phase randomization score map correction

[McHaillet]

This PR adds 'phase randomization', introduced by STOPGAP.

Explanation of what this is: The match_template command line got two additional arguments: one flag to activate this mode, another to set a seed for randomization. The seed is used to create a phase randomized version of the template, meaning the phases of the Fourier transform are randomly permuted (used often for FSC calculations). This second template is like a random noise object and is matched simultaneously with the original template. The score map of the noisy version is subtracted from the real one.

With the particle diameter updated and ctf input reworked, this is the last thing I really want to add in functionality-wise.

Once this one is merged, I would like make a PR to throw the code through ruff and maybe set up a pre-commit thingy.

[github-actions]

File	Coverage		Missing
All files	87%	✅
src/pytom_tm/correlation.py	85%	❌	94-95 126
src/pytom_tm/entry_points.py	78%	❌	28 105-122 218-263 352-367 484-501 922-933
src/pytom_tm/extract.py	74%	❌	110-121 180-187 213-216 304-322
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%	✅	286-287 299 305-307 354 457 497
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 86%

Generated by 🐒 cobertura-action against a7f2ec1

[sroet]

general comment:

• min coverage should be increased to 86 already done in fix symmetry bug #184

Other than that, one default question, one proposed refactor, one doc suggestion, one code consistency thing

Once this one is merged, I would like make a PR to throw the code through ruff and maybe set up a pre-commit thingy.

Sounds good, I can also look into that if you don't have time for that (isn't necessary 'publishable' 😉 ), just tag me into an issue

[McHaillet]

Sounds good, I can also look into that if you don't have time for that (isn't necessary 'publishable' 😉 ), just tag me into an issue

Also fine, will respond in the PR I made for it!

[sroet]

LGTM, feel free to merge