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python make_epoch_orders.py --base_dir ~/dataset2/unlabeled_processed_small --datasets all --split train --batch_size 128 --epochs 50 --out_dir ./orders --seed 42 --drop_last 1 --overwrite 1 |
./multi.sh |
python plot_mae.py --checkpoint ./models/model_MAE_ddp_test/checkpoint_e-0010.pth --base_dir ~/dataset2/unlabeled_processed_small --datasets all --split test --reducer tsne --output_png mae_tsne.png |
python plot_mae.py \ |
--checkpoint ./models/model_MAE_ddp_test/checkpoint_e-0010.pth \ |
--base_dir ~/dataset/unlabeled_processed_1.7M \ |
--datasets all \ |
--split test \ |
--reducer tsne \ |
--output_png mae_tsne.png |
./multi.sh |
python extract_embeddings.py \ |
--checkpoint ./models/model_MAE_ddp_test/checkpoint_last.pth \ |
--base_dir ~/dataset \ |
--split test \ |
--embed_dir ./embeddings/epoch_4 \ |
--seed 42 |
python plot_sp_both.py \ |
--checkpoint ./models/model_MAE_ddp_test/checkpoint_last.pth \ |
--base_dir ~/dataset \ |
--datasets all \ |
--split test \ |
--reducer tsne \ |
--species_csv ~/dataset/species.csv \ |
--output_png plot_tsne_epoch_4.png \ |
--color_map_csv colors.csv \ |
--embed_dir ./embeddings/epoch_4 |
python subplot.py \ |
--checkpoint ./models/model_MAE_ddp_test/checkpoint_last.pth \ |
--base_dir ~/dataset \ |
--datasets all \ |
--split test \ |
--reducer tsne \ |
--species_csv ~/dataset/species.csv \ |
--output_png mae_tsne_species_subplots_epoch_4.png \ |
--color_map_csv colors.csv \ |
--embed_dir ./embeddings/epoch_4 |
python process_2d.py --input_dir unlabeled_datasets --output_dir unlabeled_processed_small --img-size 256 --train-pct 70 --val-pct 10 --seed 42 |
*** From now on, we will write the processed directories to "New Volume" for space issues. |
*** as shown below |
python organize_bossdb.py \ |
--input_dir ~/connectomics/datasets/bossdb_raw \ |
--output_dir "/media/user/New Volume/connecto-data/unlabeled_datasets" \ |
--mode 2d |
python organize_bossdb.py \ |
--input_dir ~/connectomics/datasets/bossdb_raw \ |
--output_dir ~/connectomics/datasets/unlabeled_datasets_big \ |
--mode 2d |
copy other 2d datasets to there |
python process_2d.py \ |
--input_dir unlabeled_datasets \ |
--output_dir "/media/user/New Volume/connecto-data/unlabeled_processed_test" \ |
--img-size 256 \ |
--train-pct 95.0 \ |
--val-pct 0.0 \ |
--default-max-patches 3500 \ |
--seed 42 |
python process_2d_dry.py --input_dir unlabeled_datasets_big --img-size 256 --output_csv dataset_stats.csv |
python process_2d.py \ |
--input_dir unlabeled_datasets_big \ |
--output_dir unlabeled_processed_big \ |
--img-size 256 \ |
--train-pct 95.0 \ |
--val-pct 1.0 \ |
--seed 42 |
python stat_2d.py --input_dir unlabeled_processed_big --output_csv counts.csv |
python split.py \ |
--data-dir ./data \ |
--dry-run |
python split.py \ |
--data-dir labeled_datasets \ |
--train-pct 70 \ |
--val-pct 15 \ |
--seed 42 \ |
--mode copy_then_remove |
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