Xiao Furen
d167c1f7c7
Introduce a robust coordinate transformation system to manage the relationship between original CT space and rotated/standardized segmentation spaces. This includes a new directory hierarchy to separate unrotated crops from rotated outputs and utility functions for geometric mapping. Key changes: - Implement `imaging/transforms.py` to handle bounding box metadata, affine standardization, and coordinate mapping between spaces. - Restructure dataset output: unrotated segmentation files (binary, SDF, ROI, etc.) are now stored in a `<vol>/crop/` subdirectory to distinguish them from `<vol>/rotated/` aligned versions. - Add `level_file_path` utility to abstract file discovery across legacy (top-level) and new (crop-based) directory structures. - Enhance `seg_bone` to capture and export bounding box metadata (`bbox2`, `nn_bbox`, `bbox_orig`) into `transform.json`. - Implement `xfr_cbt_native.py` for mapping screw positions back to original CT space. - Update preprocessing and visualization scripts to support the new directory layout and transformation metadata. - Improve TinyDB metadata migration logic to prevent accidental corruption of existing database structures.
113 lines
No EOL
4.4 KiB
Python
113 lines
No EOL
4.4 KiB
Python
#!/home/xfr/.conda/envs/cbt/bin/python
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"""一次性的 layout 遷移：把已產出 volume 的「未旋轉 <level> 檔」移入 crop/ 子資料夾。
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新 layout（2026-09-08 起 xfr_preprocess 直接產出，無須再跑本腳本）：
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<vol>/crop/<L>_binary|_smd|_smd_resampled|_binary_sdf|_binary_nn|_roi.nii.gz
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<vol>/crop/<L>_planes.png （原 <vol>/lumbar/）
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<vol>/rotated/<L>_*.nii.gz （不變）
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<vol>/transform.json、<name>_labels.txt（頂層，不變）
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本腳本供改動前已產出、尚未重新處理的 volume 用（例：standardized-xfr-3）：
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1) <vol>/ 頂層的 <L>_*.nii.gz（L = LABEL_MAP level 名）移到 <vol>/crop/
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2) <vol>/lumbar/*.png 移到 <vol>/crop/，lumbar/ 清空後刪除
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Idempotent：已遷就的 volume 重跑無作用；crop/ 已有同名檔時不覆蓋、跳過該檔
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（頂層檔保留，人工核對）。rotated/ 與其他頂層檔不動。
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讀端（xfr_orig_labels / xfr_inverse_transform / xfr_cbt_native 等）以
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imaging.transforms.level_file_path 同時認 crop/ 與頂層，舊世代
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（standardized-xfr-2 等）不遷移也能讀；如需一致化可對該 root 跑本腳本。
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Usage:
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python xfr_migrate_crop.py [ROOT] [--dry-run]
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"""
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import argparse
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import os
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import shutil
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import sys
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sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
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from config.constant import LABEL_MAP
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DEFAULT_ROOT = '/mnt/1248/open2/cyrou/CBT/Seg/Resample/standardized-xfr-3'
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LEVEL_SET = set(LABEL_MAP.values())
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def migrate_volume(vol_dir, dry_run=False):
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"""回傳 (moved, kept) 兩個清單（人讀的說明文字）。"""
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crop_dir = os.path.join(vol_dir, 'crop')
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moved, kept = [], []
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for f in sorted(os.listdir(vol_dir)):
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if not f.endswith('.nii.gz'):
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continue
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if f.split('_', 1)[0] not in LEVEL_SET:
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kept.append(f)
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continue
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dst = os.path.join(crop_dir, f)
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if os.path.exists(dst):
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kept.append(f'{f}（crop/ 已有同名檔，未動）')
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continue
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src = os.path.join(vol_dir, f)
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if dry_run:
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moved.append(f'{f} (dry-run)')
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else:
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os.makedirs(crop_dir, exist_ok=True)
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shutil.move(src, dst)
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moved.append(f)
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lumbar_dir = os.path.join(vol_dir, 'lumbar')
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if os.path.isdir(lumbar_dir):
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for f in sorted(os.listdir(lumbar_dir)):
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dst = os.path.join(crop_dir, f)
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if os.path.exists(dst):
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kept.append(f'lumbar/{f}（crop/ 已有同名檔，未動）')
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continue
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if dry_run:
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moved.append(f'lumbar/{f} (dry-run)')
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else:
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os.makedirs(crop_dir, exist_ok=True)
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shutil.move(os.path.join(lumbar_dir, f), dst)
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moved.append(f'lumbar/{f}')
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if not dry_run:
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try:
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os.rmdir(lumbar_dir)
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except OSError:
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kept.append('lumbar/（仍有其他檔，未刪）')
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return moved, kept
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def main():
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parser = argparse.ArgumentParser(
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description='Migrate per-level pre-rotated files from <vol>/ top level '
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'to <vol>/crop/ (plus lumbar/*.png -> crop/).')
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parser.add_argument('root', nargs='?', default=DEFAULT_ROOT,
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help=f'standardized generation dir (default: {DEFAULT_ROOT})')
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parser.add_argument('--dry-run', action='store_true',
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help='Only report what would be moved.')
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args = parser.parse_args()
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if not os.path.isdir(args.root):
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sys.exit(f'not a directory: {args.root}')
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vols = sorted(d for d in os.listdir(args.root)
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if os.path.isdir(os.path.join(args.root, d)))
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tag = '[dry-run] ' if args.dry_run else ''
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n_done = n_empty = 0
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for i, vol in enumerate(vols, 1):
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vol_dir = os.path.join(args.root, vol)
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moved, kept = migrate_volume(vol_dir, dry_run=args.dry_run)
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if not moved:
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n_empty += 1
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print(f'{tag}[{i}/{len(vols)}] - {vol} (no file to move)')
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continue
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n_done += 1
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print(f'{tag}[{i}/{len(vols)}] ok {vol} moved {len(moved)} file(s)')
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for m in moved:
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print(f' -> {m}')
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for k in kept:
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print(f' !! kept: {k}')
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print(f'\n{tag}done: {n_done} volume(s) migrated, {n_empty} untouched '
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f'out of {len(vols)}')
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if __name__ == '__main__':
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main() |