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ome / ome-ngff-validator

Web page for validating OME-NGFF files
https://ome.github.io/ome-ngff-validator
BSD 2-Clause "Simplified" License
4 stars 3 forks source link

Load zarr chunks #21

Closed will-moore closed 1 year ago

will-moore commented 1 year ago

This addresses the "Load chunks with zarr.js and display" from https://github.com/ome/ome-ngff-validator/issues/6 and the feature request "how can I load a specific location in the hierarchy to check it? i.e. 1/0/0/6/10/4 and /0/0/0/8/23/2?" from https://forum.image.sc/t/error-in-import-of-ome-zarr-in-omero/74252/4

We load chunks according to the indices chosen by the user.

To test:

Screenshot 2022-11-30 at 23 04 32

https://minio-dev.openmicroscopy.org/idr/v0.4/idr0077/9836832_z_dtype_fix.zarr

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imagesc-bot commented 1 year ago

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/error-in-import-of-ome-zarr-in-omero/74252/6

ac744 commented 1 year ago

Hi anatole here, thanks again will for that.

I do not see anything on my zarr (which otherwise validate fine), ie. the image is blank whatever the coordinate I put. Actually the validator seem to crash once I check 'load chunk'...

Chunks are reported to be 7Mb, not sure if that's an issue? also data is XYZC but I do see the sliders to make them 2D.

I tried on other IDR data online and it worked as expected

will-moore commented 1 year ago

@ac744 I wonder if you could check the dev-tools Console or Network and reproduce the crash to see if you see anything useful? A screenshot would be great, thanks. I might add the ability to see the min/max values for each chunk and maybe even a histogram to check if "black" is really black.

ac744 commented 1 year ago

@will-moore yes I got that error:

index.63c4df9c.js:39 Uncaught (in promise) DOMException: Failed to construct 'ImageData': The input data length is not a multiple of (4 * width).
    at https://deploy-preview-21--ome-ngff-validator.netlify.app/assets/index.63c4df9c.js:39:2025
    at xt (https://deploy-preview-21--ome-ngff-validator.netlify.app/assets/index.63c4df9c.js:1:1342)
    at Array.map (<anonymous>)
    at https://deploy-preview-21--ome-ngff-validator.netlify.app/assets/index.63c4df9c.js:4:4319
    at nE (https://deploy-preview-21--ome-ngff-validator.netlify.app/assets/index.63c4df9c.js:4:1587)
will-moore commented 1 year ago

Thanks @ac744 I hopefully fixed that error, and I also now display the Min / Max pixel values for the chunks so you can see if it really is "black" or not.

joshmoore commented 1 year ago

Happy to get this in. Moving forward I imagine we may want to streamline and unify the terminology a bit.

For example perhaps "Load Metadata" to go with "Load Chunks".

Also, the chunks section now shows up between bits that are all "Shape" related.

Maybe something like:

> Size information (pre-loaded)
> Load Metadata
> Load Chunks (at the bottom since it's the biggest)

Random side note: clicking on .zarray might should just copy the URL rather than downloading it. (Or is even that useful?)