Center of mass fix

[McHaillet]

Fix for the center of mass. I am not fully sure about the unittest check yet though, maybe you have a better solution. Currently checking with the same method as I am using internally.

I also switched to box padding after recentering. That is the better order as the padding is anyway done with zeros.

Closes #173

The square seems to work nicely though. This is an example that was failing before:

And now works much better:

[github-actions]

File	Coverage		Missing
All files	86%	✅
src/pytom_tm/correlation.py	85%	✅	94-95 126
src/pytom_tm/entry_points.py	78%	❌	27 104-121 217-262 351-366 483-500 879-890
src/pytom_tm/extract.py	74%	❌	110-121 179-186 212-215 303-321
src/pytom_tm/io.py	80%	❌	16 26 35 44 53 62-66 75-79 83 87 95 98 144-146 199 233-234 333-336 361
src/pytom_tm/mask.py	80%	❌	70 85 94-95
src/pytom_tm/parallel.py	89%	✅	14-15 83 95-97 104 148
src/pytom_tm/plotting.py	16%	❌	20-22 25-32 36-44 48-51 54-70 73-74 77-78 98-103 119-127 133-150 165-173 177-194 198-206 210-217 223 229 234 248-398
src/pytom_tm/tmjob.py	97%	✅	276-277 289 295-297 432 472
src/pytom_tm/utils.py	78%	❌	16-18
src/pytom_tm/weights.py	96%	✅	61 292-293 300 492 495 498

Minimum allowed coverage is 85%

Generated by 🐒 cobertura-action against e624fc7

[sroet]

One preference, feel free to ignore. LGTM otherwise

I am not fully sure about the unittest check yet though, maybe you have a better solution.

Current implementation looks good
One other solution might be to compare np.abs(generate_template_from_map(template, ...) and generate_template_from_map(np.abs(template), ...) which should be identical

[McHaillet]

Current implementation looks good One other solution might be to compare np.abs(generate_template_from_map(template, ...) and generate_template_from_map(np.abs(template), ...) which should be identical

I added this in. Will merge once the tests pass.