Closed will-moore closed 3 months ago
Name | Link |
---|---|
Latest commit | 2408246e2256cb90e0e6ba2e2449ceafee9319c5 |
Latest deploy log | https://app.netlify.com/sites/ome-ngff-validator/deploys/65c25dd7e7511a00088ef8b0 |
Deploy Preview | https://deploy-preview-32--ome-ngff-validator.netlify.app/ |
Preview on mobile | Toggle QR Code...Use your smartphone camera to open QR code link. |
To edit notification comments on pull requests, go to your Netlify site configuration.
cc @joshmoore - know any good samples for testing?
I'd probably start from https://github.com/scverse/spatialdata-notebooks/tree/main/notebooks/developers_resources/storage_format
cc: @LucaMarconato
Thanks @joshmoore for tagging. Unfortunately the datasets linked could be some good starting points (and especially the code to generate variations of them), but they don't agree 100% to the current specs. As discussed here: https://github.com/scverse/spatialdata/issues/35 we wanted to wait until the transformation PR got merged, but unfortunately it didn't happen.
Testing a bunch of invalid sample files, validation is working but I find the errors can be a bit verbose.
E.g. "affine": [[1, 2, 3, 4], [5, 6, 7, 8, 9], 1],
gives me 21 Errors!
The useful ones are:
{
"instancePath": "/multiscales/0/coordinateTransformations/0/affine/0",
"schemaPath": "#/$defs/mtxFlatOrNested/oneOf/0/items/type",
"keyword": "type",
"params": {
"type": "number"
},
"message": "must be number"
}
{
"instancePath": "/multiscales/0/coordinateTransformations/0/affine/2",
"schemaPath": "#/$defs/mtxFlatOrNested/oneOf/1/items/type",
"keyword": "type",
"params": {
"type": "array"
},
"message": "must be array"
}
I tried adding an invalid arrayCoordinateSystem
block (without axes
element) but this doesn't fail validation
{
"multiscales": [
{
"version": "0.5-dev",
"name": "example",
"arrayCoordinateSystem" : {
"name" : "myDataArray",
"missing_axes" : []
},
The schema that contains arrayCoordinateSystem
spec is coordinate_systems_and_transforms.schema but that schema isn't referenced by the image.schema
or any other schemas that I can see, so I haven't loaded it in this PR.
LucaMarconato commented 2 weeks ago https://github.com/scverse/spatialdata/issues/35 we wanted to wait until the transformation PR got merged...
cc: @bogovicj but I think, @LucaMarconato, that it would now be a good time to tackle this.
@will-moore: I've updated the title to be "Transforms supports" rather than v0.5. I leave it up to you whether to change the usages internally or if we just close for the moment.
I'll close for now, thx
Adding support for https://github.com/ome/ngff/pull/138
Since that PR isn't merged yet, we need custom URL for loading schemas from that branch.
This PR build is deployed at https://deploy-preview-32--ome-ngff-validator.netlify.app - but I don't know of good sample data to test with.
To test a sample file containing various example snippets from the PR above see https://deploy-preview-32--ome-ngff-validator.netlify.app/?source=https://minio-dev.openmicroscopy.org/idr/v0.5/idr0050/4995115.zarr
NB: this is valid according to the proposed schemas, but won't make any sense to a viewer client.
I'm not loading some schemas, such as
coordinate_systems_and_transforms.schema
andcoordinateTransformations.schema
. I'm don't see that they are needed by any validation yet, but I've not tried much. Also the strict schemas aren't used (same as before).