add bioluminescence proxy correction

[messiem]

The bioluminescence proxies are currently computed using the method developed by Messié et al. (2018). We need to incorporate the correction introduced by Messié et al. (submitted) where vertical correlations between fluorescence and background bioluminescence are used as an indicator of whether "adinos" truly represents adinos, or a combination of diatoms and hdinos.

Corresponding code written by @andermi

[andermi]

need to know if

auv-python/src/data/resample.py

Line 432 in 4fd9f0e

def add_profile(self, depth_threshold: float = 15) -> None:

is called before

auv-python/src/data/resample.py

Line 470 in 4fd9f0e

def add_biolume_proxies( # noqa: PLR0913, PLR0915

So I can have access to profile_number to correct the proxies

[MBARIMike]

No, add_profile() is called after add_biolume_proxies(). I think it can be moved to be called after save_coordinates() and before resample_variable(), which calls add_biolume_proxies(). I'll run some tests to see if that can be done.

[andermi]

I was wondering if I could add a profile number column to df_r like this:

profile_series = self.resampled_nc['profile_number'].to_series()
self.df_r['profile_number'] = profile_series.reindex(self.df_r.index, method='ffill')

[MBARIMike]

I'm late in seeing this question. Is it still relevant or are the profile numbers available in self.df_r now?

[MBARIMike]

I think this has been resolved by #25.