Closed edyoshikun closed 1 week ago
What is the testing requirement on shrimPy?
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
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.
Thanks @edyoshikun! LGTM
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:
all
) by default. The config file by still expose the variables for users who want to do the cropping.