Support n5 end-chunks with chunksize differing from metadata chunksize #6890
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fm3
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Mar 6, 2023
…come_header_UI * 'master' of github.com:scalableminds/webknossos: (34 commits) Slim down view mode dropdown by using icons (#6900) Logging on password reset/change (#6901) When merging volume tracings, also merge segment lists (#6882) avoid spinner when switching tabs in dashboard (#6894) Upgrade Antd to v4.24 (#6865) Support n5 end-chunks with chunksize differing from metadata chunksize (#6890) Implement http range requests for HttpsSeekableByteChannel (#6869) new GH action for adding issues to project board Fix links in Changelog (#6881) adds dedicated explore method for zarr datasets with a datasource-properties.json (#6879) Release 23.03.0 (#6880) Fix superUser being wrongly marked as organization owners (#6876) Followups for OME-TIFF export (#6874) Fix reload-precomputed-mesh functionality (#6875) Adds OME-TIFF export (#6838) Add evolutions 99,100 to migration guide (#6871) Add link to imprint and privacy to help menu (#6870) Annotation Locking Mechanism (#6819) Update deprecated antd <Menu> (#6860) Add functions to get and set segment colors to the frontend API (#6853) ...
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Turns out N5 chunks report their own size, which may differ from the chunk size specified in metadata for end-chunks (like, at the edges of the dataset). This PR introduces code into the wk chunk reading process that handles that.
First I tried reusing the chunkSizeAtIndex from our Neuroglancer Precomputed code, but it turns out that for N5 the bounding box is not a reliable source, chunks may or may not be truncated, so the chunk size mentioned in each chunk header should be used as the source of truth here.
Additionally, I renamed the TypedChunkReader to ChunkTyper, because its job is not actually reading anything, but converting a previously read byte array to a typed multi array.
URL of deployed dev instance (used for testing):
Steps to test:
Issues: