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[WIP] Fix rng - #1411

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garrettwrong wants to merge 59 commits into

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fix_rng

Open

[WIP] Fix rng#1411
garrettwrong wants to merge 59 commits into
developfrom
fix_rng

Commits on Oct 8, 2026
- stash1 all tests still passing
  garrettwrong
  committed
  bdf183f
- remedy bot_align
  garrettwrong
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  db5f5a2
- remedy cov3d tutorial
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  a86cacd
- remediate test files
  garrettwrong
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  69fd80e
- cleanup
  garrettwrong
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  3f56385
- remedy micrograph sim
  garrettwrong
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  bd2b88e
- remedy cl cn
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  7dc2627
- minor tol adjustment
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  d051b82
- minor tol adjustment preproc
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  09f6f1e
- progress
  garrettwrong
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  26ba5fd
- Better handle and log seed init
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  7832b85
- pin denoiser utest seed similar to old sim
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  0b5e88e
- add very basic sim seeding unit test
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  7d32e0c
- seed frc/fsc test sims
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  a070aa4
- complete deprecation of randi method
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  2c57af3
- all randn methods except legacy hardcoded
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  eb67e97
- resolve choice
  garrettwrong
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  22a63b7
- remove Random from random package exports
  garrettwrong
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  dc62d87
- resolve random
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  5ae1d99
- continue choice cleanup
  garrettwrong
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  de1b286
- add missing seed in sim for shift case
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  c19b3f5
- add reminder note to NoiseAdder
  garrettwrong
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  905e51e
- Resolve test_orient_sdp failures. Add missing fixture dtype. Adjust shift search resolution and range. Adjust degree tolerance from 1 to 2. Fix eigenvalue bugs and adjust acceptable spread toleranc…
  
  j-c-c
  authored and
  garrettwrong
  committed
  b46fbcd
- Resolve test_orient_lud.py failures. Adjust shift_step resolution. Adjust spectral norm constraint based on observed ground truth spectral norms. Small max_rankZ bug.
  
  j-c-c
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  garrettwrong
  committed
  8ff5877
- Resolve test_orient_irls.py failures. Adjust spectral norm constraint based on ground truth spectral norm of grma matrix.
  
  j-c-c
  authored and
  garrettwrong
  committed
  0fe65ca
- Resolve test_orient_symmetric.py failures. Loosen tolerances for estimate_rotations and relative_viewing_directions. Fix reused index bug in test_self_relative_rotations. Add non-equator random rot…
  
  j-c-c
  authored and
  garrettwrong
  committed
  1a21e7c
- Resolve test_synthetic_volume.py failures. Adjust test tolerance.
  
  j-c-c
  authored and
  garrettwrong
  committed
  bc7c274
- Resolve test_orient_sync_voting.py failures. Increase max_shift. Add and use mean_aligned_shift_error to account for global 3D translation ambiguity. Reduce Image count. Fix dtype passthrough bug a…
  
  j-c-c
  authored and
  garrettwrong
  committed
  956ea06
- Move mean_aligned_shift_error to utils and add a unit test for it.
  
  j-c-c
  authored and
  garrettwrong
  committed
  d7b6d93
- Resolve test_rotation.py failure. Replace hardcoded common_lines test with behavioral test.
  
  j-c-c
  authored and
  garrettwrong
  committed
  e06b8f7
- Use groud truth rotations to compute aligned shift error.
  
  j-c-c
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  garrettwrong
  committed
  ab92b4b
- tox
  
  j-c-c
  authored and
  garrettwrong
  committed
  a56a735
- Resolve remaining test_orient_d.py failures. Disable fuzzy_mask in scl test. Fix to fine of shift_step resolution (unecessary). Increase image count for tests. Account for 180 degree self-commonlin…
  
  j-c-c
  authored and
  garrettwrong
  committed
  445a921
- Update to Numpy>=2.2 and update conda envs.
  garrettwrong
  committed
  1df3c6f
- stabilize cov3d kmeans calls
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  committed
  468614b
- stabilize cov3d kmeans calls some more
  garrettwrong
  committed
  c00f9df
- Resolve test_oriented_source.py sporadic failures. Set Simulation seed and use C=1 volumes.
  
  j-c-c
  authored and
  garrettwrong
  committed
  4e4529a
- Resolve test_oriented_source.py sporadic failures. Set JSync epsilon to 1e-3 for test.
  
  j-c-c
  authored and
  garrettwrong
  committed
  baac57f
- Resolve another test_oriented_source failure. C3/C4 algorithms create infeasible self-commonline search spaces for very low resolution (L=8). Setting L=12.
  
  j-c-c
  authored and
  garrettwrong
  committed
  187a3bf
- Resolve test_oriented_source.py save-roundtrip failure. Failure was due to small batch size dependent errors originating in scipy fft. Caching the source avoided this.
  
  j-c-c
  authored and
  garrettwrong
  committed
  aafb407
- stabilize the noise tests by adding more images
  garrettwrong
  committed
  07d5fa8
- migrate src code from seed to rng
  garrettwrong
  committed
  cc16936
- migrate test code from seed to rng
  garrettwrong
  committed
  06db7f3
- migrate gallery code from seed to rng
  garrettwrong
  committed
  df90f8e
- fix copy paste error per jcc
  garrettwrong
  committed
  c708851
- update minimal scipy version in conda envs and pyproj
  garrettwrong
  committed
  64a2842
- change tolerance per discussion with jcc
  garrettwrong
  committed
  364dad6
- remove semi-fixed seeds from test_orient_symmetric, replace with top of file rng
  garrettwrong
  committed
  18cfb9f
- update min_dist_cls for C2 case per jcc
  garrettwrong
  committed
  c283830
- more orient sym test patches per JCC
  garrettwrong
  committed
  de73229
- patch jcc's patch
  garrettwrong
  committed
  702e1e6
Commits on Oct 9, 2026
- split off the legacy NoiseAdder
  garrettwrong
  committed
  8cc01c2
- minor tweak denoiser test tol (by 1e-7)
  garrettwrong
  committed
  1f0a6a7
Commits on Oct 12, 2026
- remove seed refereces in gallery
  garrettwrong
  committed
  9bd5cd4
- bump white noise estimate from 1 to 2% for random seeded case
  garrettwrong
  committed
  00d7e46
Commits on Oct 13, 2026
- use emdb volume instead of builtins for fuzzy mask unit test
  garrettwrong
  committed
  a5d056a
- loosen frc/fsc tols
  garrettwrong
  committed
  16a092a
Commits on Oct 23, 2026
- add docstring for legacy white noise adder
  garrettwrong
  committed
  06b2491
- try to stablize the preproc tests with a seed
  garrettwrong
  committed
  cec9d3a

Commits

Commits on Oct 8, 2026

Commits on Oct 9, 2026

Commits on Oct 12, 2026

Commits on Oct 13, 2026

Commits on Oct 23, 2026