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scripts/extinfo_mkngff.py
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| path = f"{path}/{pos}" | ||
| else: | ||
| path = get_filepaths_info(img) | ||
| path = f"{path}/0" |
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idr0091 images weren't created with bioformats2raw, so they won't need the /0.
All the other non-HCS images will need /0.
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Ah ok thanks. Guess it needs a flag for "bioformats2raw layout" then. I'll use proper argparse then.
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Since a couple of Screens have 400 or 500 Plates, we may want an option to do a range of plates (0-50, 50-100 etc) and/or to skip ones that have already been processed, so if processing of a Screen fails after 100 Plates, you can simply run it again and it'll skip a Plate if the first image already has externalInfo set? |
scripts/extinfo_mkngff.py
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| else: | ||
| path = get_filepaths_info(img) | ||
| path = f"{path}/0" | ||
| if check(path): |
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Some idr0091 datasets e.g. https://idr.openmicroscopy.org/webclient/?show=dataset-11902 contain a mix of zarr and regular tiff images, so the check will fail with the tif images, which is fine as they can be ignored.
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That should handle bioformats layout (/0) and non bf layout images. Also skip option to skip images with existing extinfo (would still have to iterate through all plates and images, but hopefully bit faster). |
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Add script which sets the external info to the http:// URL for mkngff datasets.
Tested on:
idr0051 (Project): https://idr-testing.openmicroscopy.org/webclient/?show=project-552
idr0090 (Screen): https://idr-testing.openmicroscopy.org/webclient/?show=screen-2851
(installed ome/omero-zarr-pixel-buffer#13 on idr-testing, needed for http URL support)
(cc @jburel )