Update Pipeline Demo

[j-c-c]

Updates pipeline demo to use defaults for common-lines and class averaging. Also begins with high resolution simulation. Added BOT Align and FSC.

Related #1284

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 90.60%. Comparing base (0afa283) to head (804f212).
Report is 9 commits behind head on develop.

Additional details and impacted files

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##           develop    #1297   +/-   ##
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  Coverage    90.60%   90.60%           
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  Files          133      133           
  Lines        14346    14346           
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  Hits         12998    12998           
  Misses        1348     1348           

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[j-c-c]

Added additional preprocessing steps and switched to using ground truth rotations to align the volumes for FSC.

Attaching a pdf of the demo as it is now.
Ab-initio Pipeline Demonstration — ASPIRE 0.13.2 documentation.pdf

[garrettwrong]

Cool, couple things in there. After you tweak it, send it back and I'll render it locally for another review when rendered as the webpage. Thanks!

[garrettwrong]

Not sure if changed, was missed before, or if I'm doing something incorrect, but when I render I get the following in Download an Example Volume

sphinx_gallery_start_ignore flake8: noqa sphinx_gallery_end_ignore

[j-c-c]

Not sure if changed, was missed before, or if I'm doing something incorrect, but when I render I get the following in Download an Example Volume

Ah yeah, that needed to be in it's own cell. Fixed now. Thanks for spotting that!

[garrettwrong]

great, thanks!

[garrettwrong]

We should probably move on this so I can begin testing for release, thanks.

[garrettwrong]

Going to go ahead and merge this so we can try to get into release testing tomorrow after the delay.