#!/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