Rename WaveorderReader to ImageReader

[ziw-liu]

This PR does a shallow renaming: the legacy WaveorderReader class is now ImageReader. Otherwise API remains the same.

[ziw-liu]

This PR is related to (but not attempting to resolve) issues mentioned in #1 and #40.

Also I just briefly tested that HCS datasets written by the new NGFF API (#31) can still be opened by the legacy reader with the changes made in #16.

[talonchandler]

Great, thanks @ziw-liu.

I see that ImageReader still uses the (soon to be deprecated) ZarrReader. Can I suggest a deprecation warning on ZarrReader that points users towards the new open_ome_zarr?

[AhmetCanSolak]

happy to see this renaming @ziw-liu , I also second the deprecation suggestion from @talonchandler regarding ZarrReader

[talonchandler]

Thanks for the deprecation warning, @ziw-liu.

What do you think about reducing the default log_level to logging.WARNING, too? At least for the ImageReader?

I think it's really important to alert users that are currently using WaveorderReader (@talonchandler, @edyoshikun , @Soorya19Pradeep) that merely changing WaveorderReader to ImageReader does not finish the migration to our long term iohub solutions. There's more work to do to change to the ngff readers.

[ziw-liu]

What do you think about reducing the default log_level to logging.WARNING, too? At least for the ImageReader?

I just realized that I'm not using that custom logger in other parts of the code. So despite being a sub-optimal state the deprecation warning does show up if you invoked it in __main__ (e.g. a script). We should figure out unified logging too though.

[talonchandler]

the deprecation warning does show up if you invoked it in __main__ (e.g. a script)

If I run this script:

import logging
from iohub.reader import ImageReader
reader = ImageReader('20200812-CardiomyocyteDifferentiation14-Cycle1.zarr')
print('done')

with python test.py from a terminal I only see done. But if I add log_level=logging.WARNING to ImageReader then I receive the expected

[WARNING: zarrfile:  33 2023-02-15 10:32:08,104] `iohub.zarrfile.ZarrReader` is deprecated and will be removed in the future. For OME-NGFF (OME-Zarr) v0.4 datasets please use `iohub.ngff.open_ome_zarr` instead.
done

[ziw-liu]

with python test.py from a terminal I only see done. But if I add log_level=logging.WARNING to ImageReader then I receive the expected

Thanks for testing this! I tested in ipython and assumed the same behavior for a script. Then we do need to change log level in this PR.

[talonchandler]

Thanks for the fixes @ziw-liu!