Repository navigation
How to specify ZarrSeparator #241
Description
By default, zarr chunk files use . as the axis separator in their names, e.g. 10.20.30. But in Python, one can use a NestedDirectoryStore to store in a directory tree, effectively using / as the separator, e.g. 10/20/30.
Unfortunately, the metadata in .zarray does not specify which format is used. (This is a known shortcoming of the zarr spec.)
Is there any way to tell neuroglancer which format a zarr array uses? I notice that the source code seems to support both, at least in theory. But I can't figure out how to tell neuroglancer that my zarr array uses the / separator in chunk names instead of the default . separator. Is there a way to do it?
Reacted by Eric Perlman
Activity
jbms commentedon Sep 7, 2020
You can use the key_encoding property:
https://google.github.io/tensorstore/tensorstore/driver/zarr/index.html
stuarteberg commentedon Sep 7, 2020
Thanks very much for your reply. Sorry if I'm being dense, but I'm still confused. I'm trying to open the volume in neuroglancer. I can use either
zarrortensorstoreto create the array on disk, but either way, thekey_encodingsetting is not stored in the metadata on disk, as far as I can tell.Is there a way to somehow provide a
tensorstore-style JSON volume configuration to neuroglancer? So far, I'm just providing a source in the form ofzarr://http://localhost:9000/path/to/myarray.zarr. Are you saying neuroglancer also accepts tensorstore JSON data in that text control?Again, sorry if that's a dumb question. I'm clearly missing something here.
jbms commentedon Sep 7, 2020
Oh sorry, I didn't notice that you opened this issue on neuroglancer rather than tensorstore. Indeed, there is not at the moment support for specifying the separator. If you want to add support, I'd suggest making it a query string parameter, like
zarr://http://localhost:9000/path/to/myarray.zarr?separator=/joshmoore commentedon Feb 24, 2021
I will be looking at a PR for zarr-python at least which will use one of a small number of options for finding the key. Work on the Java side has taken place in bcdev/jzarr#17:
[pull] ndmaster from google:master (#19)
Merge Google's master branch into ndmaster and resolve conflicts (#23)
feat(zarr): support dimension_separator in .zarray file
feat(zarr): support dimension_separator in .zarray file