Code

Merge dev into main#98

Code

Merged

DSilva27 merged 40 commits intomainflatironinstitute/Cryo-EM-Heterogeneity-Challenge-1:mainfrom devflatironinstitute/Cryo-EM-Heterogeneity-Challenge-1:devCopy head branch name to clipboardSep 18, 2024

+796-210

Commits

Commits on Aug 12, 2024

• implement power spectrum and bfactor scaling

  

  DSilva27

  committed
  0ce2df1

  Copy full SHA for 0ce2df1

• merge dev

  

  DSilva27

  committed
  aab81a0

  Copy full SHA for aab81a0

• Merge branch 'dev' into 14-implement-power-spectrum-normalization

  

  DSilva27

  committed
  ae56c22

  Copy full SHA for ae56c22

• fix issue with preprocessing test

  

  DSilva27

  committed
  dd09fde

  Copy full SHA for dd09fde

• Merge branch 'dev' into 14-implement-power-spectrum-normalization

  DSilva27

  authored
  60dfc3a

  Copy full SHA for 60dfc3a

• Merge branch 'dev' into 14-implement-power-spectrum-normalization

  DSilva27

  authored
  a06b96d

  Copy full SHA for a06b96d

Commits on Aug 15, 2024

• add docstrings to tests and implemented functions

  

  DSilva27

  committed
  5c1b901

  Copy full SHA for 5c1b901

Commits on Aug 19, 2024

• added serial code for centering every volume

  Miro-Astore

  committed
  5572d97

  Copy full SHA for 5572d97

Commits on Aug 20, 2024

• element wise volume alignment

  Miro-Astore

  committed
  94b07dd

  Copy full SHA for 94b07dd

Commits on Aug 21, 2024

• Merge pull request #92 from flatironinstitute/centering_every_volume

  Show description for 21ca809
  DSilva27

  authored
  21ca809

  Copy full SHA for 21ca809

• Merge branch 'dev' into 14-implement-power-spectrum-normalization

  DSilva27

  authored
  6726c47

  Copy full SHA for 6726c47

• Merge pull request #82 from flatironinstitute/14-implement-power-spectrum-normalization

  Show description for cef000d
  DSilva27

  authored
  cef000d

  Copy full SHA for cef000d

Commits on Sep 3, 2024

• Merge branch 'dev' into current-preprocessing-pipeline

  

  DSilva27

  committed
  1b594a0

  Copy full SHA for 1b594a0

• remove centering and align only one volume in preprocessing

  

  DSilva27

  committed
  8cf8aea

  Copy full SHA for 8cf8aea

• Merge pull request #94 from flatironinstitute/current-preprocessing-pipeline

  Show description for cdc5f71
  DSilva27

  authored
  cdc5f71

  Copy full SHA for cdc5f71

Commits on Sep 4, 2024

• low memory pasisng test

  geoffwoollard

  committed
  356696c

  Copy full SHA for 356696c

Commits on Sep 10, 2024

• tests passing for low memory mode t and f

  geoffwoollard

  committed
  5e3591f

  Copy full SHA for 5e3591f

Commits on Sep 11, 2024

• l2, corr, bioem working

  geoffwoollard

  committed
  7c8e247

  Copy full SHA for 7c8e247

• fsc low memory working

  geoffwoollard

  committed
  14805d7

  Copy full SHA for 14805d7

• tests passing checking identical output

  geoffwoollard

  committed
  6f5e09e

  Copy full SHA for 6f5e09e

• all metrics implemented and test passing for matched results

  geoffwoollard

  committed
  a7290aa

  Copy full SHA for a7290aa

• all metrics implemented and test passing for matched results

  geoffwoollard

  committed
  22ec5a5

  Copy full SHA for 22ec5a5

• all metrics implemented and test passing for matched results

  geoffwoollard

  committed
  de3cddc

  Copy full SHA for de3cddc

• flags for masking and not masking

  geoffwoollard

  committed
  f20344e

  Copy full SHA for f20344e

• tests for masking and normalization

  geoffwoollard

  committed
  6def1bf

  Copy full SHA for 6def1bf

Commits on Sep 17, 2024

• code duplication for norm

  geoffwoollard

  committed
  c0f2f83

  Copy full SHA for c0f2f83

• tests passing. vmap over sub batch

  geoffwoollard

  committed
  f1f8cd8

  Copy full SHA for f1f8cd8

• tests passing. get_sub_distance_matrix

  geoffwoollard

  committed
  61608cb

  Copy full SHA for 61608cb

• tests passing with hard coded instantiation

  geoffwoollard

  committed
  1440d84

  Copy full SHA for 1440d84

• map_to_map_distance.distance_matrix_precomputation

  geoffwoollard

  committed
  555a39f

  Copy full SHA for 555a39f

• chunk_size_low_memory

  geoffwoollard

  committed
  b71e52b

  Copy full SHA for b71e52b

• on the fly sub batch normalization

  geoffwoollard

  committed
  76fdb46

  Copy full SHA for 76fdb46

• normalization and masking on the fly in sub batch

  geoffwoollard

  committed
  0a2efc0

  Copy full SHA for 0a2efc0

• tests passing

  geoffwoollard

  committed
  42525f4

  Copy full SHA for 42525f4

• tests passing for low memory off

  geoffwoollard

  committed
  e472372

  Copy full SHA for e472372

Commits on Sep 18, 2024

• tests passing. time to delete separate low memory

  geoffwoollard

  committed
  3077f6a

  Copy full SHA for 3077f6a

• all tests passing

  geoffwoollard

  committed
  cb7085e

  Copy full SHA for cb7085e

• remove low memory versions

  geoffwoollard

  committed
  1f4057e

  Copy full SHA for 1f4057e

• update configs to remove low memory metrics

  geoffwoollard

  committed
  b33a6a0

  Copy full SHA for b33a6a0

• Merge pull request #95 from flatironinstitute/51-reduce-memory-burden-of-pipeline-1

  Show description for faf7e29
  DSilva27

  authored
  faf7e29

  Copy full SHA for faf7e29