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Move all notebooks to scripts #58

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merged 38 commits into from
Nov 26, 2024
Merged

Move all notebooks to scripts #58

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d5e1942
delete hidden snakemake folder
Nov 20, 2024
beb3110
change pcna result order
Nov 20, 2024
9458d4a
add setup function to prereq to handle SDF/pc differences
Nov 20, 2024
8069271
add classes and labels to results config
ritvikvasan Nov 20, 2024
acf4055
move to run_embeddings and run_features
ritvikvasan Nov 20, 2024
be3fd45
remove hidden snakemake files
ritvikvasan Nov 20, 2024
1689542
use cytodl config path for dataloading
ritvikvasan Nov 20, 2024
c734d7f
debug runs
ritvikvasan Nov 21, 2024
cf470b3
test runs for embeddings and features pass for PCNA dataset
Nov 21, 2024
1292b7f
remove pdb
Nov 21, 2024
34447f6
move gpu stuff to utils
Nov 21, 2024
512ccd2
move fig notebooks into single analysis script
Nov 21, 2024
178a826
working analysis script for punctate structures
ritvikvasan Nov 22, 2024
4faae2b
add sdf analysis utils and merge script
ritvikvasan Nov 22, 2024
5e9e07b
fix nonetype error
ritvikvasan Nov 22, 2024
eceefa4
working sdf analysis runs
ritvikvasan Nov 22, 2024
cfd4eb7
Update data paths in the results config for other_polymorphic.yaml
fatwir Nov 22, 2024
18945d2
Update data paths in the results config for npm1_perturb.yaml
fatwir Nov 22, 2024
a8b4bb8
Update data paths in the results config for other_punctate.yaml
fatwir Nov 22, 2024
06228bb
Update other_punctate.yaml
fatwir Nov 22, 2024
11ac09d
add str2bool check
ritvikvasan Nov 22, 2024
ad6c964
rename npm1 experiment
ritvikvasan Nov 22, 2024
8371227
fix cellpack analysis error (no s key)
Nov 22, 2024
3d50c0d
remove notebooks and make script for drugdata analysis
Nov 22, 2024
d07414c
remvove selected gpu
Nov 22, 2024
e14be8c
Merge branch 'Pre-Commit-analyses' into scripts_features_rebased
pgarrison Nov 23, 2024
103b649
Modified the code to get the GPU ID based on memory utilization
Nov 25, 2024
4d42ed9
Updated the paths in configs (merged from main)
Nov 25, 2024
35e7977
Revert "Updated the paths in configs (merged from main)"
Nov 25, 2024
304d39c
Merge pull request #59 from AllenCell/fix_gpu_id
fatwir Nov 26, 2024
6ec5819
Modified the compute_evolve_dataloaders function to make this work fo…
Nov 26, 2024
dbb20b4
Revert "Modified the compute_evolve_dataloaders function to make this…
Nov 26, 2024
7da2d9c
merge main
Nov 26, 2024
d08ac35
remove leading underscores
Nov 26, 2024
34bc7b9
create dir if doesnt exist + fix cellpack evolve bug
ritvikvasan Nov 26, 2024
c35a1ba
add image path and pc path for polymorphic data
ritvikvasan Nov 26, 2024
77c2986
remove stray prints
ritvikvasan Nov 26, 2024
a4dc4e9
add new scripts to docs
ritvikvasan Nov 26, 2024
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -3,6 +3,7 @@
Code for training and benchmarking morphology appropriate representation learning methods.

# Preprocessing

This README gives instructions for running our analysis against preprocessed image data. Because the preprocessing can take a long time, we are publishing preprocessed data along with the original movies. To do the preprocessing yourself, see the instructions in [subpackages/image_preprocessing/README.md](./subpackages/image_preprocessing/README.md).

# Installation
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0 ...nt/npm1_variance/image_sdf_classical.yaml → .../experiment/npm1/image_sdf_classical.yaml
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0 ...periment/npm1_variance/image_sdf_so3.yaml → configs/experiment/npm1/image_sdf_so3.yaml
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0 ...nt/npm1_variance/image_seg_classical.yaml → .../experiment/npm1/image_seg_classical.yaml
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0 ...periment/npm1_variance/image_seg_so3.yaml → configs/experiment/npm1/image_seg_so3.yaml
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0 ...experiment/npm1_variance/pc_implicit.yaml → configs/experiment/npm1/pc_implicit.yaml
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16 changes: 9 additions & 7 deletions configs/results/cellpack.yaml
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Expand Up @@ -17,11 +17,13 @@ names:
"Rotation_invariant_pointcloud",
"Rotation_invariant_pointcloud_jitter",
]
data_paths: [
"./configs/data/cellpack/image.yaml",
"./configs/data/cellpack/image.yaml",
"./configs/data/cellpack/pc.yaml",
"./configs/data/cellpack/pc.yaml",
# "./src/br/configs/data/cellpack/pc_jitter.yaml",
"./configs/data/cellpack/pc.yaml",
data_paths:
[
"/data/cellpack/image.yaml",
"/data/cellpack/image.yaml",
"/data/cellpack/pc.yaml",
"/data/cellpack/pc.yaml",
"/data/cellpack/pc.yaml",
]
classification_label: ["rule"]
regression_label:
13 changes: 8 additions & 5 deletions configs/results/npm1.yaml
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Expand Up @@ -19,9 +19,12 @@ names:
]
data_paths:
[
"./configs/data/npm1/pc.yaml",
"./configs/data/npm1/so3_image_sdf.yaml",
"./configs/data/npm1/so3_image_seg.yaml",
"./configs/data/npm1/classical_image_sdf.yaml",
"./configs/data/npm1/classical_image_seg.yaml",
"/data/npm1/pc.yaml",
"/data/npm1/so3_image_sdf.yaml",
"/data/npm1/so3_image_seg.yaml",
"/data/npm1/classical_image_sdf.yaml",
"/data/npm1/classical_image_seg.yaml",
]
classification_label: ["STR_connectivity_cc_thresh"]
regression_label:
["mean_centroid_distances", "mean_nucleolus_volume", "mean_nucleolus_area"]
10 changes: 5 additions & 5 deletions configs/results/npm1_perturb.yaml
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Expand Up @@ -19,9 +19,9 @@ names:
]
data_paths:
[
"./configs/data/npm1_perturb/pc.yaml",
"./configs/data/npm1_perturb/classical_image_sdf.yaml",
"./configs/data/npm1_perturb/classical_image_seg.yaml",
"./configs/data/npm1_perturb/so3_image_sdf.yaml",
"./configs/data/npm1_perturb/so3_image_seg.yaml",
"/data/npm1_perturb/pc.yaml",
"/data/npm1_perturb/classical_image_sdf.yaml",
"/data/npm1_perturb/classical_image_seg.yaml",
"/data/npm1_perturb/so3_image_sdf.yaml",
"/data/npm1_perturb/so3_image_seg.yaml",
]
12 changes: 7 additions & 5 deletions configs/results/other_polymorphic.yaml
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Expand Up @@ -19,9 +19,11 @@ names:
]
data_paths:
[
"./configs/data/other_polymorphic/pc.yaml",
"./configs/data/other_polymorphic/so3_image_sdf.yaml",
"./configs/data/other_polymorphic/so3_image_seg.yaml",
"./configs/data/other_polymorphic/classical_image_sdf.yaml",
"./configs/data/other_polymorphic/classical_image_seg.yaml",
"/data/other_polymorphic/pc.yaml",
"/data/other_polymorphic/so3_image_sdf.yaml",
"/data/other_polymorphic/so3_image_seg.yaml",
"/data/other_polymorphic/classical_image_sdf.yaml",
"/data/other_polymorphic/classical_image_seg.yaml",
]
classification_label: ["structure_name"]
regression_label: ["avg_dists", "mean_volume", "mean_surface_area"]
13 changes: 6 additions & 7 deletions configs/results/other_punctate.yaml
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Expand Up @@ -6,22 +6,21 @@ model_checkpoints:
"./morphology_appropriate_representation_learning/model_checkpoints/other_punctate/Classical_image.ckpt",
"./morphology_appropriate_representation_learning/model_checkpoints/other_punctate/Rotation_invariant_image.ckpt",
"./morphology_appropriate_representation_learning/model_checkpoints/other_punctate/Classical_pointcloud.ckpt",
"./morphology_appropriate_representation_learning/model_checkpoints/other_punctate/Rotation_invariant_pointcloud.ckpt",
"./morphology_appropriate_representation_learning/model_checkpoints/other_punctate/Rotation_invariant_pointcloud_structurenorm.ckpt",
]
names:
[
"Classical_image",
"Rotation_invariant_image",
"Classical_pointcloud",
"Rotation_invariant_pointcloud",
"Rotation_invariant_pointcloud_structurenorm",
]
data_paths:
[
"./configs/data/other_punctate/image.yaml",
"./configs/data/other_punctate/image.yaml",
"./configs/data/other_punctate/pc.yaml",
"./configs/data/other_punctate/pc_intensity.yaml",
"./configs/data/other_punctate/pc_intensity_structurenorm.yaml",
"/data/other_punctate/image.yaml",
"/data/other_punctate/image.yaml",
"/data/other_punctate/pc.yaml",
"/data/other_punctate/pc_intensity_structurenorm.yaml",
]
classification_label: ["structure_name", "cell_stage"]
regression_label:
20 changes: 11 additions & 9 deletions configs/results/pcna.yaml
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Expand Up @@ -3,25 +3,27 @@ image_path: ./morphology_appropriate_representation_learning/preprocessed_data/p
pc_path: ./morphology_appropriate_representation_learning/preprocessed_data/pcna/manifest.csv
model_checkpoints:
[
"./morphology_appropriate_representation_learning/model_checkpoints/pcna/Classical_pointcloud.ckpt",
"./morphology_appropriate_representation_learning/model_checkpoints/pcna/Rotation_invariant_pointcloud.ckpt",
"./morphology_appropriate_representation_learning/model_checkpoints/pcna/Classical_image.ckpt",
"./morphology_appropriate_representation_learning/model_checkpoints/pcna/Rotation_invariant_image.ckpt",
"./morphology_appropriate_representation_learning/model_checkpoints/pcna/Classical_pointcloud.ckpt",
"./morphology_appropriate_representation_learning/model_checkpoints/pcna/Rotation_invariant_pointcloud.ckpt",
"./morphology_appropriate_representation_learning/model_checkpoints/pcna/Rotation_invariant_pointcloud_jitter.ckpt",
]
names:
[
"Classical_pointcloud",
"Rotation_invariant_pointcloud",
"Classical_image",
"Rotation_invariant_image",
"Classical_pointcloud",
"Rotation_invariant_pointcloud",
"Rotation_invariant_pointcloud_jitter",
]
data_paths: [
"./configs/data/pcna/pc.yaml",
"./configs/data/pcna/pc_intensity.yaml",
"./configs/data/pcna/image.yaml",
"./configs/data/pcna/image.yaml",
"/data/pcna/image.yaml",
"/data/pcna/image.yaml",
"/data/pcna/pc.yaml",
"/data/pcna/pc_intensity.yaml",
# "./src/br/configs/data/pcna/pc_intensity_jitter.yaml",
"./configs/data/pcna/pc_intensity.yaml",
"/data/pcna/pc_intensity.yaml",
]
classification_label: ["cell_stage_fine", "flag_comment"]
regression_label:
0 src/br/models/.gitkeep → src/br/analysis/__init__.py
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