New Spec TODO

[constantinpape]

Tentative Spec-Changes:

• [x] sourceLocations -> dataLocations or xmlLocations?
• [x] dataset metadata: exact definition of dataset?
• [x] do we need project metadata in project.json? I think references should be in there.
• [x] grid-view table layout: https://github.com/mobie/mobie/issues/22#issuecomment-803476419
• [x] menuItem format: https://github.com/mobie/mobie-viewer-fiji/issues/200#issuecomment-803475881

Json Schema and spec description: Proper string regex:

• [x] source.menuItem: menuName/itemName
• [x] source.sourceLocations: pattern for xml file path
• [x] segmentationSource.tableRootLocation: pattern for folder
• [x] imagedisplays.color: RGBApattern ("\\(r=(.+),g=(.+),b=(.+),a=(.+)\\)") and randomFromGlasbey
• [x] segmentationDisplays.color: double check allowed values, color map from file, example
• [x] segmentationDisplays.selectedSegmentIds: sourceName;timepoint;labelId
• [x] project.specVersion: MAJOR.MINOR.PATCH
• [x] all name fields: no whitespaces, no ;, no /

Tooling:

• [x] Auto generate parts of spec from json schema, useful tools: fake-schema-cli, jsonschema2md, json-schema-to-markdown
• [ ] CI for static json schema validation (create github actions? https://docs.github.com/en/actions/creating-actions/creating-a-docker-container-action)
• [x] Fix issue with example generation for source.schema

Spec description:

• [ ] The examples generated by schema-faker don't look very nice (weird names where it needs to match the regexps) and are inconsistent where consistency cannot be enforced through the schema (e.g. sources not matching name). Would be best to write some code around this to choose better names and make things consistent or write the examples manually once we fix the current spec version.

[constantinpape]

From discussion with @tischi

• imageDataLocations, tableDataLocations
• references to project, dimensions: {is2d: true/false}

[constantinpape]

Also, the bookmark description will be outdated with the new spec: https://mobie.github.io/tutorials/bookmarks.html

[constantinpape]

Remaining regex issues:

• [^\/]+\/[^\/]+ matches the menuItem a/b pattern, but it still allows for matching a/b/c/...

[constantinpape]

More spec changes:

• Move description and is2d to root level and get rid of dataset in dataset spec; move description and references to root level and get rid of project in project spec, see #6.
• Remove name in sourceTrasforms:affine and sourceTransforms:autoGrid see #7
• Rename tableDataRootLocation to tableDataLocation for segmentationSource and autoGrid, see #9
• imageDisplays -> imageDisplay, segmentationDisplays -> segmentationDisplay, see #10
• Move menuItem from source to view, see #11

[constantinpape]

Add viewerTransform to the example.

[constantinpape]

Above is done, new set of changes:

• Rename color to lut in segmentationDisplay, see #16.
• Add initial fields for scatterplot to segmentationDisplay, see https://github.com/mobie/mobie-viewer-fiji/issues/224
• Don't require sourceDisplays in view? See #19.
• menuItem -> uiSelectionGroup See https://github.com/mobie/mobie.github.io/issues/20#issuecomment-805578633
• Write proper setup names in the xml (not part in the spec, but needs to be changed in mobie-python)