`attributes/ome/omero/channels/label` gets incorrectly coerced to integer
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- Python
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Description
Related to https://github.com/Huber-group-EMBL/SpatialData.validate/pull/3. Visible in the blobs example dataset.
"attributes": {
"ome": {
"omero": {
"channels": [
{
"label": 0
},
{
"label": 1
},
{
"label": 2
}
]
}
Should be
"attributes": {
"ome": {
"omero": {
"channels": [
{
"label": "0"
},
{
"label": "1"
},
{
"label": "2"
}
]
}
The OME-NGFF spec says attributes/ome/omero/channels/label must be a string, but if it's a string containing just an integer, this is silently converted to an integer, making elements in images/ non-compliant with the OME-NGFF spec.
(I know elements in images/ still won't be completely compliant with the OME-NGFF spec after this because of the transformations that are not available in 0.5, but it's a separate issue.)
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by tracing the type-coercion handling for attributes/ome/omero/channels/label and reproduce the behavior with the blobs example dataset. The change is complete when numeric-looking labels remain strings, matching the OME-NGFF requirement shown in the issue.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Active
- Clarity
- Mostly clear
- Newbie friendliness
- 55/100