Move all notebooks to scripts #55
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…y script that essentially is used to compute features which will then be used to plot the figures!
Reverted this change!
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A lot of these changes appear to be due to running a linter or other pre-commit hooks.
The github action identified that |
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@fatwir will work on splitting this PR up. Im going to work on another PR for the missing analysis in this repo The linting config is here - https://github.com/AllenCell/benchmarking_representations/blob/main/.pre-commit-config.yaml |
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So all the commits upto |
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@ritvikvasan closing this in favor of #58. Please take over that PR |
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This PR does a few things
run_embeddingsscript to compute embeddingse.g.
python src/br/analysis/run_embeddings.py --save_path "./outputs/" --sdf False --dataset_name "pcna" --batch_size 5 --debug Falserun_featuresscript to compute featurese.g.
python src/br/analysis/run_features.py --save_path "./outputs/" --embeddings_path "./morphology_appropriate_representation_learning/model_embeddings/pcna" --sdf False --dataset_name "pcna"run_analysisscript to run all analysis.e.g.
python src/br/analysis/run_analysis.py --save_path "./outputs_pcna/" --embeddings_path "./morphology_appropriate_representation_learning/model_embeddings/pcna" --dataset_name "pcna" --run_name "Rotation_invariant_pointcloud_jitter" --sdf Falserun_drugdata_analysisscript to run drug data perturbation detection analysispython src/br/analysis/run_drugdata_analysis.py --save_path "./outputs_npm1_perturb/" --embeddings_path "./morphology_appropriate_representation_learning/model_embeddings/npm1_perturb/" --dataset_name "npm1_perturb"To test these runs, you will need a local copy of the
morphology_appropriate_representation_learningfolder with the preprocessed data. This dataset currently lives here/allen/aics/modeling/ritvik/projects/latest_clones/benchmarking_representations/morphology_appropriate_representation_learning/