Xiao Furen
2ae08ac2cd
Refactor the preprocessing and segmentation pipeline to handle AP orientation variations and improve anatomical boundary detection. Key changes include: - Implement automated AP orientation detection in `process_single_image` to handle prone scans by flipping CT and labels when necessary. - Enhance `segment_spinous_process` using a gap-based approach to identify the spinal canal, providing more stable thresholds for spinous process and vertebral body segmentation. - Improve optimization search space by using the vertebral body (VBODY) projection for x/z bounding box calculation instead of the whole bone. - Refactor `render_bone_figure` to unify 2D/3D visualization and support detailed anatomical coloring (VBODY, spinous process). - Update `cl_score_torch_xfr` with more robust penalty handling for out-of-bone and null-voxel regions. - Add `retry_robust` utility to handle transient NFS file system errors. - Update `xfr_preprocess.py` to include anatomical segmentation coloring in rotated level visualizations.
128 lines
No EOL
5 KiB
Python
128 lines
No EOL
5 KiB
Python
#!/home/xfr/.conda/envs/cbt/bin/python
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"""掃 standardize 輸出目錄中「前後（AP）方向翻轉」的個案（prone 伏位掃描，
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前側落在 y 小側，例：colon 0003），供重跑修正用。
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判定：對每個 volume 的 L1~L6 輸出遮罩（優 _binary_sdf、次 _binary_nn、
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再 _binary）個別跑 orientation.anterior_y_side（中線帶椎管兩側質量比較，
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見該函式 docstring），多 level 票決：
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flip : y_min 票 > y_max 票（前後翻轉，需重跑）
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ok : y_max 票 > y_min 票（方向正常）
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mixed : 平手（需人工確認）
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unknown : 全部無法判定（無明顯前後質量差，如鏡稱面異常案例）
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Usage:
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python xfr_reprocess_ap.py <output_dir> # 只回報
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python xfr_reprocess_ap.py <output_dir> --fix # 另刪 flip volume 的輸出
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# 資料夾 + progress.json
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# 條目，之後重跑
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# xfr_preprocess.py 即可
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"""
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import argparse
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import json
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import os
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import shutil
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import sys
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import time
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import SimpleITK as sitk
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sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
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from imaging.orientation import anterior_y_side
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LEVELS = ('L1', 'L2', 'L3', 'L4', 'L5', 'L6')
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MASK_SUFFIXES = ('_binary_sdf.nii.gz', '_binary_nn.nii.gz', '_binary.nii.gz')
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def volume_decision(vol_dir):
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"""回傳 (decision, per_level dict)。decision ∈ flip/ok/mixed/unknown/nomask。"""
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per = {}
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for lvl in LEVELS:
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for suf in MASK_SUFFIXES:
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p = os.path.join(vol_dir, f'{lvl}{suf}')
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if os.path.exists(p):
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m = sitk.GetArrayFromImage(sitk.ReadImage(p, sitk.sitkUInt8))
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per[lvl] = anterior_y_side(m)
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break
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if not per:
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return 'nomask', per
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votes = [v for v in per.values() if v is not None]
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if not votes:
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return 'unknown', per
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n_min = votes.count('y_min')
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n_max = votes.count('y_max')
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if n_min > n_max:
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return 'flip', per
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if n_max > n_min:
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return 'ok', per
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return 'mixed', per
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def main():
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parser = argparse.ArgumentParser(
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description='Find AP-flipped (prone) volumes in a standardized output dir.')
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parser.add_argument('output_dir')
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parser.add_argument('--fix', action='store_true',
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help='Also delete flipped volumes\' output dirs and '
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'their progress.json entries')
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args = parser.parse_args()
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outdir = args.output_dir
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if not os.path.isdir(outdir):
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print(f'not a directory: {outdir}')
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return
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vols = sorted(d for d in os.listdir(outdir)
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if os.path.isdir(os.path.join(outdir, d)))
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flip, mixed, unknown, ok, nomask = [], [], [], [], []
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t0 = time.time()
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for i, vol in enumerate(vols, 1):
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dec, per = volume_decision(os.path.join(outdir, vol))
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tag = {'flip': 'FLIP', 'ok': 'ok ', 'mixed': 'MIXED',
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'unknown': '?!?', 'nomask': '- '}[dec]
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detail = ' '.join(f'{k}={v}' for k, v in per.items())
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print(f'[{i}/{len(vols)}] {tag} {vol} {detail}')
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{'flip': flip, 'mixed': mixed, 'unknown': unknown,
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'ok': ok, 'nomask': nomask}[dec].append(vol)
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if (i % 25) == 0:
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print(f' ... {i}/{len(vols)} ({(time.time()-t0)/60:.1f} min)', flush=True)
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print(f'\n=== Summary: {len(vols)} volumes ===')
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print(f' ok (normal) : {len(ok)}')
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print(f' FLIP (AP-flipped) : {len(flip)}')
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for v in flip:
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print(f' - {v}')
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print(f' mixed (need check) : {len(mixed)}')
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for v in mixed:
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print(f' - {v}')
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print(f' unknown (no vote) : {len(unknown)}')
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for v in unknown:
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print(f' - {v}')
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print(f' no level mask : {len(nomask)}')
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if args.fix and flip:
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# 1) progress.json：刪掉 flip 的條目（備份）
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prog_path = os.path.join(outdir, 'progress.json')
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if os.path.exists(prog_path):
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with open(prog_path) as f:
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prog = json.load(f)
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removed = [v for v in flip if prog.pop(v, None) is not None]
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bak = f'{prog_path}.apfix-{time.strftime("%Y%m%d_%H%M%S")}'
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shutil.copyfile(prog_path, bak)
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with open(prog_path, 'w') as f:
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json.dump(prog, f, indent=2)
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print(f'\nprogress.json: removed {len(removed)} entr(y/ies) '
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f'[{", ".join(v.split(".")[-1] or v for v in removed)}]; '
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f'backup {bak}')
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# 2) 刪輸出資料夾
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for v in flip:
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shutil.rmtree(os.path.join(outdir, v))
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print(f'removed {os.path.join(outdir, v)}')
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print('\nNext: rerun `python xfr_preprocess.py` — only the removed '
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'volumes will be reprocessed (with the AP flip applied).')
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elif not args.fix and flip:
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print('\nRerun with --fix to delete the flipped outputs and progress '
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'entries, then run `python xfr_preprocess.py`.')
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if __name__ == '__main__':
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main() |