Closed will-moore closed 7 months ago
Testing on idr-ftp
NB: we need #147 for name_option AND #156, so I've merged them together with this PR in a new branch to allow installing together (https://github.com/snoopycrimecop/omero-cli-zarr/ doesn't exist yet):
conda activate omero_zarr_export
pip install 'omero-cli-zarr @ git+https://github.com/will-moore/omero-cli-zarr@merge_prs'
...
Successfully installed omero-cli-zarr-0+untagged.486.g0b26417
https://github.com/snoopycrimecop/omero-cli-zarr/ doesn't exist yet
That just requires adding the submodule to https://github.com/ome/omero-plugins if you'd like to do that.
Looks good to me. Tested it with the same image 10648046 "dtype": "<f4"
👍
cat 0/.zarray
{
"chunks": [
1,
1,
1024,
1024
],
"compressor": {
"blocksize": 0,
"clevel": 5,
"cname": "lz4",
"id": "blosc",
"shuffle": 1
},
"dimension_separator": "/",
"dtype": "<f4",
"fill_value": 0.0,
"filters": null,
"order": "C",
"shape": [
600,
3,
432,
101
],
"zarr_format": 2
}%
Anyone up for another release in 2023?
Merged, but can't release without fixing the versioning issue: see https://github.com/ome/omero-cli-zarr/pull/156
Images in OMERO with
float
pixelType arefloat-32
(f4
: 4 bytes per pixel) but are currently exported asf8
. E.g. https://idr.openmicroscopy.org/webclient/?show=image-10648046 was exported as https://ome.github.io/ome-ngff-validator/?source=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD852/971f2809-c748-4259-8044-81ba6c774fdd/971f2809-c748-4259-8044-81ba6c774fdd.zarrThis is because we have previously used
np.dtype(omeroDtype)
which gives thefloat64
dtype by default:To test:
Should see
Type: <f4