CT/liver/scripts/run_benchmark.sh

#!/usr/bin/env bash
set -euo pipefail

ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
cd "$ROOT_DIR"

export PYTHONPATH="$ROOT_DIR/src:${PYTHONPATH:-}"
CONDA_ENV="${CONDA_ENV:-ct}"
CONFIG="${1:-configs/benchmark.yaml}"

run_py() {
  conda run --no-capture-output -n "$CONDA_ENV" python "$@"
}

mkdir -p logs experiments/benchmark

echo "[benchmark] tabular clinical_logistic"
run_py -m liver_tace.tabular_benchmark --config "$CONFIG" --method clinical_logistic

echo "[benchmark] tabular radiomics_svm"
run_py -m liver_tace.tabular_benchmark --config "$CONFIG" --method radiomics_svm

echo "[benchmark] tabular radiomics_clinical_rf"
run_py -m liver_tace.tabular_benchmark --config "$CONFIG" --method radiomics_clinical_rf

echo "[benchmark] deep CT-only resnet18"
run_py -m liver_tace.deep_outcome_baseline --config configs/benchmark/resnet18_ct_only.yaml

echo "[benchmark] deep CT-only densenet121"
run_py -m liver_tace.deep_outcome_baseline --config configs/benchmark/densenet121_ct_only.yaml

echo "[benchmark] SegResNet segmentation-only"
run_py -m liver_tace.train --config configs/benchmark/waw_seg_only.yaml
run_py -m liver_tace.evaluate \
  --config configs/benchmark/waw_seg_only.yaml \
  --checkpoint experiments/benchmark/segresnet_seg_only/checkpoints/best.pt \
  --output-dir experiments/benchmark/segresnet_seg_only

echo "[benchmark] current full multitask with clean clinical columns"
run_py -m liver_tace.train --config configs/benchmark/full_multitask_clean.yaml
run_py -m liver_tace.evaluate \
  --config configs/benchmark/full_multitask_clean.yaml \
  --checkpoint experiments/benchmark/full_multitask/checkpoints/best.pt \
  --output-dir experiments/benchmark/full_multitask

echo "[benchmark] VISTA3D/NV-Segment-CT external prediction evaluation"
run_py -m liver_tace.external_segmentation_benchmark --config "$CONFIG" --method vista3d_external --split val || true

echo "[benchmark] aggregate"
run_py -m liver_tace.aggregate_benchmark --config "$CONFIG" --output-dir experiments/benchmark

echo "[benchmark] done: experiments/benchmark/benchmark_summary.csv"