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Minor fix to caching embeddings in AIS evaluation #800

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merged 1 commit into from
Nov 25, 2024
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Minor fix to caching embeddings in AIS evaluation #800

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17 changes: 10 additions & 7 deletions micro_sam/evaluation/instance_segmentation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -247,7 +247,7 @@ def run_instance_segmentation_grid_search(
def run_instance_segmentation_inference(
segmenter: Union[AMGBase, InstanceSegmentationWithDecoder],
image_paths: List[Union[str, os.PathLike]],
embedding_dir: Union[str, os.PathLike],
embedding_dir: Optional[Union[str, os.PathLike]],
prediction_dir: Union[str, os.PathLike],
generate_kwargs: Optional[Dict[str, Any]] = None,
) -> None:
Expand Down Expand Up @@ -279,13 +279,16 @@ def run_instance_segmentation_inference(
image = imageio.imread(image_path)

if embedding_dir is None:
segmenter.initialize(image)
embedding_path = None
else:
assert predictor is not None
embedding_path = os.path.join(embedding_dir, f"{os.path.splitext(image_name)[0]}.zarr")
image_embeddings = util.precompute_image_embeddings(
predictor, image, embedding_path, ndim=2, verbose=verbose_embeddings
)
segmenter.initialize(image, image_embeddings)

image_embeddings = util.precompute_image_embeddings(
predictor, image, embedding_path, ndim=2, verbose=verbose_embeddings
)

segmenter.initialize(image, image_embeddings)

masks = segmenter.generate(**generate_kwargs)

Expand Down Expand Up @@ -365,7 +368,7 @@ def run_instance_segmentation_grid_search_and_inference(
val_image_paths: List[Union[str, os.PathLike]],
val_gt_paths: List[Union[str, os.PathLike]],
test_image_paths: List[Union[str, os.PathLike]],
embedding_dir: Union[str, os.PathLike],
embedding_dir: Optional[Union[str, os.PathLike]],
prediction_dir: Union[str, os.PathLike],
experiment_folder: Union[str, os.PathLike],
result_dir: Union[str, os.PathLike],
Expand Down
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