util to convert the masks to bool + ruff bump - #319
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TeunHuijben merged 4 commits intoJul 27, 2026
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TeunHuijben
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JoOkuma
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Hi @TeunHuijben , thanks for the PR, I left a few comments to make it a bit more general
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| def _copy_geff(geff_store: StoreLike, output_path: StoreLike) -> Path: | ||
| """Copy a geff directory to ``output_path`` and return the new path.""" | ||
| try: | ||
| src = Path(os.fspath(geff_store)) | ||
| dst = Path(os.fspath(output_path)) | ||
| except TypeError as e: | ||
| raise TypeError("output_path is only supported for filesystem-path geff stores.") from e | ||
| if dst.exists(): | ||
| raise FileExistsError(f"output_path already exists: {dst}") | ||
| shutil.copytree(src, dst) | ||
| return dst |
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Is there a zarr copy function that processes the storelike objects?
I'm thinking of the case where it cannot be loaded as a os.fspath
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zarr.copy_store doesn't exist for zarr3
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What about this implementation?
JoOkuma
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Jul 27, 2026
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The latest version of tracksdata stores masks as booleans in a GEFF. But previously exported GEFFs are saved as
uint64, which causes memory to explode upon loading.This PR implements a utility that converts the mask elements to booleans, either duplicating the geff or doing so in place.
Sorry for doing the
ruffstuff as well in this PR, but GitHub CI takes the latest ruff, so I had to be compliant.