Add support for "sig" and "nav" to index axes_manager

[ericpre]

This is a simple change but very convenient!

Progress of the PR

• Add support for "sig" and "nav" to index axes_manager,
• update docstring (if appropriate),
• update user guide (I may have another to see where best to update),
• add an changelog entry in the upcoming_changes folder (see upcoming_changes/README.rst),
• Check formatting changelog entry in the readthedocs doc build of this PR (link in github checks)
• add tests,
• ready for review.

Minimal example of the bug fix or the new feature

import hyperspy.api as hs
import numpy as np
s = hs.signals.Signal1D(np.ones((10, 10, 10)))

assert s.axes_manager["nav"] == s.axes_manager.navigation_axes
assert s.axes_manager["sig"] == s.axes_manager.signal_axes

# Sum over navigation axis
s_sum_nav = s.sum(axis="nav")

# Sum over signal axis
s_sum_sig = s.sum(axis="sig")

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 80.65%. Comparing base (70b9669) to head (daba5e9).

Additional details and impacted files

@@                  Coverage Diff                   @@
##           RELEASE_next_minor    #3385      +/-   ##
======================================================
+ Coverage               80.63%   80.65%   +0.01%     
======================================================
  Files                     146      146              
  Lines                   21918    21929      +11     
  Branches                 5174     5178       +4     
======================================================
+ Hits                    17674    17687      +13     
+ Misses                   3027     3026       -1     
+ Partials                 1217     1216       -1     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[ericpre]

The failure on CI is related to sympy 1.13.0rc1 - see sympy/sympy#26663 and potential fix in sympy/sympy#26678.

[bjodah]

@ericpre, I saw the mention in the PR over at SymPy: I'm curious, do you know what Derivative instances are present in the expressions you use lambdify on? If so, we should try to amend my PR against the sympy repo with some relevant test cases. In particular, I'd like to add test(s) to test_lambdify.py analogous to this one:
https://github.com/sympy/sympy/pull/26678/files#diff-a9bc959f22b154b22a706c75d4927a5a2806ce36f499b8e5b6f993470aebafa3

[ericpre]

Thanks @bjodah, I will try to make a minimum example representation of the failure here in the coming days. From a quick look at the log, it most likely have to do with the computation of derivative of these expression:

hyperspy/hyperspy/_components/voigt.py

Lines 97 to 99 in 95c194c

	expression="area * real(V); \
	V = wofz(z) / (sqrt(2.0 * pi) * sigma); \
	z = (x - centre + 1j * gamma_) / (sigma * sqrt(2.0))",

and

hyperspy/hyperspy/_components/heaviside.py

Line 61 in 95c194c

expression="A*heaviside(x-n,0.5)",

[ericpre]

xref #814.

[ericpre]

The test failure with sympy 1.13.0rc1 is fixed in #3388.

[CSSFrancis]

@ericpre I can look at this on Tuesday! I'm very excited for this one :)

+1 to following this up with something like what had been previously proposed.

s.axes_manager["nav"].scale=.2

s.axes_manager["nav"](scale=0.2, units="nm", offsets=0.2)

The second one looks kind of weird, although still correct and you could do s.axes_manager.signal_axes(...)

On another note there are so many more ways to index axes than I previously realized. It would be nice to have an example of how to use things like the imaginary number indexing indexing with the axis name etc in order to set things like the scale.

Maybe just a basic example showing how to sum data along different axes.

[ericpre]

See #2756 for the setter.

[francisco-dlp]

LGTM!

[jlaehne]

We should probably add a section on accessing the axes and their properties in the documentation on the Axes handling page right before "setting axis properties".

[ericpre]

Yes, the documentation on AxesManager will need an overhaul and integrating with the gallery of example, etc. I was thinking that it would be a good time to do after #2756.