Porting `create_empty_zarr` to iohub

czbiohub-sf / iohub

Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata

https://czbiohub-sf.github.io/iohub/

BSD 3-Clause "New" or "Revised" License

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Porting `create_empty_zarr` to iohub #234

Closed edyoshikun closed 1 week ago

edyoshikun commented 2 months ago

This PR adds shrimPy utility functions relevant to iohub listed below:

create_empty_zarr: enables the creation of an empty zarr
process_single_position: function that can apply a czyx in czyx out function to a zarr store.

TODO:

[x] Add docstring documentation to functions
[ ] ~Decide on the processing BaseFOV vs Position level~ moved to #249
[x] Names of the functions
[x] Hypothesis testing

mattersoflight commented 2 months ago

TODO: Implement tests via hypothesis

ieivanov commented 2 months ago

Heads up, I'll have a bunch of comments and edits here, WIP

ieivanov commented 2 months ago

P.S. I'm leaving a bunch of comments here so we can agree on the structure, but I'm also happy to implement some of these suggestions, I'm not asking others (Ed) to implement all of these.

ieivanov commented 1 month ago