Download via rawpixelsstore #1
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I need to install bioformats2raw to test that this all still works as before. |
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Would it be easier to create an official OME 'omero-cli-zarr' repository from scratch and just use the rawpixelstore approach for that? 'bioformats2raw' isn't actually needed then. This repository was just an attempt to play around with it a little bit, and is probably unneccessary now. |
| parser.add_argument("--tile_height", default=None) | ||
| parser.add_argument("--resolutions", default=None) | ||
| parser.add_argument("--max_workers", default=None) | ||
| ProxyStringType("Image") |
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This line can be removed, no?
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The name of this file probably isn't conflict-safe enough.
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| parser.add_argument("--bf", action="store_true", | ||
| help="Use bioformats2raw to read from managed repo") | ||
| parser.add_argument("--tile_width", default=None, |
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These might also be of use for the numpy version.
| "--cache_numpy", action="store_true", | ||
| help="Save planes as .npy files in case of connection loss") | ||
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| parser.add_argument("--bf", action="store_true", |
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I could see naming this --local and pass it the ManagedRepository location directly.
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Merging. I'll try to handle Josh's remarks myself in a follow-up PR. Passing in the ManagedRepository location as argument is definitely a good idea! |
img_group named image.getName() added to collection
Ported the script from https://github.com/ome/omero-ms-zarr/blob/master/src/scripts/omero_to_zarr.py and updated with omero metadata
To test:
Also test the other arguments mentioned in the README (
--outputand--cache_numpy).Use napari and the https://github.com/ome/ome-zarr-py to open in napari:
To export with bioformats2raw, use the
--bfflag.