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Description
- meshfiles Read Zarr Mesh Files #8682
- agglomerate files Read Zarr Agglomerate Files #8633
- segment index files Read Zarr Segment Index Files #8711
- connectome files Read Zarr Connectome Files #8717
- cumsum files (currently looks next to the hdf5 agglomerate files; unused in zarr case)
- legacy json mappings (registered in json but not inside of attachments)
- remove double scanning (once for reporting to wk and once during list request)
- migrate existing jsons and remove directory scanning completely?
Detailed Description
We want meshfiles, agglomerate files, or segment index files to be explicitly listed in the datasource-properties.json
in the future. WK should be able to parse these and use the information, if available, instead of probing the filesystem.
{
"id": {
"name": "l4_sample",
"team": "scalable_minds"
},
"version": 1, # or bump to 2
"scale": [
11.24,
11.24,
28.0
],
"dataLayers": [
{
"name": "color",
...
},
{
"name": "segmentation",
"category": "segmentation",
"boundingBox": {
"topLeft": [
3072,
3072,
512
],
"width": 1024,
"height": 1024,
"depth": 1024
},
"elementClass": "uint32",
"wkwResolutions": [
{
"resolution": [
1,
1,
1
],
"cubeLength": 1024
},
...
],
"dataFormat": "wkw",
"numChannels": 1,
"largestSegmentId": 2504697,
"attachments": {
"meshes": [{ "name": "meshfile", "dataFormat": "hdf5", "path": "segmentation/meshes/meshfile.hdf5" }], # path relative to dataset
"agglomerates": [
{ "name": "agglomerate_view_5", "dataFormat": "zarr3", "path": "segmentation/agglomerates/agglomerate_view_5" },
{ "name": "agglomerate_view_10", "dataFormat": "zarr3", "path": "segmentation/agglomerates/agglomerate_view_10" },
...
],
"cumsum": { "name": "cumsum", "dataFormat": "json", "path": "segmentation/agglomerates/cumsum.json" }, # or null
"segmentIndex": { "name": "segmentIndex", "dataFormat": "zarr3", "path": "segmentation/segmentIndex" }, # or null
"connectomes": [{ "name": "connectome", "dataFormat": "zarr3", "path": "segmentation/connectomes/connectome" }]
}
}
]
}