code/launch_phase2b.sh

#!/bin/bash
# Phase 2b — retrain failed DINOv2 + RETFound and re-run Phase 3 ensemble.
set -e
cd ~/fundus_project
source ~/.venv/bin/activate

echo "=== Phase 2b: DINOv2 + RETFound (fixed) ==="
python comparison_experiment/run_foundation_models.py \
    --manifest holdout_split_augmented.json \
    --out-dir final_experiments_v3 \
    --weights-dir weights_v3 \
    --retfound-weights weights_retfound.pth \
    --models dinov2_l retfound \
    --batch-size 24 \
    --workers 4 \
    --lp-epochs 20 \
    --ft-epochs 15 \
    --patience 8

echo "=== Phase 3: ensemble all models ==="
mkdir -p final_experiments_all
cp final_experiments_v2/*_test_preds.json final_experiments_all/ 2>/dev/null || true
cp final_experiments_v2/*_test.json       final_experiments_all/ 2>/dev/null || true
cp final_experiments_v3/*_test_preds.json final_experiments_all/ 2>/dev/null || true
cp final_experiments_v3/*_test.json       final_experiments_all/ 2>/dev/null || true

python comparison_experiment/ensemble_and_stats.py \
    --results-dir final_experiments_all \
    --out final_experiments_all/ensemble_report.json

echo "=== Done. Final outputs: ==="
ls -la final_experiments_all/