Transformations0.6

[AlexSurtees]

Description

Implements scene specification and 0.6 multiscales coordinateSystems.

Adds test images including scene. URL can be found at fixtures/scene.yaml e.g.

https://uk1s3.embassy.ebi.ac.uk/idr/zarr/test-data/v0.6.dev3/idr0050/4995115_scene.zarr

NOTE

Due to image metadata mis-specification, the image WILL NOT align correctly while conforming to the specification rules. However, if the additional 'rotated' transformations are included the image DOES align correctly (i.e. the rotation transformation logic is correctly implemented). This is because the scene-level transformations specified here

https://will-moore.github.io/ome-ngff-validator/?source=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/test-data/v0.6.dev3/idr0050/4995115_scene.zarr

for each image have input coordinate system 'physical', meaning we should only apply the coordinate transformations with coordinate system 'physical' from these images.

[codecov]

Codecov Report

❌ Patch coverage is 81.09756% with 31 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
viewer/src/coordinate-transformations.ts	58.00%	19 Missing and 2 partials ⚠️
viewer/src/io.ts	57.14%	5 Missing and 1 partial ⚠️
viewer/src/ome.ts	97.26%	2 Missing ⚠️
viewer/tests/metadata.js	33.33%	2 Missing ⚠️

📢 Thoughts on this report? Let us know!

[will-moore]

It would be good to test this with @jo-mueller's test samples listed at https://forum.image.sc/t/ngff-weekly-dev-update-thread/110810/98.
I tried running locally with e.g. http://localhost:5173/?source=https://s3.zih.tu-dresden.de/johamuel:rfc5-transform-sanity-checks/logan_shepp_rotation_30_degree_anticlockwise_around_center.ome.zarr/
but it seems this fails due to no validParsers being found for this data.

const parser = validParsers[validParsers.length - 1];

  return {
->    data: parser.schema.parse(data),

TypeError: Cannot read properties of undefined (reading 'schema')
    at parse (parse.ts:34:18)
    at createSourceData (io.ts:81:24)
    at async VizarrViewer.tsx:68:30