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"""
Batch process all 10 MSD tasks.
This script processes all MSD tasks sequentially:
- Converts each task to HF format
- Creates 10% processed datasets
- Output structure:
RL_dataset/
MSD_task01/
Task01_BrainTumour/
Task01_BrainTumour_10percent_processed/
MSD_task02/
Task02_Heart/
Task02_Heart_10percent_processed/
...
"""
import os
import sys
import subprocess
from pathlib import Path
# Add script directory to path
SCRIPT_DIR = Path(__file__).resolve().parent
sys.path.insert(0, str(SCRIPT_DIR))
# MSD task configurations
MSD_TASKS = [
{
"name": "Task01_BrainTumour",
"raw_dir": "/projects/p32685/MSD/Task01_BrainTumour",
"description": "Brain Tumour Segmentation"
},
{
"name": "Task02_Heart",
"raw_dir": "/projects/p32685/MSD/Task02_Heart",
"description": "Heart Segmentation"
},
{
"name": "Task03_Liver",
"raw_dir": "/projects/p32685/MSD/Task03_Liver",
"description": "Liver Segmentation"
},
{
"name": "Task04_Hippocampus",
"raw_dir": "/projects/p32685/MSD/Task04_Hippocampus",
"description": "Hippocampus Segmentation"
},
{
"name": "Task05_Prostate",
"raw_dir": "/projects/p32685/MSD/Task05_Prostate",
"description": "Prostate Segmentation"
},
{
"name": "Task06_Lung",
"raw_dir": "/projects/p32685/MSD/Task06_Lung",
"description": "Lung Tumor Segmentation"
},
{
"name": "Task07_Pancreas",
"raw_dir": "/projects/p32685/MSD/Task07_Pancreas",
"description": "Pancreas Segmentation"
},
{
"name": "Task08_HepaticVessel",
"raw_dir": "/projects/p32685/MSD/Task08_HepaticVessel",
"description": "Hepatic Vessel Segmentation"
},
{
"name": "Task09_Spleen",
"raw_dir": "/projects/p32685/MSD/Task09_Spleen",
"description": "Spleen Segmentation"
},
{
"name": "Task10_Colon",
"raw_dir": "/projects/p32685/MSD/Task10_Colon",
"description": "Colon Tumor Segmentation"
}
]
# Configuration
OUTPUT_BASE_DIR = "/projects/p32685/RL_dataset"
TEMPLATE_PERCENT = 10
DEVICE = "cuda:0"
def process_task(task_config, skip_convert=False, skip_packing=False, skip_precompute=False):
"""
Process a single MSD task.
Args:
task_config: Dictionary with task configuration
skip_convert: Skip step 1 (conversion)
skip_packing: Skip step 2 (packing)
skip_precompute: Skip step 3 (precompute)
"""
task_name = task_config["name"]
raw_dir = task_config["raw_dir"]
print("\n" + "="*80)
print(f"Processing {task_name}: {task_config['description']}")
print("="*80)
print(f"Raw data: {raw_dir}")
print(f"Output base: {OUTPUT_BASE_DIR}")
print(f"Template percent: {TEMPLATE_PERCENT}%")
# Check if raw directory exists
if not os.path.exists(raw_dir):
print(f"✗ Error: Raw data directory does not exist: {raw_dir}")
return False
# Build command
cmd = [
"python3",
os.path.join(SCRIPT_DIR, "end_to_end_preprocessing.py"),
"--dataset_name", task_name,
"--template_percent", str(TEMPLATE_PERCENT),
"--raw_data_dir", raw_dir,
"--output_base_dir", OUTPUT_BASE_DIR,
"--device", DEVICE
]
if skip_convert:
cmd.append("--skip_convert")
if skip_packing:
cmd.append("--skip_packing")
if skip_precompute:
cmd.append("--skip_precompute")
print(f"\nRunning: {' '.join(cmd)}")
try:
result = subprocess.run(cmd, check=True, cwd=SCRIPT_DIR)
if result.returncode == 0:
print(f"\n✓ {task_name} processed successfully!")
return True
else:
print(f"\n✗ {task_name} failed with return code {result.returncode}")
return False
except subprocess.CalledProcessError as e:
print(f"\n✗ {task_name} failed: {e}")
return False
except Exception as e:
print(f"\n✗ {task_name} failed with exception: {e}")
import traceback
traceback.print_exc()
return False
def main():
"""Main function to process all MSD tasks."""
import argparse
parser = argparse.ArgumentParser(description="Batch process all MSD tasks")
parser.add_argument("--start_from", type=int, default=1,
help="Start from task number (1-10)")
parser.add_argument("--end_at", type=int, default=10,
help="End at task number (1-10)")
parser.add_argument("--skip_convert", action="store_true",
help="Skip step 1 (conversion) for all tasks")
parser.add_argument("--skip_packing", action="store_true",
help="Skip step 2 (packing) for all tasks")
parser.add_argument("--skip_precompute", action="store_true",
help="Skip step 3 (precompute) for all tasks")
parser.add_argument("--device", type=str, default="cuda:0",
help="Device for template precomputation")
args = parser.parse_args()
global DEVICE
DEVICE = args.device
print("â•”" + "="*78 + "â•—")
print("â•‘" + " "*15 + "BATCH PROCESS ALL MSD TASKS" + " "*38 + "â•‘")
print("â•”" + "="*78 + "â•—")
print(f"\nTotal tasks: {len(MSD_TASKS)}")
print(f"Processing tasks: {args.start_from} to {args.end_at}")
print(f"Output base: {OUTPUT_BASE_DIR}")
print(f"Template percent: {TEMPLATE_PERCENT}%")
print(f"Device: {DEVICE}")
if args.skip_convert:
print("âš Skipping Step 1 (conversion)")
if args.skip_packing:
print("âš Skipping Step 2 (packing)")
if args.skip_precompute:
print("âš Skipping Step 3 (precompute)")
# Process tasks
success_count = 0
failed_tasks = []
for i, task_config in enumerate(MSD_TASKS, start=1):
if i < args.start_from or i > args.end_at:
continue
print(f"\n{'='*80}")
print(f"Task {i}/{len(MSD_TASKS)}: {task_config['name']}")
print(f"{'='*80}")
success = process_task(
task_config,
skip_convert=args.skip_convert,
skip_packing=args.skip_packing,
skip_precompute=args.skip_precompute
)
if success:
success_count += 1
else:
failed_tasks.append(task_config['name'])
# Summary
print("\n" + "="*80)
print("BATCH PROCESSING SUMMARY")
print("="*80)
print(f"Successfully processed: {success_count}/{args.end_at - args.start_from + 1} tasks")
if failed_tasks:
print(f"\nFailed tasks:")
for task in failed_tasks:
print(f" - {task}")
else:
print("\n✓ All tasks processed successfully!")
print(f"\nOutput structure:")
print(f" {OUTPUT_BASE_DIR}/")
for i in range(args.start_from, args.end_at + 1):
task_name = MSD_TASKS[i-1]['name']
task_num = f"task{i:02d}"
print(f" MSD_{task_num}/")
print(f" {task_name}/")
print(f" {task_name}_{TEMPLATE_PERCENT}percent_processed/")
if __name__ == "__main__":
main()
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