Closed bnmajor closed 8 months ago
loving it!
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@thewtex @PaulHax A new example notebook has been added but if there is better data to use (maybe a large dataset that is typically stuck to a lower scale?) I'd be happy to update with a different example. This data was more or less selected at random.
@bnmajor awesome job!
A few requests inline.
This is a good dataset, but another to consider is:
https://data.kitware.com/#item/63476e0911dab81428208e27
for more scales / variety.
@bnmajor awesome job!
A few requests inline.
This is a good dataset, but another to consider is:
https://data.kitware.com/#item/63476e0911dab81428208e27
for more scales / variety.
Awesome!
@thewtex Two last items:
@bnmajor what is your ngff_zarr.__version__
?
Checking this branch out locally, I could not reproduce with ngff-Zarr 0.6.0.
Checking this branch out locally, I could not reproduce with ngff-Zarr 0.6.0.
I was on 0.4.7
... Sorry about that!
EDIT: Actually, still seeing it with 0.6.0
...
I seem to recall an older version of itk-vtk-viewer causing this behavior -- is it possible that an old version is used locally?
I tried again with a fresh conda environment and repository checkout, the spacing was correct and consistent across scales.
I'm not using a local instance of the itk-vtk-viewer and we're currently using the latest release...
Oh, I was just looking and viewer1
-- I do see that with viewer2
:-)
roi = multiscales.images[loaded_scale].data[roi_slices]
This is extracting only the array and discarding the metadata.
with:
# Create a new viewer using only the data in the ROI determined above
loaded_image = multiscales.images[loaded_scale]
roi_data = loaded_image.data[roi_slices]
from ngff_zarr import to_ngff_image
roi_image = to_ngff_image(roi_data, dims=loaded_image.dims, scale=loaded_image.scale, translation={'x': roi_region[0][0], 'y': roi_region[0][1], 'z': roi_region[0][2]})
from ngff_zarr import to_ngff_image
?
- update the notebook according to the above.
- could you please update get_roi_region to output a list of dictionaries, 'x', 'y', etc.
?
Updates have been pushed, thank you
Sorry, I was not too clear -- I will push a patch with a minor tweak.
Sorry, I was not too clear -- I will push a patch with a minor tweak.
I see, sorry about my misunderstanding! Thanks for the fix!
@thewtex This is good to go from my end if everything is looking good for you as well
Depends on Kitware/itk-vtk-viewer#724 and #702