cornerstone: Display NIfTI and dicom image previews

[kousu]

Use CornerstoneJS to render previews of .nii and .dcm on the web, making Gitea more helpful for clinicians and researchers building medical databases.

Here's a DICOM:

and here's a NIfTI:

Fixes #23

[kousu]

This also works naturally with LFS files. If combined with #1 (-> #24), it works equally well for annexed files.

[kousu]

As a reminder to the future: I was very confused by the current rewrite Cornerstone is going through. It went from cornerstone-core ^2.6.1 to @cornerstonejs/core ^0.22.0. The docs are based on the rewrite, but don't actually explain how to use NIfTIs (or many other things), and the docs for the old version have disappeared from the internet.

It turns out the new version is at best unfinished and at worst vaporware, since not even the flagship app currently uses the rewrite (it's still on 2.6.1) and neither has the author of the NIfTI plugin ported to the new API (even though that plugin has started being published under the new namespace at @cornerstonejs/nifti-image-loader ^1.0.8 with cornerstone-nifti-image-loader being abandoned and only running up to 1.0.0).

The upshot is that if the dependencies look inconsistent to you:

https://github.com/neuropoly/gitea/blob/c528c18ae17a52c6a9dc9f71722309270a3bf9ea/package.json#L10-L13

it's because they are.

For future reference: the way I actually figured out how to use this plugin was with the help of GitHub's downstream tab; it helped me find ChRIS_UI whose package.json clearly shows a working configuration and code shows how to actually use all the different filetypes together.

[kousu]

Testing ⚔️

I don't know how to write tests for this since it's mostly frontend code so I'm just not going to do it. I don't think upstream even bothers to test the frontend automatically that much, there only really seems to be these two files:

https://github.com/neuropoly/gitea/blob/fa43bce541507c8a702723f84764a48db9278506/web_src/js/features/repo-code.test.js#L1-L18

https://github.com/neuropoly/gitea/blob/fa43bce541507c8a702723f84764a48db9278506/web_src/js/features/repo-findfile.test.js#L1-L35

which don't actually test loading any pages or images, they are just unit tests on some utils that happen to be in javascript instead of go.

[kousu]

Oh, whoops. Looks like Gitea has a hook for doing just this that can be configured via app.ini. It would be something like

[markup.nifti]
ENABLED = true
FILE_EXTENSIONS = .nii.gz .nii
RENDER_COMMAND = "cornerstone-wrapper.sh"
IS_INPUT_FILE = false

and then we would have to make sure that cornerstone.js and everything else it needs is in custom/public/.

[kousu]

There is a competitor, (thanks @valosekj for the tip): https://brainsprite.github.io/.

We used this in the past: spine-generic/spine-generic#218; it's live on https://spine-generic.readthedocs.io/data-acquisition.html#example-of-datasets.

I am not motivated to rewriting what I already have working, and I found something to support my bias: brainsprite requires server-side pre-processing:

The brainsprite python library uses nilearn in order to generate the sprites, as well as the html and javascript code required above. This code can be inserted into an html page template based on the tempita library.

We'd need a route that turns a .nii.gz image into a .jpg of stitched together sprites, and maybe a place on-disk to cache those, separate from the usual Gitea folders. This is possible, but complicates things a lot.

[valosekj]

There is a competitor, (thanks @valosekj for the tip): https://brainsprite.github.io/.

Another potential competitor is NiiVue. It is used, for example, by AFNI QC HTML report; see NV figure under Methods and Results section:

[kousu]

Lovely, good find!