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Feature selection and documentation #54

Merged
merged 42 commits into from
Dec 9, 2024
Merged

Feature selection and documentation #54

merged 42 commits into from
Dec 9, 2024

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chantelleleveille
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@chantelleleveille chantelleleveille commented Dec 7, 2024 •
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Feature selection

Features used in development were pruned and the final set of updated features remain.

  • all calls to the old density column have been removed
  • features not used in analysis workflows have been dropped
  • features for TFE have been updated

Feature documentation

  • documentation tables have been updated
  • glossary definitions for TFE have been updated.

TFE outputs are being generated here: /allen/aics/assay-dev/users/Chantelle/colorizer/final/

chantelleleveille and others added 30 commits November 13, 2024 11:01
@chantelleleveille
remove unused whole colony LRM feats
6dd62d3
@chantelleleveille
optionally add mother or sister features for full tracks
dc643ab
@chantelleleveille
only add sister features used in LRM
72c23bf
@chantelleleveille
dont calc neighborhood avg for dxdt feats automatically
e846f20
@chantelleleveille
remove unused lrm ft
89fe2b7
@chantelleleveille
temp sorting through old vs new columns
0fd10a8
@chantelleleveille
Merge remote-tracking branch 'origin/dev' into feature_documentation
7668a39
@chantelleleveille
update
0e5827b
@chantelleleveille
Merge remote-tracking branch 'origin/dev' into feature_documentation
7d56b83
@cfrick13
inv_cyto and others removed
d3d5728
@cfrick13
determine neighbor_of_X columns to keep
e3705b8
@chantelleleveille
more feature pruning
85a9f0e
@cfrick13
first pass going through new features to keep and drop
1ab84ea
@cfrick13
clean up keep and drop lists
f9bdd0b
@cfrick13
add code to remove columns to be dropped
1b4b969
@cfrick13
move extra neighbor_of_X code into examples folder
1719987
@cfrick13
clarify var names
06169b5
@cfrick13
remove unused number_of_frame_X_neighbor columns and corresponding ex…
e8080d9 
…ample code
@cfrick13
add code to remove those columns using global_dataset_filtering
dc516b5
@jcass11
remove dropped columns from label_tables
6ef56f6
@jcass11
remove density
9a42385
@cfrick13
make fast load_local run all
1e0dcc8
@cfrick13
Merge branch 'dev' of github.com:AllenCell/nuc-morph-analysis into fe…
df10a28 
…ature_doc_test_density_frick
@chantelleleveille
Merge remote-tracking branch 'origin/dev' into feature_documentation
be138ba
@chantelleleveille
update TFE to reflect new features
d64ce32
@cfrick13
restore load_local=False
b81fdc1
@jcass11
Merge pull request #53 from AllenCell/feature_doc_test_density_frick
08741ba 
Quick run_all_manuscript_workflow error catching
@jcass11
remove old density feature from repo
8d7aa2d
@jcass11
use glossary file from tfe update commit d64ce32
3d0b3f8
@chantelleleveille
boolean feature correction
e5b537b
@chantelleleveille chantelleleveille marked this pull request as ready for review December 7, 2024 01:32
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jcass11 commented Dec 7, 2024

Tests are fixed. Re-running run_all_manuscript_workflows.py for good measure.

@jcass11 jcass11 self-requested a review December 9, 2024 00:06
jcass11
jcass11 approved these changes Dec 9, 2024
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====== Successes ======
figure_1_dataset (3050.4s) (56.2GB)
figure_3_s4_height_density (3218.3s) (50.0GB)
figure_4_s8_volume_trajectories (726.0s) (43.8GB)
figure_5_s9_s10_local_growth (2187.3s) (53.8GB)
figure_6_s11_compensation (730.5s) (43.9GB)
figure_7_s13_s14_lineage (899.5s) (43.8GB)
figure_s12_feeding_control (561.2s) (26.8GB)
figure_s15_linear_regression_model (1950.7s) (43.9GB)
figure_s19_transition_point (678.2s) (43.8GB)
figure_s1_cell_health (670.0s) (43.8GB)
figure_s20_precision_error (6.5s)
figure_s2_s3_s18_segmentation_model_validation (132.0s) (4.4GB)
figure_s6_s16_inhibitors (606.6s) (14.7GB)
figure_s7_growth_outliers (733.8s) (44.1GB)
====== 14 succeeded ======
YES!

cfrick13
cfrick13 approved these changes Dec 9, 2024
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Excellent work! So exciting to see this pushed to the finish line!

nuc_morph_analysis/lib/visualization/label_tables.py Outdated Show resolved Hide resolved
@chantelleleveille chantelleleveille added this pull request to the merge queue Dec 9, 2024
Merged via the queue into dev with commit 5cd9c51 Dec 9, 2024
1 check passed
@chantelleleveille chantelleleveille deleted the feature_documentation branch December 9, 2024 17:51
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@jcass11 jcass11 jcass11 approved these changes

@cfrick13 cfrick13 cfrick13 approved these changes

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@chantelleleveille @jcass11 @cfrick13