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.
242 lines
No EOL
9.1 KiB
Python
242 lines
No EOL
9.1 KiB
Python
#!/usr/bin/env python
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"""
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從 optimizer 存的 output.csv 重新渲染既有螺絲模式四視角圖（X-ray 圖）。
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用途：render_bone_figure 改了純顯示層（例如棘突改半透明 + 依深度正確遮擋
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螺絲路徑）之後，不需要重跑優化，直接從 CSV 的 best_position 重新出圖。
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原圖先備份到 Output/{date}/backup_opaque_spinous/{vol}/，再重渲染同檔名覆蓋。
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mask 取法與 xfr_debug / xfr_plot_level 相同（level_file_path：
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binary_sdf 優先、缺則 binary；cortical 同），spacing 讀自 mask 檔。
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Usage:
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python xfr_rerender_spinous.py # 預設 20260912，多 GPU 並行
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python xfr_rerender_spinous.py 20260911 # 指定日期
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python xfr_rerender_spinous.py 20260912 0001 # 只該 volume（全名或末段）
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python xfr_rerender_spinous.py --dry-run 20260912 # 只列出會重新渲染的圖
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python xfr_rerender_spinous.py --cpus 20260912 # 純 CPU 循序
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"""
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import argparse
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import csv
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import multiprocessing
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import os
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import re
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import shutil
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import sys
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import numpy as np
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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.transforms import level_file_path
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from visualization.res_bone_figure import render_bone_figure
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OUTPUT_BASE = '/mnt/1248/open2/cyrou/Output'
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MASK_DIR = '/mnt/1248/open2/cyrou/CBT/Seg/Resample/standardized-xfr'
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BACKUP = 'backup_opaque_spinous'
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# {level}_{way}_L{d}_{l}_R{d}_{l}_{swarm}_{iter}.png（單側跑法該側可為空）
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PNG_RE = re.compile(
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r'^(?P<level>[A-Z]\d+?)_(?P<way>CBT|TPS)'
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r'_L(?P<dl>\d+(?:\.\d+)?|)_(?P<ll>\d+(?:\.\d+)?|)'
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r'_R(?P<dr>\d+(?:\.\d+)?|)_(?P<lr>\d+(?:\.\d+)?|)'
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r'_(?P<sw>\d+|)_(?P<it>\d+|)\.png$')
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def _f(s):
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s = (s or '').strip()
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return float(s) if s else None
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def _parse_pos(s):
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"""CSV '(x, y, z)' -> (z, y, x)（best_position 慣例）。"""
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v = re.findall(r'[-+]?\d*\.?\d+(?:[eE][-+]?\d+)?', s or '')
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if len(v) < 3:
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return None
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x, y, z = (float(t) for t in v[:3])
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return z, y, x
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def _pos(row):
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if row is None:
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return None
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p = _parse_pos(row.get('Position_XYZ'))
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if p is None:
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return None
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az, alt = _f(row.get('Raw_Azimuth')), _f(row.get('Raw_Altitude'))
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if az is None or alt is None:
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return None
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return (p[0], p[1], p[2], az, alt)
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def read_csv_rows(vol_out_dir):
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path = os.path.join(vol_out_dir, 'output.csv')
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if not os.path.isfile(path):
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return None
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with open(path, newline='') as f:
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return [r for r in csv.DictReader(f) if any(c.strip() for c in r.values())]
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def find_row(rows, side, d, l):
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if d is None or l is None:
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return None
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for r in rows:
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if r.get('Side') != side:
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continue
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rd, rl = _f(r.get('Diameter')), _f(r.get('Length'))
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if rd is not None and rl is not None \
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and abs(rd - d) < 1e-6 and abs(rl - l) < 1e-6:
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return r
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return None
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def collect_figs(date_dir, vol_filter=None):
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"""回傳 (tasks, skipped)：tasks 為可重新渲染的圖（dict），skipped 為 (原因, 路徑)。"""
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vols = sorted(d for d in os.listdir(date_dir)
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if os.path.isdir(os.path.join(date_dir, d)) and d != BACKUP)
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if vol_filter:
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vols = [v for v in vols
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if v == vol_filter or v.rsplit('.', 1)[-1] == vol_filter]
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if not vols:
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raise SystemExit(f'volume not found: {vol_filter}')
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tasks, skipped = [], []
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for vol in vols:
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vdir = os.path.join(date_dir, vol)
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rows = read_csv_rows(vdir) or []
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for name in sorted(os.listdir(vdir)):
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m = PNG_RE.match(name)
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if not m:
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continue
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png = os.path.join(vdir, name)
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level, way = m['level'], m['way']
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d_l, l_l = _f(m['dl']), _f(m['ll'])
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d_r, l_r = _f(m['dr']), _f(m['lr'])
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row_l = find_row(rows, 'L', d_l, l_l)
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row_r = find_row(rows, 'R', d_r, l_r)
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if (d_l is not None and row_l is None) or (d_r is not None and row_r is None) \
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or (d_l is None and d_r is None):
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skipped.append((vol, name, 'CSV 無對應 L/R 行'))
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continue
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mask_dir = os.path.join(MASK_DIR, vol)
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sdf = level_file_path(mask_dir, level, 'binary_sdf')
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binary_path = sdf if os.path.exists(sdf) \
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else level_file_path(mask_dir, level, 'binary')
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if not os.path.exists(binary_path):
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skipped.append((vol, name, f'無 bone mask: {binary_path}'))
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continue
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cortical_path = level_file_path(mask_dir, level, 'cortical')
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row_any = row_l or row_r
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tt = _f(row_any.get('Total_Time'))
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tt = None if (tt is None or not np.isfinite(tt)) else tt
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tasks.append({
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'vol': vol, 'name': name, 'png': png, 'level': level, 'way': way,
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'd_l': d_l, 'l_l': l_l, 'd_r': d_r, 'l_r': l_r,
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'pos_l': _pos(row_l), 'pos_r': _pos(row_r),
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'binary': binary_path,
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'cortical': cortical_path if os.path.exists(cortical_path) else None,
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'swarm': int(_f(m['sw']) or 0), 'iter': int(_f(m['it']) or 0),
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'time': tt,
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})
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return tasks, skipped
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def _run_batch(batch):
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"""一個 worker 固定綁一個 GPU，依序渲染分到的圖（CUDA_VISIBLE_DEVICES
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須在 torch 首次 init CUDA 前設好，故綁定後不再變）。"""
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gpu, g_tasks = batch
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os.environ['CUDA_VISIBLE_DEVICES'] = str(gpu)
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os.environ.setdefault('OMP_NUM_THREADS', '4')
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import matplotlib
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matplotlib.use('Agg')
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return [render_one(t) for t in g_tasks]
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def render_one(task):
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import torch
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device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
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img = sitk.ReadImage(task['binary'], sitk.sitkUInt8)
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spacing = list(img.GetSpacing())
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# 備份原圖（同目錄同檔名會重複跑時，備份檔保留第一份）
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backup_dir = os.path.join(os.path.dirname(os.path.dirname(task['png'])), BACKUP, task['vol'])
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bpath = os.path.join(backup_dir, task['name'])
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os.makedirs(backup_dir, exist_ok=True)
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if not os.path.exists(bpath):
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shutil.move(task['png'], bpath)
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try:
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out = render_bone_figure(
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task['vol'], task['level'], task['binary'], task['cortical'],
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base_folder=OUTPUT_BASE, spacing=spacing, way=task['way'],
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best_position_l=task['pos_l'], best_position_r=task['pos_r'],
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diameter_l=task['d_l'], length_l=task['l_l'],
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diameter_r=task['d_r'], length_r=task['l_r'],
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image2_path=None, device=device,
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swarm_size=task['swarm'], max_iter=task['iter'], total_time=task['time'],
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write_csv=False, output_path=task['png'])
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except Exception as e:
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if not os.path.exists(task['png']) and os.path.exists(bpath):
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shutil.move(bpath, task['png'])
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return (task['vol'], task['name'], 'fail', f'{type(e).__name__}: {e}')
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if out is None:
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if os.path.exists(bpath):
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shutil.move(bpath, task['png'])
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return (task['vol'], task['name'], 'fail', 'render 回傳 None（無/空遮罩）')
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if out != task['png']:
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os.replace(out, task['png'])
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return (task['vol'], task['name'], 'ok', f'{out} ({device})')
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def main():
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ap = argparse.ArgumentParser(description='從 output.csv 重新渲染螺絲模式四視角圖')
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ap.add_argument('date', nargs='?', default='20260912')
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ap.add_argument('volume', nargs='?', default=None)
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ap.add_argument('--dry-run', action='store_true')
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ap.add_argument('--cpus', action='store_true', help='CPU 循序（不佔 GPU）')
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args = ap.parse_args()
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date_dir = os.path.join(OUTPUT_BASE, args.date)
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if not os.path.isdir(date_dir):
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raise SystemExit(f'no such date dir: {date_dir}')
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tasks, skipped = collect_figs(date_dir, args.volume)
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print(f'{args.date}: {len(tasks)} figure(s) to re-render, {len(skipped)} skip(s)')
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for vol, name, why in skipped:
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print(f' [skip] {vol}/{name}: {why}')
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if args.dry_run:
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for t in tasks:
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print(f" [dry] {t['vol']}/{t['name']} "
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f"L=({t['d_l']},{t['l_l']}) R=({t['d_r']},{t['l_r']})")
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return
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if not tasks:
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return
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if args.cpus or not _cuda_count():
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os.environ['CUDA_VISIBLE_DEVICES'] = ''
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for i, t in enumerate(tasks, 1):
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r = render_one(t)
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print(f'[{i:3d}/{len(tasks)}] {r[2]:4s} {r[0]}/{r[1]} {r[3]}', flush=True)
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else:
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n = min(_cuda_count(), 4)
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ctx = multiprocessing.get_context('spawn')
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batches = [(i, tasks[i::n]) for i in range(n)]
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with ctx.Pool(n) as pool:
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for results in pool.map(_run_batch, batches):
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for vol, name, status, detail in results:
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print(f'[{status:4s}] {vol}/{name} {detail}', flush=True)
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print('=' * 60)
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print('Done.')
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def _cuda_count():
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try:
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import torch
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return torch.cuda.device_count()
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except Exception:
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return 0
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if __name__ == '__main__':
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main() |