Xiao Furen
332226f843
- Created a new pixi.toml file to manage project dependencies and tasks. - Defined workspace metadata including authors, channels, name, platforms, and version. - Specified tasks for preprocessing, PSO, DE, and other scripts. - Listed dependencies for Python and various libraries with specific versions. - Configured additional PyPI options for PyTorch installation from a custom index.
214 lines
No EOL
8.3 KiB
Python
214 lines
No EOL
8.3 KiB
Python
#!/usr/bin/env python
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"""補記既有 volume 的 transform.json rotated 段平面（sym / endplate）。
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core/optimizer 的 xfr 管線（run_pso_torch_xfr / run_de_torch_xfr）不再於影像
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上重新估算兩平面（best_symmetry_plane / best_upper_endplate_plane），改直接
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讀 <vol>/transform.json levels[L*]['rotated']['sym' / 'endplate']
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（imaging.transforms.load_rotated_planes_from_path）：
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- 新世代：xfr_preprocess._write_rotated_level 旋轉時即記錄（rotated/ 局部系）；
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- 舊世代（進度 progress.json 已標完成、重跑 preprocess 會整支跳過）：跑本腳本
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補記——用與舊 optimizer 相同函式、相同預設值，對
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rotated/<level>_binary_sdf.nii.gz（完整 mask、SP 移除前）重新估算，
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併入既有 rotated 段（只加 sym / endplate 兩鍵，不動 template / R / center /
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start / size 等既有鍵、不重寫任何 nii）。補記後 optimizer 讀到的平面與
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改前行為一致（同輸入、同演算法）。
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預設跳過已有 sym 記錄的 level（部分失敗後重跑只補缺者）；--force 全數重記。
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Usage:
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python xfr_record_planes.py [--force] [--dir <standardized dir>] [volume_id ...]
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volume_id 可用完整 ID 或末段（如 0001）；省略 = 全部 volume。
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"""
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import argparse
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import logging
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import os
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import re
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import sys
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import time
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import numpy as np
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import SimpleITK as sitk
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from imaging.orientation import best_symmetry_plane, best_upper_endplate_plane
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from imaging.transforms import load_transform, save_transform
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STANDARDIZED_DIR = '/mnt/1248/open2/cyrou/CBT/Seg/Resample/standardized-xfr-3/'
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LOG_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'logs')
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logger = logging.getLogger('xfr_record_planes')
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# 基準系健全閾值：對齊良好時 theta_v / tau_y 應近似 0（xfr_preprocess 的 R
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# 已把鏡稱面法線轉到 +x、終板法線轉到 z>0）
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SANITY_DEG = 5.0
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class _Tee:
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"""同時輸出到 console 與 log 檔，逐行寫入。"""
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def __init__(self, console, log_fh):
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self.console = console
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self.log_fh = log_fh
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self.buf = ''
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def _emit(self, line):
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self.console.write(line + '\n')
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self.log_fh.write(line + '\n')
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def write(self, data):
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if not data:
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return
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self.buf += data
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while True:
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idx_n = self.buf.find('\n')
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idx_r = self.buf.find('\r')
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candidates = [i for i in (idx_n, idx_r) if i != -1]
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if not candidates:
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break
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idx = min(candidates)
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self._emit(self.buf[:idx])
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self.buf = self.buf[idx + 1:]
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def flush(self):
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if self.buf:
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self._emit(self.buf)
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self.buf = ''
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self.console.flush()
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self.log_fh.flush()
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def isatty(self):
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return False
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def setup_tee(log_path):
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log_fh = open(log_path, 'a', buffering=1)
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sys.stdout = _Tee(sys.stdout, log_fh)
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sys.stderr = _Tee(sys.stderr, log_fh)
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def rotated_levels(vol_dir):
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"""該 volume rotated/ 中有 _binary_sdf.nii.gz 的 lumbar level（排序）。"""
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rotated_dir = os.path.join(vol_dir, 'rotated')
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if not os.path.isdir(rotated_dir):
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return ()
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levels = set()
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for fn in os.listdir(rotated_dir):
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m = re.fullmatch(r'(L[1-9]\d*)_binary_sdf\.nii\.gz', fn)
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if m:
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levels.add(m.group(1))
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return tuple(sorted(levels, key=lambda lv: int(lv[1:])))
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def record_level(vol_dir, level, sdf_path):
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"""估算該 level 兩平面併入 transform.json rotated 段；回傳 (sym, endplate)。"""
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arr = sitk.GetArrayFromImage(sitk.ReadImage(sdf_path))
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sym = best_symmetry_plane(arr)
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endplate = best_upper_endplate_plane(arr)
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meta = load_transform(vol_dir)
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lv = meta['levels'].setdefault(level, {})
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rot = lv.setdefault('rotated', {})
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rot['sym'] = sym
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rot['endplate'] = endplate
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save_transform(vol_dir, meta)
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s_nx, s_ny, _ = sym['normal']
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theta_v = float(np.degrees(np.arctan2(s_ny, s_nx)))
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if endplate is not None:
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e_nx, e_ny, e_nz = endplate['normal']
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tau_y = float(np.degrees(np.arctan2(e_ny, e_nz)))
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else:
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tau_y = None
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note = f'endplate={endplate is not None}'
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if abs(theta_v) > SANITY_DEG or (tau_y is not None and abs(tau_y) > SANITY_DEG):
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logger.warning(f'{os.path.basename(vol_dir)} {level}: 基準系殘差偏大 '
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f'(theta_v={theta_v:+.2f} deg, tau_y='
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f'{tau_y if tau_y is None else round(tau_y, 2)}) — '
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f'該 level 的 xfr_preprocess 對齊可能失效，建議人工核對')
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else:
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logger.info(f'{os.path.basename(vol_dir)} {level}: recorded '
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f'(mirror ratio={sym["ratio"]:.3f}, theta_v={theta_v:+.2f} deg, '
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f'tau_y={tau_y if tau_y is None else round(tau_y, 2)}, {note})')
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return sym, endplate
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def main():
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parser = argparse.ArgumentParser(
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description='Record sym/endplate planes into transform.json for '
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'existing volumes (old generation, before xfr_preprocess '
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'recording them at rotation time).')
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parser.add_argument('volume_ids', nargs='*',
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help='Full ID or trailing segment (e.g. 0001); '
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'default: all volumes')
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parser.add_argument('--dir', default=STANDARDIZED_DIR,
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help='Standardized output dir (default: standardized-xfr-3)')
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parser.add_argument('--force', action='store_true',
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help='Re-record levels that already have sym/endplate')
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args = parser.parse_args()
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os.makedirs(LOG_DIR, exist_ok=True)
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log_path = os.path.join(
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LOG_DIR, f'xfr_record_planes_{time.strftime("%Y%m%d_%H%M%S")}.log')
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setup_tee(log_path)
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logging.basicConfig(level=logging.INFO,
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format='%(asctime)s [%(levelname)s] %(name)s: %(message)s',
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datefmt='%Y-%m-%d %H:%M:%S')
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logger.info(f'Log file: {log_path}')
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logger.info(f'Command: {sys.executable} {" ".join(sys.argv)}')
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if not os.path.isdir(args.dir):
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sys.exit(f'Standardized dir not found: {args.dir}')
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volumes = [d for d in sorted(os.listdir(args.dir))
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if os.path.isdir(os.path.join(args.dir, d))]
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if args.volume_ids:
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keys = [v.lower() for v in args.volume_ids]
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vols = [v for v in volumes
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if v.lower() in keys or v.rsplit('.', 1)[-1].lower() in keys]
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if not vols:
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sys.exit(f'No volume matches: {", ".join(args.volume_ids)}')
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volumes = vols
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logger.info(f'{len(volumes)} volume(s) under {args.dir}'
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+ (' (force)' if args.force else ''))
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t0 = time.time()
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n_rec, n_skip_done, n_err, n_no_levels = 0, 0, 0, 0
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no_ep = []
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for vid in volumes:
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vol_dir = os.path.join(args.dir, vid)
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levels = rotated_levels(vol_dir)
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if not levels:
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n_no_levels += 1
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continue
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try:
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meta = load_transform(vol_dir)
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except FileNotFoundError:
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logger.warning(f'{vid}: transform.json 缺失，跳過 '
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f'（舊世代可先在 xfr_inverse_transform.py 加 --rebuild）')
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n_err += 1
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continue
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for level in levels:
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rot = meta['levels'].get(level, {}).get('rotated') or {}
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if not args.force and rot.get('sym') is not None:
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n_skip_done += 1
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continue
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sdf_path = os.path.join(vol_dir, 'rotated', f'{level}_binary_sdf.nii.gz')
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try:
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_, ep = record_level(vol_dir, level, sdf_path)
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n_rec += 1
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if ep is None:
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no_ep.append(f'{vid} {level}')
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except Exception as e:
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n_err += 1
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logger.error(f'{vid} {level}: {e}')
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dt = time.time() - t0
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logger.info(f'Done in {dt / 60:.1f} min: recorded {n_rec} level(s), '
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f'skipped(already) {n_skip_done}, no rotated levels '
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f'{n_no_levels} volume(s), errors {n_err}')
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if no_ep:
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logger.warning(f'{len(no_ep)} level(s) 無上終板面記錄（資料不足），'
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f'optimizer 對應 level 終板入口剪除停用: {", ".join(no_ep[:10])}'
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f'{" ..." if len(no_ep) > 10 else ""}')
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if __name__ == '__main__':
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main() |