Support opening of masks #30
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With that last commit, and with loads masks along with the Image:
And this works locally (with images exported as above) loading masks with the Image:
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In testing against a local array, I was failing to load the masks, @will-moore. I tried unifying the logic and this now works. This, however, removes your directory listing code. Two thoughts:
cc: @tlambert03 |
masks: unify remote and local handling
ome_zarr.py
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| data = da.from_zarr(mask_path) | ||
| # mask data is 5D (t, c, z, y, x) but each layer in napari is 4D (no C) | ||
| # NB: Assume we want 'first Channel' | ||
| data = data[:,0,:,:,:] |
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Shouldn't this be handled on the napari side, instead of in this library?
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ah interesting. There does seem to be a limitation here in napari if you have multiple (image) channels along with a mask for each one. In the near(ish) future, we'll have layer "groups" that would let you associate each labels layer with a given image layer... but for now, you basically have no choice but to have nC x 2 unassociated layers in napari if you have a mask for every image channel.
So for here, doing data[:, 0, :, :, :] will make sure you only have a single labels layer, but will obviously omit some data. So you could return a list of [(data[:,n,:,:,:],meta,'labels') for n in range(nChannels)] if you want to (and, until we provide layer groups, give them names that indicate which image layer they go with?)
lastly, singleton dimensions are handled well in napari, so if nC == 1, you wouldn't need to squeeze it.
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Without that line, the masks shape is 5D: (40, 1, 31, 256, 256) whereas the Image channels have 4D shape (40, 31, 256, 256), so you get a mismatch of dimensions (masks and Image have independent T sliders):
In 9f7f878 I've split mask channels into layers, as suggested by @tlambert03 - Thanks.
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@joshmoore Your logic from ec13afd for detecting masks relies on ome/omero-cli-zarr#12 ? |
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Yes. Happy to roll that back if you need to get this in before 12 lands. |
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This works now (loading masks): |
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Merging this as is. I'll updated ome/omero-ms-zarr#55 to list labeled images as zarrays rather than multiscale zgroups and then we can make that move in a follow up. (It'll be the first test of a breaking change!) |
Currently supports opening of local zarr masks.
To test:
$ omero napari view Image:5514375napariconsole, doviewer.open('path/to/5514375.zarr/masks/')