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.

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

Export of segmentations to n5 doesn't use nearest neighbour interpolation #183

Closed
K-Meech opened this issue Feb 2, 2021 · 10 comments
Closed
Labels
bug Something isn't working

Comments

@K-Meech
Copy link
Collaborator

K-Meech commented Feb 2, 2021

ExportImagePlusAsN5Plugin in Fiji doesn't have options for the interpolation used during downsampling.
For segmentations, this results in values outside the labels for downsampled layers.

Would have to dig into this code https://github.com/bigdataviewer/bigdataviewer-core/blob/master/src/main/java/bdv/export/n5/WriteSequenceToN5.java / or put an issue on their repo.

@tischi tischi added the bug Something isn't working label Feb 3, 2021
@tischi
Copy link
Contributor

tischi commented Feb 3, 2021

Sounds good, let's do both, modify the code you copied and also raise an issue in the bdv-core repo.

@tischi
Copy link
Contributor

tischi commented Feb 9, 2021

@K-Meech

There are now two PR pending fixing this:

If need be, we could think about copying the code to MoBIE until this is merged.

@K-Meech
Copy link
Collaborator Author

K-Meech commented Feb 9, 2021

Great - thanks @tischi!
Let's leave it for now. I won't have time until the end of next week anyway. So we can always copy it over then, if needs be.

@K-Meech
Copy link
Collaborator Author

K-Meech commented Feb 18, 2021

@tischi Would you be happy to copy this over to MoBIE for now? I should have time next week to make a project creator 2.0 with Matt's suggestions, and it'd be great to include this.

@tischi
Copy link
Contributor

tischi commented Feb 18, 2021

@K-Meech Could you first poke Tobias about the PRs? That is, go into the PRs, ping him, and say that you are very interested as well and need this rather soon :)

@K-Meech
Copy link
Collaborator Author

K-Meech commented Mar 3, 2021

@tischi I'm going to start rewriting parts of the project creator soon. Could we copy this over at some point?
I poked Tobias about the PRs, but no response as of yet.

@tischi
Copy link
Contributor

tischi commented Mar 3, 2021

I asked in gitter again, let's wait until tomorrow.

@tischi
Copy link
Contributor

tischi commented Mar 3, 2021

@K-Meech Tobias will not look into it within the next 2 weeks => copy it over, I guess.

@K-Meech
Copy link
Collaborator Author

K-Meech commented Mar 9, 2021

@tischi I'm copying over this code now, and I noticed an issue.
Currently, if you select a downsampling method it persists throughout that imageJ session i.e. if you export your first image with Average downsampling, then all later images have Average downsampling too.

I added a quick fix here: K-Meech@84a9d1a
I'm not sure if this affects the h5 export too. Probably worth updating the request on bdv-core?

@K-Meech
Copy link
Collaborator Author

K-Meech commented Mar 15, 2021

This is fixed now. When the PRs above get merged, we can remove: ExportScalePyramid, DownsampleBlock and WriteSequenceToN5 from MoBIE

@K-Meech K-Meech closed this as completed Mar 15, 2021
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working
Projects
None yet
Development

No branches or pull requests

2 participants