Add filter_zero_loss_peak argument to spikes_removal_tool and fix one bug.

[ericpre]

It should be PR to next_minor, but I initially check out from next_patch... I can change it to next_minor if necessary.
It may also be a good opportunity to add some tests (not for the ui) for the spikes_removal_tool, I guess it should be possible to test the different method/functions without using the ui?

• Add filter_zero_loss_peak argument
• Add documentation
• Add tests
• Fix bug with update pointer position

[francisco-dlp]

Wouldn't this be equivalent?:

s.isig[start:end].spikes_removal_tool()

[ericpre]

Yes, it is! Thanks :) I will add it to the documentation!

Is there a clever way to set two intervals, that I would have miss? For example to ignore a zero-loss peak?

[francisco-dlp]

You can pass a signal_mask to do that. That's simply a boolean matrix. Model1D has a sort of interactive signal mask editor (e.g. set_signal_range etc) that would be useful to turn into an independent function to create signal masks more conveniently.

[ericpre]

Adding a get_signal_range method to Signal1D, that works in a similar manner than set_signal_range and returns a mask?

[francisco-dlp]

Something like that. Currently Model1D has:

• set_signal_range
• remove_signal_range
• reset_signal_range

They enable editing a mask interactively. Because the mask is stored in the model as an attribute for internal consumption there is no method to get the mask as you propose.

For the model it makes sense to store it internally, but does it make sense to store it internally for the signal? If not, it could be implemented as a Signal that includes the above methods e.g.

mask = s.get_signal_mask() # This returns a mask masking nothing by default
mask.set_signal_range() # It remembers its parent mask and, if no signal range is passed, it plots s for interactive selection
mask.set_signal_range(signal=s2) # Interactively edit the mask with a different signal
s.spikes_removal_tool(signal_mask=mask)

[ericpre]

Ready for review.

[ericpre]

Merged with upstream and resolved conflict.

[tjof2]

Minor doc change @ericpre otherwise looks good!

[codecov]

Codecov Report

Merging #1412 into RELEASE_next_minor will increase coverage by 0.07%.
The diff coverage is 77.91%.

@@                  Coverage Diff                   @@
##           RELEASE_next_minor    #1412      +/-   ##
======================================================
+ Coverage               75.56%   75.63%   +0.07%     
======================================================
  Files                     202      202              
  Lines                   29544    29614      +70     
  Branches                 6439     6449      +10     
======================================================
+ Hits                    22324    22398      +74     
+ Misses                   5401     5390      -11     
- Partials                 1819     1826       +7     

Impacted Files	Coverage Δ
hyperspy/signal.py	75.38% <ø> (ø)
hyperspy/_signals/signal1d.py	75.19% <71.42%> (+3.91%)	⬆️
hyperspy/signal_tools.py	65.64% <76.92%> (+0.08%)	⬆️
hyperspy/_signals/eels.py	75.48% <81.48%> (+0.13%)	⬆️
hyperspy/docstrings/signal.py	100.00% <100.00%> (ø)
hyperspy/docstrings/signal1d.py	100.00% <100.00%> (ø)
hyperspy/drawing/signal1d.py	75.07% <0.00%> (+0.61%)	⬆️

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[tjof2]

If you can resolve the conflicts this should be good to go?

[tjof2]

@francisco-dlp can you check this over again since you initially reviewed it?

[tjof2]

Subject to resolving conflicts.