Functions adapted to hyperspy-based methods

[jordiferrero]

Some functions currently in LumiSpy have created their own methods while there are similar functionalities in Hyperspy which can do the same.
In this PR, a better integration of Hyperspy-based methods is intended.
(Former #40)

TODO:

• Cosmic ray removal function
• Background subtraction methods
• Create tests for each function

[jordiferrero]

I am struggling with an error I get when running the Tests in this function:

spikes_removal = SpikesRemoval(signal=signal, navigation_mask=navigation_mask, signal_mask=signal_mask,
                                       threshold=threshold, default_spike_width=default_spike_width,
>                                      add_noise=add_noise,)
E       TypeError: __init__() got an unexpected keyword argument 'threshold'

However, the SpikesRemoval class, inherited from hyperspy.signal_tools here, does indeed have a threshold argument. I don't know why it is raising this issue.

When I run the tests internally in my computer (py3.7 in PyCharm) all tests pass...

Can you @ericpre @jlaehne have a quick look if you see any obvious mistake? Thank you.

After resolving this issue, this PR is ready for review.

[ericpre]

I am struggling with an error I get when running the Tests in this function:

spikes_removal = SpikesRemoval(signal=signal, navigation_mask=navigation_mask, signal_mask=signal_mask,
                                       threshold=threshold, default_spike_width=default_spike_width,
>                                      add_noise=add_noise,)
E       TypeError: __init__() got an unexpected keyword argument 'threshold'

However, the SpikesRemoval class, inherited from hyperspy.signal_tools here, does indeed have a threshold argument. I don't know why it is raising this issue.

When I run the tests internally in my computer (py3.7 in PyCharm) all tests pass...

Can you @ericpre @jlaehne have a quick look if you see any obvious mistake? Thank you.

After resolving this issue, this PR is ready for review.

This is not released and this is only on the RELEASE_next_minor branch.

[ericpre]

If you check the py3.8/coverage which uses the non_uniform branch and is ahead of (include) RELEASE_next_minor, you will notice that there is no error, but the test fails.

[jordiferrero]

Oh. I assumed it was released already :-) Since I am always in the non_uniform branch....

So how should I deal with this?
My guess it to add a check whether SpikesRemovalTool is released. If yes, then the function can be used. If not, then it is not available yet for the user until the hyperspy new version is released (I could leave my old simpler function for such cases as a temporal thing, but I would rather not).
Does this make sense @ericpre? Thanks for the help!

[jlaehne]

spikes_removal_tool is an old function, which is released: https://hyperspy.org/hyperspy-doc/current/api/hyperspy._signals.signal1d.html?highlight=spikes_removal_tool#hyperspy._signals.signal1d.Signal1D.spikes_removal_tool

However, the threshold parameter was only introduced in hyperspy/hyperspy#1412, which was merged last September. So you could maybe check for the availability of that parameter. As the use of lumispy is still limited without the non_uniform_axes, I would not bother providing alternative implementations.

[jordiferrero]

All comments have been adressed and accepted.
This PR has been closed.
Thank you all for your help.