janelia-cellmap / openorganelle

A portal for viewing FIB-SEM datasets
Other
10 stars 2 forks source link

Fiji links do not point to container roots #118

Open bogovicj opened 8 months ago

bogovicj commented 8 months ago

My recollection is that the "Copy Fiji Link" buttons used to point to the root of the n5 (or soon, zarr) containers, and that seems not to be the case anymore.

For example, the button on this page https://openorganelle.janelia.org/datasets/jrc_hela-2 should copy this url: s3://janelia-cosem-datasets/jrc_hela-2/jrc_hela-2.n5

but it currently copies this one: s3://janelia-cosem-datasets/jrc_hela-2 which can cause problems (1)

This behavior seems consistent across the site, here's the next three I tried:

(1) Fiji will have to guess what the storage format it will be, and the extension is a strong hint that the urls currently being copied don't have.

d-v-b commented 8 months ago

this is fixed via #119 . the current solution is a hack -- it checks whether there are more n5-formatted images than zarr-formatted images, and associates the url behind the "fiji link" button with the majority. I think most datasets today are essentially 99% or more n5, or 99% or more zarr, so this hack will work.

But the long-term solution is to associate a fiji link with an individual image, not an entire dataset. this will require some more changes to the site that are planned but not in motion yet (see #115 )

bogovicj commented 8 months ago

Looks good now, thanks @d-v-b , feel free to close this issue if you'd like, or leave it open until your preferred solution is ready - up to you.