_view: bool) -> None:
+def main(zarr_paths: list[Path], output: Path, resolution: float) -> None:
     """For each path set, load the data and write the combined annotations."""
     annotations = []
-    for path_set in paths:
-        input_metadata_path, input_annotations_path = path_set
+    for path_set in zarr_paths:
+        input_metadata_path = path_set
+        input_annotations_path = path_set.parent / (path_set.stem + ".ndjson")
         metadata, data = load_data(input_metadata_path, input_annotations_path)
         annotations.append({"metadata": metadata, "data": data})
 
     coordinate_space = neuroglancer.CoordinateSpace(
-        names=["x", "y", "z"], units=["", "", ""], scales=[1, 1, 1]
+        names=["x", "y", "z"],
+        units=["nm", "nm", "nm"],
+        scales=[resolution, resolution, resolution],
     )
     colors = [(255, 0, 0, 255), (0, 255, 0, 255)]
-    write_annotations(output_dir, annotations, coordinate_space, colors)
-    print("Wrote annotations to", output_dir)
-
-    if should_view:
-        view_data(coordinate_space, output_dir)
-
-
-if __name__ == "__main__":
-    base_dir = Path("/media/starfish/LargeSSD/data/cryoET/data")
-    input_metadata_path = base_dir / "sara_goetz-ribosome-1.0.json"
-    input_annotations_path = base_dir / "sara_goetz-ribosome-1.0.ndjson"
-    paths = [(input_metadata_path, input_annotations_path)]
-    input_metadata_path = base_dir / "sara_goetz-fatty_acid_synthase-1.0.json"
-    input_annotations_path = base_dir / "sara_goetz-fatty_acid_synthase-1.0.ndjson"
-    paths.append((input_metadata_path, input_annotations_path))
-    should_view = False
-    main(paths, base_dir / "annotations", should_view)
+    write_annotations(output, annotations, coordinate_space, colors)
+    print("Wrote annotations to", output)