Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Select roi rechunk filter itkwasm #717

Merged
merged 4 commits into from
Dec 19, 2023
Merged

Select roi rechunk filter itkwasm #717

Show file tree
Hide file tree
Changes from 3 commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
d5193ec
BUG: rechunk roi data after slicing
thewtex Dec 19, 2023
c5e46f6
DOC: Add filtering, save itk.Image content to SelectROI
thewtex Dec 19, 2023
b8deb3a
DOC: Add itkwasm version of SelectROI
thewtex Dec 19, 2023
653f5c0
BUG: Add required skip-execution tags to new SelectROI cells
thewtex Dec 19, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 7 additions & 0 deletions .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,3 +27,10 @@ docs/jupyterlite/_output/

# autodoc2 generated
docs/apidocs

examples/integrations/itk/roi.zarr/
examples/integrations/itk/roi_gradient.nrrd
examples/integrations/itk/roi_image.nrrd

examples/integrations/itkwasm/roi.zarr/
examples/integrations/itkwasm/roi_image.nrrd
113 changes: 78 additions & 35 deletions examples/integrations/itk/SelectROI.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

635 changes: 635 additions & 0 deletions examples/integrations/itkwasm/SelectROI.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

1 change: 1 addition & 0 deletions itkwidgets/viewer.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -429,6 +429,7 @@ async def get_roi_image(self, scale: int = -1, name: str = 'Image') -> NgffImage
multiscales = from_ngff_zarr(store)
loaded_image = multiscales.images[scale]
roi_data = loaded_image.data[roi_slices]
roi_data = roi_data.rechunk(loaded_image.data.chunksize)
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Ah, I did not encounter this error in my testing - I'm glad you caught this!

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Yes, it seemed to happen occasionally, especially with thin slabs.

return to_ngff_image(
roi_data,
dims=loaded_image.dims,
Expand Down
Loading