czbiohub-sf / shrimPy

shrimPy: Smart High-throughput Robust Imaging & Measurement in Python
BSD 3-Clause "New" or "Revised" License
7 stars 1 forks source link

CLI for concatenating zarr stores #145

Closed edyoshikun closed 1 week ago

edyoshikun commented 3 weeks ago

NOTE: this function might have to be ported to iohub or iphub later

This PR adds a CLI for concatenating zarr stores. The main purpose is to merge multiples stores similar to append_channels.

Additionally, since this relies on the copy_n_paste_czyx() function to crop the arrays, one can pass cropping parameters for T,Z,Y, and X in the config file.

This helps create toy datasets and merge the datasets at the end of our pipelines and assumes that all the datasets have the same folder structure.

Edit:

ziw-liu commented 1 week ago

What is the testing requirement on shrimPy?

edyoshikun commented 1 week ago

I don't think we had a strict requirement, however, I will add a test function that runs the CLI. The config is checked with the pydantic models.

Thanks @ziw-liu

edyoshikun commented 1 week ago

I added the test and made some changes to make sure the config and cli files have consistent naming w.r.t. to the other CLIs.

talonchandler commented 1 week ago

Thanks @edyoshikun! LGTM