Merge pull request #84 from computational-cell-analytics/update-im-loader

Remove unused ndim from load_image_data

Author: constantinpape

micro_sam/sam_annotator/annotator_2d.py

@@ -246,12 +246,12 @@ def annotator_2d(
 def main():
     parser = _initialize_parser(description="Run interactive segmentation for an image.")
     args = parser.parse_args()
-    raw = util.load_image_data(args.input, ndim=2, key=args.key)
+    raw = util.load_image_data(args.input, key=args.key)
 
     if args.segmentation_result is None:
         segmentation_result = None
     else:
-        segmentation_result = util.load_image_data(args.segmentation_result, args.segmentation_key)
+        segmentation_result = util.load_image_data(args.segmentation_result, key=args.segmentation_key)
 
     if args.embedding_path is None:
         warnings.warn("You have not passed an embedding_path. Restarting the annotator may take a long time.")

micro_sam/sam_annotator/annotator_3d.py

@@ -294,12 +294,12 @@ def main():
 
     parser = _initialize_parser(description="Run interactive segmentation for an image volume.")
     args = parser.parse_args()
-    raw = util.load_image_data(args.input, ndim=3, key=args.key)
+    raw = util.load_image_data(args.input, key=args.key)
 
     if args.segmentation_result is None:
         segmentation_result = None
     else:
-        segmentation_result = util.load_image_data(args.segmentation_result, args.segmentation_key)
+        segmentation_result = util.load_image_data(args.segmentation_result, key=args.segmentation_key)
 
     if args.embedding_path is None:
         warnings.warn("You have not passed an embedding_path. Restarting the annotator may take a long time.")

micro_sam/sam_annotator/annotator_tracking.py

@@ -504,12 +504,12 @@ def main():
     )
 
     args = parser.parse_args()
-    raw = util.load_image_data(args.input, ndim=3, key=args.key)
+    raw = util.load_image_data(args.input, key=args.key)
 
     if args.tracking_result is None:
         tracking_result = None
     else:
-        tracking_result = util.load_image_data(args.tracking_result, args.tracking_key)
+        tracking_result = util.load_image_data(args.tracking_result, key=args.tracking_key)
 
     if args.embedding_path is None:
         warnings.warn("You have not passed an embedding_path. Restarting the annotator may take a long time.")

micro_sam/util.py

@@ -479,15 +479,13 @@ def get_centers_and_bounding_boxes(
 
 def load_image_data(
     path: str,
-    ndim: Optional[int] = None,
     key: Optional[str] = None,
     lazy_loading: bool = False
 ) -> np.ndarray:
     """Helper function to load image data from file.
 
     Args:
         path: The filepath to the image data.
-        ndim: The data dimensionality.
         key: The internal filepath for complex data formats like hdf5.
         lazy_loading: Whether to lazyly load data. Only supported for n5 and zarr data.