Prevent (most) NaN propagation in Background and BoxcarExtract

[ojustino]

This pull request should be part 1 of a multi-pronged response to #158. Tests are forthcoming.

Background

Goal: NaNs outside the user-specified window should not propagate into the 1D spectrum of the background or the background-subtracted image. NaNs inside the user-specified window should be ignored.

Approach:

• Adjusted _bkg_array:
  • Take the user-provided mask (if it exists) into account by bringing in the or_mask approach from HorneExtract that also masks non-finite pixels.
  • Fixed a possible mistake in the statistic='median' case that may have previously allowed zero-weighted pixels to still make it into the median calculation.
• bkg_image() and sub_image() don't appear to need changes as long as _bkg_array handles NaNs appropriately.
• bkg_spectrum() and sub_spectrum() just need np.sum changed to np.nansum.

BoxcarExtract

Goal: As with Background, NaNs outside the user-specified window should not propagate into the extracted 1D spectrum. Unlike with Background, NaNs inside the user-specified window should propagate to the extracted 1D spectrum. Zeroing them out of the sum could lure less careful users into finding spectral features that don't actually exist.

Approach:

• Assign no weight to non-finite pixels while summing each column. This case needs to be handled specially because np.nan * 0 = np.nan, not 0. _parse_image() can't help because, for now, it only either adopts the user's mask or, if none is provided, masks every non-finite pixel. It can't only mask non-finite pixels outside the window.
  • The better approach going forward may be for _parse_image() to always defer to the user's mask, even if none is provided. Making our operations more resistant to unmasked NaNs we may see as a result would require major changes in another ticket.

[codecov]

Codecov Report

Merging #159 (bd72fae) into main (7be9a76) will increase coverage by 0.80%.
The diff coverage is 91.66%.

@@            Coverage Diff             @@
##             main     #159      +/-   ##
==========================================
+ Coverage   75.77%   76.58%   +0.80%     
==========================================
  Files           9        9              
  Lines         706      709       +3     
==========================================
+ Hits          535      543       +8     
+ Misses        171      166       -5     

Impacted Files	Coverage Δ
specreduce/background.py	93.75% <90.00%> (+5.45%)	⬆️
specreduce/extract.py	95.09% <100.00%> (+0.03%)	⬆️

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[kecnry]

Acts as I'd expect in the cases that used to result in a column of nans in the background image, and the implementation seems reasonable and clean to me! Happy to re-review/approve once test coverage is added and passes. Thanks!

[tepickering]

looks good to me, too. thanks for this! approved pending the added test coverage codecov is requesting.