Automatic/interactive dark spot counter for CL maps

[aidanc151]

Performs HyperSpy's find_peaks_log on Signal2D, creates markers using obtained peak positions and then applies markers to signal. Secondly, interactive marker placement and removal is enabled by mouse clicking inside the figure. Either of the functionalities can be used independently. Using the signal area and the number of markers placed, the density of dark spots is calculated, applied to the signal metadata, and also displayed as the figure title.

Description of the change

A few sentences and/or a bulleted list to describe and motivate the change:

• For automation of the counting of threading dislocations/dark spots in Cathodoluminescence maps
• Laplacian of Gaussian (LoG) algorithm enables quantitative identification of dark spots
• Saving of calculated density and markers to metadata for convenience and reproducibility of results

Progress of the PR

• [ ] add writing of LoG parameters to metadata functionality,
• [ ] add tests,
• [ ] add a changelog entry,
• [ ] ready for review.

Minimal example of the bug fix or the new feature

import hyperspy.api as hs
from lumispy.utils.signals import dark_spot_counter

# Interactive functionality does not work well with qt6
%matplotlib widget

panchromatic_map_arr = np.loadtxt('CL_panchromatic_map.txt')
panchromatic_map = hs.signals.Signal2D(panchromatic_map_arr,
                                       axes = [dict(units='µm', scale=5.66563),
                                               dict(units='µm', scale=5.66563)])


dark_spot_counter(panchromatic_map, log_algorithm=True, threshold = 0.005, min_sigma=8, color='blue', r=0.14, click_tolerance=0.1)

CL_panchromatic_map.txt

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Codecov Report

Attention: Patch coverage is 9.43396% with 48 lines in your changes missing coverage. Please review.

Project coverage is 91.95%. Comparing base (9c402c0) to head (f820e99). Report is 20 commits behind head on main.

Files with missing lines	Patch %	Lines
lumispy/utils/signals.py	9.43%	48 Missing :warning:

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Additional details and impacted files

@@             Coverage Diff             @@
##              main     #214      +/-   ##
===========================================
- Coverage   100.00%   91.95%   -8.05%     
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  Files           12       12              
  Lines          556      597      +41     
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- Hits           556      549       -7     
- Misses           0       48      +48     

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[jlaehne]

For me widget/ipympl is the backend that gives inline display and it I neither see the markers nor can I add/remove some.

@cssfrancis you have more experience with markers and matplotlib, can you give some guidance to implement the interactive display/adding/removing of markers to work with the different backends?

[CSSFrancis]

@jlaehne Hopefully I can get around to looking at this today :)