rename_acdc_specific.py

#!/usr/bin/env python3
"""
Specific renaming script for ACDC dataset (adapted for HuggingFace download structure)
Input:  flat Images/ and Masks/ folders with patient###_frameXX[_gt].nii.gz
Output: per-patient subdirectories with renamed files:
- patient###_frameXX.nii.gz -> lvsa_SR_ED.nii.gz (lower frame) or lvsa_SR_ES.nii.gz (higher frame)
- patient###_frameXX_gt.nii.gz -> seg_lvsa_SR_ED.nii.gz (lower frame) or seg_lvsa_SR_ES.nii.gz (higher frame)
"""

import re
import shutil
from pathlib import Path
from collections import defaultdict
import argparse


def rename_acdc_files(source_dir: str, output_dir: str, dry_run: bool = True):
    """
    Reorganise flat Images/Masks folders into per-patient directories with renamed files.

    Args:
        source_dir: Directory containing Images/ and Masks/ subdirectories
        output_dir: Directory where per-patient folders will be created
        dry_run: If True, only show what would be done
    """
    source_path = Path(source_dir)
    output_path = Path(output_dir)
    images_dir = source_path / "Images"
    masks_dir = source_path / "Masks"

    if not images_dir.exists() or not masks_dir.exists():
        print(f"Error: Expected Images/ and Masks/ subdirectories in {source_path}")
        return

    print(f"\n{'DRY RUN MODE' if dry_run else 'EXECUTING'}")
    print("=" * 50)

    # Group files by patient
    patients = defaultdict(dict)  # patient_id -> {frame_num: {'img': path, 'gt': path}}

    for img_file in sorted(images_dir.glob("patient*_frame*.nii.gz")):
        match = re.match(r'(patient\d+)_frame(\d+)\.nii\.gz', img_file.name)
        if match:
            pid, fnum = match.group(1), int(match.group(2))
            patients[pid].setdefault(fnum, {})['img'] = img_file

    for gt_file in sorted(masks_dir.glob("patient*_frame*_gt.nii.gz")):
        match = re.match(r'(patient\d+)_frame(\d+)_gt\.nii\.gz', gt_file.name)
        if match:
            pid, fnum = match.group(1), int(match.group(2))
            patients[pid].setdefault(fnum, {})['gt'] = gt_file

    for pid in sorted(patients):
        frame_files = patients[pid]
        frame_numbers = sorted(frame_files.keys())

        print(f"\nProcessing: {pid}")

        if len(frame_numbers) < 2:
            print(f"  Warning: Only {len(frame_numbers)} frame found, expected 2")
            continue

        ed_frame = frame_numbers[0]
        es_frame = frame_numbers[-1]
        print(f"  ED frame: {ed_frame}, ES frame: {es_frame}")

        patient_out = output_path / pid
        if not dry_run:
            patient_out.mkdir(parents=True, exist_ok=True)

        rename_map = {
            (ed_frame, 'img'): 'lvsa_SR_ED.nii.gz',
            (ed_frame, 'gt'):  'seg_lvsa_SR_ED.nii.gz',
            (es_frame, 'img'): 'lvsa_SR_ES.nii.gz',
            (es_frame, 'gt'):  'seg_lvsa_SR_ES.nii.gz',
        }

        for (fnum, ftype), new_name in rename_map.items():
            if ftype in frame_files.get(fnum, {}):
                src = frame_files[fnum][ftype]
                dst = patient_out / new_name
                if dry_run:
                    print(f"  Would copy: {src.name} -> {pid}/{new_name}")
                else:
                    shutil.copy2(src, dst)
                    print(f"  Copied: {src.name} -> {pid}/{new_name}")

    print("\n" + "=" * 50)
    if dry_run:
        print("DRY RUN COMPLETE - No files were actually copied")
        print("To execute, run with --execute flag")
    else:
        print(f"COMPLETE - Output at {output_path}")


def main():
    parser = argparse.ArgumentParser(description='Reorganise and rename ACDC dataset files')
    parser.add_argument('--source', type=str,
                       default='/mnt/storage/home/ym1413/QC_data_preprocessing/raw_dataset/ACDC',
                       help='Source directory containing Images/ and Masks/')
    parser.add_argument('--output', type=str,
                       default='/mnt/storage/home/ym1413/QC_data_preprocessing/sabotaged_dataset',
                       help='Output directory for per-patient folders')
    parser.add_argument('--dry-run', action='store_true', default=True,
                       help='Show what would be done without executing (default)')
    parser.add_argument('--execute', action='store_true',
                       help='Actually perform the copy and rename')

    args = parser.parse_args()

    if args.execute:
        args.dry_run = False

    rename_acdc_files(args.source, args.output, dry_run=args.dry_run)


if __name__ == "__main__":
    main()