Add scripts

scripts/amos/00_make_manifests.sh

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+#!/usr/bin/env bash
+set -euo pipefail
+# Backward-compatible alias for the current shared-13 manifest creation script.
+exec bash scripts/amos/create_manifests_shared13.sh

scripts/amos/01_smoke_source_ct.sh

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+#!/usr/bin/env bash
+set -euo pipefail
+CFG=${CFG:-configs/experiments/amos_source_ct_shared13.yaml}
+TMP_CFG=${TMP_CFG:-configs/experiments/amos_source_ct_shared13_smoke.yaml}
+python - <<'PY'
+from sacflow.utils.config import load_yaml, save_yaml
+cfg = load_yaml('configs/experiments/amos_source_ct_shared13.yaml')
+cfg['output_dir'] = 'outputs/amos/shared13/source_ct_smoke'
+cfg['train']['epochs'] = 1
+cfg['train']['steps_per_epoch'] = 2
+cfg['train']['val_every'] = 1
+cfg['train']['save_every'] = 1
+cfg['wandb']['enabled'] = False
+save_yaml(cfg, 'configs/experiments/amos_source_ct_shared13_smoke.yaml')
+PY
+NPROC=${NPROC:-1}
+torchrun --standalone --nnodes=1 --nproc_per_node=$NPROC tools/train.py --config "$TMP_CFG" --name amos_source_ct_smoke

scripts/amos/cleanup_checkpoints_keep_last_best.sh

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+#!/usr/bin/env bash
+set -euo pipefail
+for d in outputs/amos/source_ct_shared13/checkpoints outputs/amos/oracle_mri_shared13/checkpoints; do
+  if [ -d "$d" ]; then
+    echo "Before cleanup: $d"
+    du -sh "$d" || true
+    find "$d" -maxdepth 1 -type f -name 'epoch_*.pt' -print -delete
+    find "$d" -maxdepth 1 -type f -name '*.tmp' -print -delete
+    echo "After cleanup: $d"
+    du -sh "$d" || true
+  fi
+done

scripts/amos/create_manifests_shared13.sh

@@ -0,0 +1,23 @@
+#!/usr/bin/env bash
+set -euo pipefail
+AMOS_ROOT=${AMOS_ROOT:-datasets/amos22}
+mkdir -p data_json
+python tools/create_amos_ct_mr_manifest.py \
+  --amos-root ${AMOS_ROOT} \
+  --source ct \
+  --target mri \
+  --output data_json/amos_ct2mr.json \
+  --name amos_ct2mr \
+  --id-scheme one_based
+python tools/remap_labels_in_manifest.py \
+  --input data_json/amos_ct2mr.json \
+  --output data_json/amos_ct2mr_shared13.json \
+  --label-root datasets/amos22_shared13_labels \
+  --map 14:0 15:0 \
+  --num-classes 14 \
+  --protocol-name amos_ct2mr_shared13
+python tools/make_sfda_manifest.py \
+  --input data_json/amos_ct2mr_shared13.json \
+  --output data_json/amos_ct2mr_shared13_sfda.json \
+  --drop-splits target_train
+python tools/inspect_dataset.py --manifest data_json/amos_ct2mr_shared13_sfda.json

scripts/amos/eval_all_main.sh

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+#!/usr/bin/env bash
+set -euo pipefail
+declare -A CFGS
+CFGS[source_ct]=configs/experiments/amos_source_ct_shared13.yaml
+CFGS[oracle_mri]=configs/experiments/amos_oracle_mri_shared13.yaml
+CFGS[selftrain]=configs/experiments/amos_selftrain_ct2mri_shared13.yaml
+CFGS[peft]=configs/experiments/amos_peft_ct2mri_shared13.yaml
+CFGS[proto_align]=configs/experiments/amos_proto_align_ct2mri_shared13.yaml
+CFGS[sacflow]=configs/experiments/amos_sacflow_ct2mri_shared13.yaml
+for name in source_ct oracle_mri selftrain peft proto_align sacflow; do
+  outdir=$(python - <<PY
+from sacflow.utils.config import load_yaml
+print(load_yaml('${CFGS[$name]}')['output_dir'])
+PY
+)
+  echo "=== Evaluating $name from $outdir ==="
+  python tools/eval.py --config "${CFGS[$name]}" --checkpoint "$outdir/checkpoints/best.pt" --split target_val
+ done

scripts/amos/eval_sacflow_ct2mri_shared13.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+set -euo pipefail
+python tools/eval.py \
+  --config configs/experiments/amos_sacflow_ct2mri_shared13.yaml \
+  --checkpoint outputs/amos/sacflow_ct2mri_shared13/checkpoints/best.pt \
+  --split target_val

scripts/amos/eval_source_ct2mri.sh

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+#!/usr/bin/env bash
+set -euo pipefail
+exec bash scripts/amos/eval_source_ct2mri_shared13.sh

scripts/amos/eval_source_ct2mri_shared13.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+set -euo pipefail
+python tools/eval.py \
+  --config configs/experiments/amos_source_ct_shared13.yaml \
+  --checkpoint outputs/amos/source_ct_shared13/checkpoints/best.pt \
+  --split target_val

scripts/amos/export_memory_ct.sh

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+#!/usr/bin/env bash
+set -euo pipefail
+exec bash scripts/amos/export_memory_ct_shared13.sh

scripts/amos/export_memory_ct_shared13.sh

@@ -0,0 +1,7 @@
+#!/usr/bin/env bash
+set -euo pipefail
+python tools/export_source_memory.py \
+  --config configs/experiments/amos_source_ct_shared13.yaml \
+  --checkpoint outputs/amos/source_ct_shared13/checkpoints/best.pt \
+  --output outputs/amos/source_ct_shared13/source_memory.pt \
+  --num-passes ${NUM_PASSES:-3}

scripts/amos/resume_oracle_mri_shared13.sh

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+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=${NPROC} tools/train.py \
+  --config configs/experiments/amos_oracle_mri_shared13.yaml \
+  --name amos_oracle_mri_shared13 \
+  --resume auto

scripts/amos/resume_source_ct_shared13.sh

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+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=${NPROC} tools/train.py \
+  --config configs/experiments/amos_source_ct_shared13.yaml \
+  --name amos_source_ct_shared13 \
+  --resume auto

scripts/amos/run_peft_ct2mri.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=$NPROC tools/train.py \
+  --config configs/experiments/amos_peft_ct2mri_shared13.yaml \
+  --name amos_peft_ct2mri_shared13

scripts/amos/run_peft_ct2mri_shared13.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=${NPROC} tools/train.py \
+  --config configs/experiments/amos_peft_ct2mri_shared13.yaml \
+  --name amos_peft_ct2mri_shared13

scripts/amos/run_proto_align_ct2mri.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=$NPROC tools/train.py \
+  --config configs/experiments/amos_proto_align_ct2mri_shared13.yaml \
+  --name amos_proto_align_ct2mri_shared13

scripts/amos/run_proto_align_ct2mri_shared13.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=${NPROC} tools/train.py \
+  --config configs/experiments/amos_proto_align_ct2mri_shared13.yaml \
+  --name amos_proto_align_ct2mri_shared13

scripts/amos/run_sacflow_ct2mri.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=$NPROC tools/train.py \
+  --config configs/experiments/amos_sacflow_ct2mri_shared13.yaml \
+  --name amos_sacflow_ct2mri_shared13

scripts/amos/run_sacflow_ct2mri_shared13.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=${NPROC} tools/train.py \
+  --config configs/experiments/amos_sacflow_ct2mri_shared13.yaml \
+  --name amos_sacflow_ct2mri_shared13

scripts/amos/run_sacflow_linear_ct2mri.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=$NPROC tools/train.py \
+  --config configs/experiments/amos_sacflow_linear_ct2mri_shared13.yaml \
+  --name amos_sacflow_linear_ct2mri_shared13

scripts/amos/run_sacflow_linear_ct2mri_shared13.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=${NPROC} tools/train.py \
+  --config configs/experiments/amos_sacflow_linear_ct2mri_shared13.yaml \
+  --name amos_sacflow_linear_ct2mri_shared13

scripts/amos/run_sacflow_random_subspace_ct2mri.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=$NPROC tools/train.py \
+  --config configs/experiments/amos_sacflow_random_subspace_ct2mri_shared13.yaml \
+  --name amos_sacflow_random_subspace_ct2mri_shared13

scripts/amos/run_sacflow_random_subspace_ct2mri_shared13.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=${NPROC} tools/train.py \
+  --config configs/experiments/amos_sacflow_random_subspace_ct2mri_shared13.yaml \
+  --name amos_sacflow_random_subspace_ct2mri_shared13

scripts/amos/run_sacflow_whole_feature_ct2mri.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=$NPROC tools/train.py \
+  --config configs/experiments/amos_sacflow_whole_feature_ct2mri_shared13.yaml \
+  --name amos_sacflow_whole_feature_ct2mri_shared13

scripts/amos/run_sacflow_whole_feature_ct2mri_shared13.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=${NPROC} tools/train.py \
+  --config configs/experiments/amos_sacflow_whole_feature_ct2mri_shared13.yaml \
+  --name amos_sacflow_whole_feature_ct2mri_shared13

scripts/amos/run_selftrain_ct2mri.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=$NPROC tools/train.py \
+  --config configs/experiments/amos_selftrain_ct2mri_shared13.yaml \
+  --name amos_selftrain_ct2mri_shared13

scripts/amos/run_selftrain_ct2mri_shared13.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=${NPROC} tools/train.py \
+  --config configs/experiments/amos_selftrain_ct2mri_shared13.yaml \
+  --name amos_selftrain_ct2mri_shared13

scripts/amos/train_oracle_mri.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=$NPROC tools/train.py \
+  --config configs/experiments/amos_oracle_mri_shared13.yaml \
+  --name amos_oracle_mri_shared13

scripts/amos/train_oracle_mri_shared13.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=${NPROC} tools/train.py \
+  --config configs/experiments/amos_oracle_mri_shared13.yaml \
+  --name amos_oracle_mri_shared13

scripts/amos/train_source_ct.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=$NPROC tools/train.py \
+  --config configs/experiments/amos_source_ct_shared13.yaml \
+  --name amos_source_ct_shared13

scripts/amos/train_source_ct_shared13.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=${NPROC} tools/train.py \
+  --config configs/experiments/amos_source_ct_shared13.yaml \
+  --name amos_source_ct_shared13

scripts/amos/train_source_ct_smoke.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-1}
+torchrun --standalone --nnodes=1 --nproc_per_node=${NPROC} tools/train.py \
+  --config configs/experiments/amos_source_ct_smoke.yaml \
+  --name amos_source_ct_smoke

scripts/mmwhs/eval_sacflow_ct2mr.sh

@@ -0,0 +1,3 @@
+#!/usr/bin/env bash
+set -euo pipefail
+python tools/eval.py --config configs/experiments/mmwhs_sacflow_ct2mr.yaml --checkpoint outputs/mmwhs/sacflow_ct2mr/checkpoints/best.pt --split target_test

scripts/mmwhs/eval_source_ct2mr.sh

@@ -0,0 +1,3 @@
+#!/usr/bin/env bash
+set -euo pipefail
+python tools/eval.py --config configs/experiments/mmwhs_source_ct.yaml --checkpoint outputs/mmwhs/source_ct/checkpoints/best.pt --split target_test

scripts/mmwhs/export_memory_ct.sh

@@ -0,0 +1,3 @@
+#!/usr/bin/env bash
+set -euo pipefail
+python tools/export_source_memory.py --config configs/experiments/mmwhs_source_ct.yaml --checkpoint outputs/mmwhs/source_ct/checkpoints/best.pt --output outputs/mmwhs/source_ct/source_memory.pt

scripts/mmwhs/run_peft_ct2mr.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=${NPROC} tools/train.py --config configs/experiments/mmwhs_peft_ct2mr.yaml --name mmwhs_peft_ct2mr

scripts/mmwhs/run_proto_align_ct2mr.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=${NPROC} tools/train.py --config configs/experiments/mmwhs_proto_align_ct2mr.yaml --name mmwhs_proto_align_ct2mr

scripts/mmwhs/run_sacflow_ct2mr.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=${NPROC} tools/train.py --config configs/experiments/mmwhs_sacflow_ct2mr.yaml --name mmwhs_sacflow_ct2mr

scripts/mmwhs/run_sacflow_linear_ct2mr.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=${NPROC} tools/train.py --config configs/experiments/mmwhs_sacflow_linear_ct2mr.yaml --name mmwhs_sacflow_linear_ct2mr

scripts/mmwhs/run_sacflow_random_subspace_ct2mr.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=${NPROC} tools/train.py --config configs/experiments/mmwhs_sacflow_random_subspace_ct2mr.yaml --name mmwhs_sacflow_random_subspace_ct2mr

scripts/mmwhs/run_sacflow_whole_feature_ct2mr.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=${NPROC} tools/train.py --config configs/experiments/mmwhs_sacflow_whole_feature_ct2mr.yaml --name mmwhs_sacflow_whole_feature_ct2mr

scripts/mmwhs/run_selftrain_ct2mr.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=${NPROC} tools/train.py --config configs/experiments/mmwhs_selftrain_ct2mr.yaml --name mmwhs_selftrain_ct2mr

scripts/mmwhs/train_oracle_mr.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=${NPROC} tools/train.py --config configs/experiments/mmwhs_oracle_mr.yaml --name mmwhs_oracle_mr

scripts/mmwhs/train_source_ct2mr.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NPROC=${NPROC:-8}
+torchrun --standalone --nnodes=1 --nproc_per_node=${NPROC} tools/train.py --config configs/experiments/mmwhs_source_ct.yaml --name mmwhs_source_ct