EELS functional fine structure

[francisco-dlp]

Main feature

Currently the fine structure of EELSCLEdges is hardcoded as a spline. This adds the possibilty to use other Components as EELSCLEdge fine strucuture.

To implement the feature, this adds 3 attributes to EELSModel:

• ext_fine_structure fine_structure_components: a set to add the fine structure components
• int_fine_structure fine_structure_spline fine_structure_spline_active: bool. When True, the spline fine structure feature is active. It can be combined with fine_structure_components.
• fine_structure_onset fine_structure_spline_onset: the energy (from the onset) from where to use the "standard" fine structure. This can be None.
• where_ext_fine_structure_zero

Other changes

• Automatic update of model figure when changing the fine structure configuration
• New EELSCLEdge methods fix_fine_structure and free_fine_structure

Example

import hyperspy.api as hs

s = hs.datasets.eelsdb(title="Hexagonal Boron Nitride",
                       spectrum_type="coreloss")[0]
ll = hs.datasets.eelsdb(title="Hexagonal Boron Nitride",
                        spectrum_type="lowloss")[0]

s.set_microscope_parameters(beam_energy=300,
                            convergence_angle=0.2,
                            collection_angle=2.55)

s.add_elements(('B', 'N'))
m = s.create_model(ll=ll)
m.enable_fine_structure()

m.set_signal_range(160.)
m.components.B_K.onset_energy.value = 194
m.components.N_K.onset_energy.value = 402.5
m.components.B_K.fine_structure_width = 40
m.components.N_K.fine_structure_width = 45
m.components.B_K.fine_structure_smoothing = 0.4


g1 = hs.model.components1D.GaussianHF(centre=194.7, fwhm=3., height=5)
g1.name = "B_K_l1"
g2 = hs.model.components1D.GaussianHF(centre=201.9, fwhm=5., height=5)
g2.name = "B_K_l2"
m.extend((g1, g2,))

m.components.B_K.fine_structure_components.update((g1, g2))

m.components.B_K.fine_structure_spline_onset = 205. - m.components.B_K.onset_energy.value

m.smart_fit()
m.plot(plot_components=True)

TODO

• User Guide documentation
• Docstrings
• Tests

[francisco-dlp]

I would like this to be included in the 2.0 release if possible (in the splitted EELS package), but I am leaving on holidays tomorrow and I won't be able to work on the documentation and thte tests until the week of the 28th of August.

[codecov]

Codecov Report

Patch coverage: 86.76% and project coverage change: +0.10% 🎉

Comparison is base (b586b9b) 81.29% compared to head (003d5c7) 81.40%.

Additional details and impacted files

@@                  Coverage Diff                   @@
##           RELEASE_next_major    #3206      +/-   ##
======================================================
+ Coverage               81.29%   81.40%   +0.10%     
======================================================
  Files                     173      173              
  Lines                   24212    24312     +100     
  Branches                 5627     5672      +45     
======================================================
+ Hits                    19684    19792     +108     
+ Misses                   3225     3208      -17     
- Partials                 1303     1312       +9     

Files Changed	Coverage Δ
hyperspy/_components/eels_cl_edge.py	84.38% <86.71%> (+0.08%)	⬆️
hyperspy/models/eelsmodel.py	79.89% <87.50%> (+3.13%)	⬆️

... and 2 files with indirect coverage changes

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[CSSFrancis]

@francisco-dlp This looks good! My plan was to finish splitting the EDS and EELS once #3148 is finished. The good thing about splitting things is that once the EELS EDS is split it doesn't really matter if this is released before/after 2.0.0 as we can just make a minor release in the EELS EDS package.

That being said, I was hoping that we can make a release candidate for the 2.0.0 in the next month or so and then we can go through the process of updating the downstream packages so most likely this won't occur in that time frame (unless people have substantial time to work on these things.

[ericpre]

@francisco-dlp, not much happen in August, would you be able to add documentation and tests in the coming week? If not, maybe just an example to check that this is working when moving code around?

[francisco-dlp]

Yes, I'll add docs this week.

[ericpre]

This is very nice!

I suspect that they will conflict with #3082 when it get merge with RELEASE_next_major. I can do the rebase if this helps.

[ericpre]

Since #3082, there is support for other GOS?

[francisco-dlp]

Thanks. What about "HyperSpy only supports atomic simulations" instead?

Once I polish this a little and add the test, it'll be ready for review.

[francisco-dlp]

This is now ready for review.