source_code/sam3/medsam3_brats/run_pipeline.sh

#!/bin/bash
# MedSAM3 BraTS 分割完整流程脚本

# 配置路径
BRATS_RAW_DIR="/data/yty/brats2023/ASNR-MICCAI-BraTS2023-GLI-Challenge-TrainingData"
PROCESSED_DIR="/data/yty/brats23_sam3_processed"
OUTPUT_DIR="/data/yty/brats23_sam3_results"
SAM3_CHECKPOINT="/data/yty/sam3/sam3.pt"

# 处理参数
MODALITY=0  # 0=t1c, 1=t1n, 2=t2f, 3=t2w
TARGET_SIZE="512 512"
NUM_CASES=5  # 先测试5个病例，设为空处理所有

echo "============================================"
echo "MedSAM3 BraTS Segmentation Pipeline"
echo "============================================"

# Step 1: 预处理数据
echo ""
echo "Step 1: Preprocessing BraTS data..."
echo "--------------------------------------------"

if [ ! -z "$NUM_CASES" ]; then
    NUM_CASES_ARG="--num_cases $NUM_CASES"
else
    NUM_CASES_ARG=""
fi

python preprocess_brats.py \
    --input_dir "$BRATS_RAW_DIR" \
    --output_dir "$PROCESSED_DIR" \
    --modality $MODALITY \
    --target_size $TARGET_SIZE \
    $NUM_CASES_ARG

if [ $? -ne 0 ]; then
    echo "Error in preprocessing!"
    exit 1
fi

# Step 2: SAM3 推理
echo ""
echo "Step 2: Running SAM3 inference..."
echo "--------------------------------------------"

python infer_brats_sam3.py \
    --input_dir "$PROCESSED_DIR" \
    --output_dir "$OUTPUT_DIR" \
    --checkpoint "$SAM3_CHECKPOINT" \
    --prompt_type box \
    --visualize

if [ $? -ne 0 ]; then
    echo "Error in inference!"
    exit 1
fi

echo ""
echo "============================================"
echo "Pipeline completed!"
echo "Results saved to: $OUTPUT_DIR"
echo "============================================"