use `ok` in `normalize`

zkbt / chromatic

Tools for visualizing spectrosopic light curves, with flux as a function of wavelength and time.

MIT License

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use `ok` in `normalize` #223

Closed zkbt closed 1 year ago

zkbt commented 1 year ago

Add get_ok_data as (possibly pointless) wrapper to get flux with bad data replaced with nan.
Fix normalize to now use ok.
Add warning to normalize if any of the normalization factors are negative, with suggestion for fix.
Add more tests for normalize. Closes #222 . Passes tests.

zkbt commented 1 year ago

@catrionamurray , this should now at least ignore values that are not ok in the normalization. It will still happily normalize by a negative number and therefore produce negative uncertainties, but at least it warns you about it now. I think for the vast majority of applications you could probably consider negative median flux as making a wavelength effectively useless.

catrionamurray commented 1 year ago

This is great, thank you! I think that maybe a statement in the init file is missing? Should there be from .fluxlike import * in the /get/init.py?

zkbt commented 1 year ago

Oh, yeah, I guess so. I think it works for me without it because the only place it's needed is as a direct import into the Rainbow class definition...

https://github.com/zkbt/chromatic/blob/567e1319414d0b37935b2ca061efe78d67fcad6e/chromatic/rainbows/rainbow.py#L1018

...but it's possible that including in the get/__init__.py helps for some other versions of Python?

zkbt commented 1 year ago

(Just updated this directly in the develop branch).