Upgrade n5 zarr #48
Upgrade n5 zarr #48
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I have this file checked in for convenience when I debug it, but if you don't want it here I can remove it.
| <n5-universe.version>2.3.0</n5-universe.version> | ||
| <n5.version>3.5.0</n5.version> | ||
| <n5-zarr.version>1.5.1</n5-zarr.version> | ||
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the correct property is n5-zarr.version not n5-zarr-version
StephanPreibisch
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krokicki
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Why are changes for getContainerGroupPath() mixed into this PR? Is it necessary to upgrade the Zarr version?
Can you please explain why this is added? I also think it will break the export for BDV-projects, where the XML is created alongside the the OME-ZARR/N5/HDF5. |
This is useful for EASI-FISH pipeline to put all rounds in the same zarr container as different groups for example: stitched.ome.zarr
@StephanPreibisch I will remove this from this PR, but I found this feature really useful especially for our EASI-FISH workflow. |
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Good to know, but we have to make sure it also works outside your use-case @cgoina |
N5-Zarr 1.3.5 has a bug when it writes fill_value attribute. This was fixed in the latest version so I am upgrading n5-zarr.
I also added an additional parameter for CreateFusionContainer and SparkAffineFusion that allowed me to specify the zarr group for the output. This is useful for EASI-FISH pipeline to put all rounds in the same zarr container as different groups for example:
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- r1
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- r2
Currently I could set the output parameter as '-o /stitched.ome.zarr/r1' to put the container where I want it but in this case there is no .zgroup file created under stitched.ome.zarr folder and some tools fail to read the zarr container properly. Adding the '--group' parameter fixes this issue