#!/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 \

)

# --------------------------------------------------------------------------------------