#!/bin/bash
# -------------------------------- Prepare datasets ------------------------------------
(cd ../rocaseg/datasets &&
echo "prepare_dataset" &&
python prepare_dataset_oai_imo.py \
../../../data_raw/OAI_iMorphics_scans \
../../../data_raw/OAI_iMorphics_annotations \
../../../data/91_OAI_iMorphics_full_meta \
--margin 20 \
)
(cd ../rocaseg/datasets &&
echo "prepare_dataset" &&
python prepare_dataset_okoa.py \
../../../data_raw/OKOA \
../../../data/31_OKOA_full_meta \
--margin 0 \
)
(cd ../rocaseg/datasets &&
echo "prepare_dataset" &&
python prepare_dataset_maknee.py \
../../../data_raw/MAKNEE \
../../../data/41_MAKNEE_full_meta \
--margin 0 \
)
# --------------------------------------------------------------------------------------
# -------------------------------- Resample datasets -----------------------------------
(cd ../rocaseg/ &&
echo "resample" &&
python resample.py \
--path_root_in ../../data/31_OKOA_full_meta \
--spacing_in 0.5859375 0.5859375 \
--path_root_out ../../data/32_OKOA_full_meta_rescaled \
--spacing_out 0.36458333 0.36458333 \
--num_threads 12 \
--margin 0 \
)
(cd ../rocaseg/ &&
echo "resample" &&
python resample.py \
--path_root_in ../../data/41_MAKNEE_full_meta \
--spacing_in 0.5859375 0.5859375 \
--path_root_out ../../data/42_MAKNEE_full_meta_rescaled \
--spacing_out 0.36458333 0.36458333 \
--num_threads 12 \
--margin 0 \
)
# --------------------------------------------------------------------------------------
# --------------------------------- Train models ---------------------------------------
(cd ../rocaseg/ &&
echo "train" &&
python train_baseline.py \
--path_data_root ../../data \
--path_experiment_root ../../results/0_baseline \
--model_segm unet_lext \
--input_channels 1 \
--output_channels 5 \
--center_depth 1 \
--lr_segm 0.001 \
--batch_size 32 \
--epoch_num 50 \
--fold_num 5 \
--fold_idx -1 \
--num_workers 12 \
)
(cd ../rocaseg/ &&
echo "train" &&
python train_baseline.py \
--path_data_root ../../data \
--path_experiment_root ../../results/1_mixup \
--model_segm unet_lext \
--input_channels 1 \
--output_channels 5 \
--center_depth 1 \
--lr_segm 0.001 \
--batch_size 32 \
--epoch_num 50 \
--fold_num 5 \
--fold_idx -1 \
--with_mixup \
--mixup_alpha 0.7 \
--num_workers 12 \
)
(cd ../rocaseg/ &&
echo "train" &&
python train_baseline.py \
--path_data_root ../../data \
--path_experiment_root ../../results/2_mixup_nowd \
--model_segm unet_lext \
--input_channels 1 \
--output_channels 5 \
--center_depth 1 \
--lr_segm 0.001 \
--wd_segm 0.0 \
--batch_size 32 \
--epoch_num 50 \
--fold_num 5 \
--fold_idx -1 \
--with_mixup \
--mixup_alpha 0.7 \
--num_workers 12 \
)
(cd ../rocaseg/ &&
echo "train" &&
python train_uda1.py \
--path_data_root ../../data \
--path_experiment_root ../../results/3_uda1 \
--model_segm unet_lext \
--center_depth 1 \
--model_discr discriminator_a \
--input_channels 1 \
--output_channels 5 \
--mask_mode all_unitibial_unimeniscus \
--loss_segm multi_ce_loss \
--lr_segm 0.0001 \
--lr_discr 0.00004 \
--batch_size 32 \
--epoch_num 30 \
--fold_num 5 \
--fold_idx 0 \
--num_workers 12 \
)
(cd ../rocaseg/ &&
echo "train" &&
python train_uda1.py \
--path_data_root ../../data \
--path_experiment_root ../../results/4_uda2 \
--model_segm unet_lext_aux \
--center_depth 1 \
--model_discr_out discriminator_a \
--model_discr_aux discriminator_a \
--input_channels 1 \
--output_channels 5 \
--mask_mode all_unitibial_unimeniscus \
--loss_segm multi_ce_loss \
--lr_segm 0.0001 \
--lr_discr 0.00004 \
--batch_size 32 \
--epoch_num 30 \
--fold_num 5 \
--fold_idx 0 \
--num_workers 12 \
)
(cd ../rocaseg/ &&
echo "train" &&
python train_uda1.py \
--path_data_root ../../data \
--path_experiment_root ../../results/5_uda1_mixup_nowd \
--model_segm unet_lext \
--center_depth 1 \
--model_discr discriminator_a \
--input_channels 1 \
--output_channels 5 \
--mask_mode all_unitibial_unimeniscus \
--loss_segm multi_ce_loss \
--lr_segm 0.0001 \
--lr_discr 0.00004 \
--wd_segm 0.0 \
--batch_size 32 \
--epoch_num 30 \
--fold_num 5 \
--fold_idx 0 \
--num_workers 12 \
--with_mixup \
--mixup_alpha 0.7 \
)
# --------------------------------------------------------------------------------------
# ------------------------------- Run model inference ----------------------------------
for EXP in 0_baseline 1_mixup 2_mixup_nowd 3_uda1 5_uda1_mixup_nowd
do
(cd ../rocaseg/ &&
echo "evaluate" &&
python evaluate.py \
--path_data_root ../../data \
--path_experiment_root ../../results/${EXP} \
--model_segm unet_lext \
--center_depth 1 \
--restore_weights \
--output_channels 5 \
--dataset oai_imo \
--subset test \
--mask_mode all_unitibial_unimeniscus \
--batch_size 64 \
--fold_num 5 \
--fold_idx -1 \
--num_workers 12 \
--predict_folds \
--merge_predictions \
)
done
for EXP in 4_uda2
do
(cd ../rocaseg/ &&
echo "evaluate" &&
python evaluate.py \
--path_data_root ../../data \
--path_experiment_root ../../results/${EXP} \
--model_segm unet_lext_aux \
--center_depth 1 \
--restore_weights \
--output_channels 5 \
--dataset oai_imo \
--subset test \
--mask_mode all_unitibial_unimeniscus \
--batch_size 64 \
--fold_num 5 \
--fold_idx -1 \
--num_workers 12 \
--predict_folds \
--merge_predictions \
)
done
for EXP in 0_baseline 1_mixup 2_mixup_nowd 3_uda1 5_uda1_mixup_nowd
do
(cd ../rocaseg/ &&
echo "evaluate" &&
python evaluate.py \
--path_data_root ../../data \
--path_experiment_root ../../results/${EXP} \
--model_segm unet_lext \
--center_depth 1 \
--restore_weights \
--output_channels 5 \
--dataset okoa \
--subset all \
--mask_mode background_femoral_unitibial \
--batch_size 64 \
--fold_num 5 \
--fold_idx -1 \
--num_workers 12 \
--predict_folds \
--merge_predictions \
)
done
for EXP in 4_uda2
do
(cd ../rocaseg/ &&
echo "evaluate" &&
python evaluate.py \
--path_data_root ../../data \
--path_experiment_root ../../results/${EXP} \
--model_segm unet_lext_aux \
--center_depth 1 \
--restore_weights \
--output_channels 5 \
--dataset okoa \
--subset all \
--mask_mode background_femoral_unitibial \
--batch_size 64 \
--fold_num 5 \
--fold_idx -1 \
--num_workers 12 \
--predict_folds \
--merge_predictions \
)
done
# --------------------------------------------------------------------------------------
# ------------------------------- Analyze model predictions ----------------------------
for EXP in 0_baseline 1_mixup 2_mixup_nowd 3_uda1 4_uda2 5_uda1_mixup_nowd
do
(cd ../rocaseg/ &&
echo "analyze_predictions" &&
python analyze_predictions_single.py \
--path_experiment_root ../../results/${EXP} \
--dirname_pred mask_foldavg \
--dirname_true mask_prep \
--dataset oai_imo \
--atlas segm \
--ignore_cache \
--num_workers 12 \
)
done
for EXP in 0_baseline 1_mixup 2_mixup_nowd 3_uda1 4_uda2 5_uda1_mixup_nowd
do
(cd ../rocaseg/ &&
echo "analyze_predictions" &&
python analyze_predictions_single.py \
--path_experiment_root ../../results/${EXP} \
--dirname_pred mask_foldavg \
--dirname_true mask_prep \
--dataset okoa \
--atlas okoa \
--ignore_cache \
--num_workers 12 \
)
done
# --------------------------------------------------------------------------------------
# --------------------------------- Compare models -------------------------------------
(cd ../rocaseg/ &&
echo "analyze_predictions_multi" &&
python analyze_predictions_multi.py \
--path_results_root ../../results \
--experiment_id 0_baseline \
--experiment_id 2_mixup_nowd \
--experiment_id 4_uda2 \
--dataset oai_imo \
--atlas segm \
--num_workers 12 \
)
(cd ../rocaseg/ &&
echo "analyze_predictions_multi" &&
python analyze_predictions_multi.py \
--path_results_root ../../results \
--experiment_id 0_baseline \
--experiment_id 2_mixup_nowd \
--experiment_id 4_uda2 \
--dataset okoa \
--atlas okoa \
--num_workers 12 \
)
# --------------------------------------------------------------------------------------
