Zarr group arg #49
Open
Zarr group arg #49
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…e saalfeld stitching hierarchy, i.e., c<x>/s<x>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This adds an '--group' command line argument for CreateFusionContainer and SparkAffineFusion. For EASI-FISH pipeline I found it useful to have an the fused result in a round specific group such as 'fused.ome.zarr/r1'. I tried to use timepoints but I might have missed something because they were not working for me. The other option I tried was to use as the output the directory 'fused.ome.zarr/r1'. This worked if I specified the '--storage' argument but other tools could not read the data properly becase .zgroup was no present in the 'fused.ome.zarr' folder and I had to create that manually. If the parameter is not specified it works as before using the root group ('/') for the output.
@StephanPreibisch please take a look and let me know if you can think of any other places that need to be changed. I tested with the '--bdv' option and I was able to open the created project.