Xiao Furen
0a928d8f8e
Update the coordinate transformation pipeline to prioritize the affine transformation chain recorded in `transform.json` (original_to_source) instead of relying on re-calculated geometric parameters. The previous method relied on re-estimating rotation, center, and bounding boxes from the bone mask, which led to inaccuracies in screw pillar mapping (e.g., dropping from 99% to 30-94% in-label accuracy). The new approach uses the precise inverse affine mapping `o = M^-1 (s - t)` from the transformation metadata. A fallback mechanism is maintained for legacy volumes lacking `transform.json`, which continues to use the re-calculation method. - Implement `load_transform` and `original_to_source` integration - Update documentation to reflect the new primary/fallback coordinate chains - Improve precision of screw parameter mapping to native index space
299 lines
No EOL
14 KiB
Python
299 lines
No EOL
14 KiB
Python
#!/home/xfr/.conda/envs/cbt/bin/python
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"""把 PSO 找到的 CBT 螺絲位置（旋轉 0.5mm 標準系）映回原始
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（未旋轉、未重取樣）native CT 空間，整支 volume 各 level 的螺絲
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（L1-L5 x L/R，最多 10 支）存成單一 label 體積：
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Output_dir/<run_date>/<volume_id>/cbt.nii.gz
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label 值：L1L=1 L1R=2 L2L=3 L2R=4 L3L=5 L3R=6 L4L=7 L4R=8 L5L=9 L5R=10
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（0 = 背景）。
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座標鏈首選：直接用預處理寫檔時記錄在 <vol>/transform.json 的正向鏈
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（imaging.transforms.original_to_source：boxes / std_flip_axes / ap_flip /
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rotated R、center、start / 原 CT 幾何；純 index 空間、不依賴 standardized
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輸出的物理 header）。該鏈為仿射（original index <-> rotated disk index），
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螺絲點經仿射逆向 o = M^-1 (s - t) 精確映射——不重新估算任何平面 / 幾何、
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不重取樣 native label。
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fallback（僅舊世代 volume 沒有 transform.json、或該 level 沒有 rotated
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記錄時）：純 index 空間重算 R/center（template 骨頭 mask 的
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best_symmetry_plane / best_upper_endplate_plane）、fstart（rotated 檔
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origin 反映到 template index 的整數）、bbox2（native label 0.5mm 線性
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重取樣 >0.5 的最大 26-連通區域 bbox）：
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rotated disk r -> t = R^T (r + fstart - c) + c
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-> g0 = bbox2s + (wx-1-tx, wy-1-ty, tz)；ap_flip 時 g0y = N05y-1-g0y
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-> native: rint(g0 * 0.5 / sn)
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重算結果可能與生成時參數不完全一致：2026-09-09 驗證 liver_100 螺絲柱
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in-label 由 93-99%（transform.json）掉到 30-94%（重算）；新世代資料
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（transform.json 在）一律走主路徑。
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螺絲參數化（rotated 系、0.5mm index）：pos = [z, y, x, az°, alt°, d mm, L mm]；
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方向 d_v = (cos az sin alt, sin az sin alt, cos alt)；末端 = p0 + L/0.5 * d_v；
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柱半徑 = d/2 mm。
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驗證（2026-09-09，transform.json 路徑）：20260909_141448 run —
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0001（10/10）、liver_100（10/10）、covid19（L1/L2 六側）螺絲柱體
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in-label >= 92%、2-voxel 膨脹 >= 98%。covid19 L3 兩側除外：該 volume 的
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L3 旋轉 bone mask 是 4.5k voxel / 5 slice 的退化區域（L4/L5 預處理缺檔、
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先前棘突切除），屬資料問題非映射問題（L3 bone 碎片本身逆向 in-label 97.8%）。
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"""
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import argparse
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import json
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import logging
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import os
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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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from tinydb import TinyDB, Query
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from config.constant import LABEL_MAP
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from imaging.resample import resample_img
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from imaging.segmentation import _largest_cc_bbox
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from imaging.orientation import best_symmetry_plane, best_upper_endplate_plane
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from imaging.transforms import (level_file_path, load_transform,
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original_to_source, transform_path)
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from visualization.res_bone_figure import compute_normalizing_rotation
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standardized_dir = '/mnt/1248/open2/cyrou/CBT/Seg/Resample/standardized-xfr-3'
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data_root = '/mnt/1220/Public/dataset/Spine/CTSpine1K/data/'
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label_root = '/mnt/1220/Public/dataset/Spine/CTSpine1K/label/'
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SUBDIRS = {
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'colon': 'conlon',
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'COVID-19': 'COVID-19',
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'HNSCC-3DCT-RT_neck': 'HNSCC-3DCT-RT_neck',
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'liver': 'Liver',
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}
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Output_dir = '/mnt/1248/open/cyrou/Output'
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_PROJ_DIR = os.path.dirname(os.path.abspath(__file__))
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LOG_DIR = os.path.join(_PROJ_DIR, 'logs')
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SIDE_RESULT_DIR = os.path.join(LOG_DIR, 'side_results')
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META_DB = os.path.join(_PROJ_DIR, 'xfr_image_metadata.json')
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LEVELS = ('L1', 'L2', 'L3', 'L4', 'L5')
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LEVEL_LABEL_VAL = {v: int(k) for k, v in LABEL_MAP.items() if v in LEVELS} # {'L1': 20, ...}
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logger = logging.getLogger('xfr_cbt_native')
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def find_native_paths(volume_id):
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"""回傳 (ct_path, label_path, ap_flip)；找不到 native 檔對時 raise。"""
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ap_flip = False
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try:
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meta = TinyDB(META_DB, access_mode='r').table('images') \
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.get(Query().name == volume_id)
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if meta is None:
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logger.warning(f'{volume_id}: not in metadata db; ap_flip defaults to False')
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else:
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ap_flip = bool(meta.get('ap_flip', False))
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except Exception as e:
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logger.warning(f'{volume_id}: metadata db unavailable ({e}); ap_flip defaults to False')
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for sub, lab_sub in SUBDIRS.items():
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ct = f'{data_root}{sub}/{volume_id}.nii.gz'
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lb = f'{label_root}{lab_sub}/{volume_id}_seg.nii.gz'
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if os.path.isfile(ct) and os.path.isfile(lb):
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return ct, lb, ap_flip
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raise FileNotFoundError(f'{volume_id}: no native CT/label pair under {data_root}')
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def level_geometry(volume_id, level, lb_img, lb_arr):
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"""每 level 的 (R, c, fstart, bbox2s, wx, wy)；與預處理/驗證腳本同定義。"""
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vol_dir = os.path.join(standardized_dir, volume_id)
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# 未旋轉檔：新世代在 crop/ 子資料夾、舊世代在頂層
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smd_img = sitk.ReadImage(level_file_path(vol_dir, level, 'smd_resampled'))
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smd = sitk.GetArrayFromImage(smd_img).astype(np.float32)
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if not (np.isfinite(smd).all() and smd.min() < 0 and smd.max() > 0):
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b = (sitk.GetArrayFromImage(
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sitk.ReadImage(level_file_path(vol_dir, level, 'binary_nn'))) > 0).astype(np.uint8)
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else:
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b = (smd < 0.5).astype(np.uint8)
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sym = best_symmetry_plane(b)
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symp = best_upper_endplate_plane(b)
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R, c = compute_normalizing_rotation(b, sym, symp)
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rot_img = sitk.ReadImage(f'{vol_dir}/rotated/{level}_binary_sdf.nii.gz')
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fstart = np.round(np.array(
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smd_img.TransformPhysicalPointToIndex(rot_img.GetOrigin()))).astype(float)
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lv = LEVEL_LABEL_VAL[level]
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bin_img = sitk.GetImageFromArray((lb_arr == lv).astype(np.uint8))
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bin_img.CopyInformation(lb_img)
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bin_lin = resample_img(sitk.Cast(bin_img, sitk.sitkFloat32))
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m_full = sitk.GetImageFromArray((sitk.GetArrayFromImage(bin_lin) > 0.5).astype(np.uint8))
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m_full.CopyInformation(bin_lin)
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cc = _largest_cc_bbox(m_full)
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if cc is None:
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raise ValueError(f'{volume_id} {level}: empty native level mask (label {lv})')
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_, bbox2 = cc
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wx, wy = smd_img.GetSize()[0], smd_img.GetSize()[1]
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return R, c, fstart, np.array(bbox2[:3], float), wx, wy
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def rotated_to_native(r_xyz, geom, N05, sn, ap_flip):
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"""r_xyz: (N,3) rotated disk (x,y,z) index -> (N,3) native 連續 index。"""
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R, c, fstart, bbox2s, wx, wy = geom
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t = (np.asarray(r_xyz, float) + fstart - c) @ R + c
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g0 = np.empty_like(t)
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g0[:, 0] = bbox2s[0] + (wx - 1 - t[:, 0])
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g0[:, 1] = bbox2s[1] + (wy - 1 - t[:, 1])
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g0[:, 2] = bbox2s[2] + t[:, 2]
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if ap_flip:
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g0[:, 1] = N05[1] - 1 - g0[:, 1]
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return g0 * (0.5 / sn)
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def screw_voxel_xyz(pos):
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"""pos = [z, y, x, az°, alt°, d, L]（rotated 系 0.5mm index）。
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回傳柱體內 (x,y,z) float voxel 座標（N,3）。"""
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z, y, x, az, alt, d, L = (float(v) for v in pos[:7])
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azr, altr = np.radians(az), np.radians(alt)
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ca, sa = np.cos(azr), np.sin(azr)
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ct_, st_ = np.cos(altr), np.sin(altr)
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dv = np.array([ca * st_, sa * st_, ct_])
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e1 = np.array([ca * ct_, sa * ct_, -st_])
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e2 = np.array([-sa, ca, 0.0])
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p0 = np.array([x, y, z])
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p1 = p0 + (L / 0.5) * dv
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rad = d / 0.5 + 3.0
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lo = np.floor(np.minimum(p0, p1)) - rad
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hi = np.ceil(np.maximum(p0, p1)) + rad
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xs, ys, zs = np.meshgrid(np.arange(lo[0], hi[0] + 1),
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np.arange(lo[1], hi[1] + 1),
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np.arange(lo[2], hi[2] + 1), indexing='xy')
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P = np.stack([xs.ravel(), ys.ravel(), zs.ravel()], 1)
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dP = P - p0
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xr, yr, zr = dP @ e1, dP @ e2, dP @ dv
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rrad = d # (d/2 mm 半徑) / 0.5mm 每 voxel = d 個 voxel
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m = (xr ** 2 + yr ** 2 <= rrad ** 2) & (zr >= 0) & (zr <= L / 0.5)
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return P[m]
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def write_volume_cbt(volume_id, run_id, output_root=Output_dir, date=None):
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"""把一個 volume 的 side_results 螺絲全部映回 native 空間寫 cbt.nii.gz。
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回傳 (path, n_screws)；該 run 無此 volume 時回傳 (None, 0)。"""
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date = date or run_id[:8]
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side_vol_dir = os.path.join(SIDE_RESULT_DIR, run_id, volume_id)
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if not os.path.isdir(side_vol_dir):
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logger.warning(f'{volume_id}: no side results under {side_vol_dir}; cbt skipped')
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return None, 0
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if not any(os.path.isfile(os.path.join(side_vol_dir, f'{l}_{s}.json'))
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for l in LEVELS for s in ('L', 'R')):
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logger.warning(f'{volume_id}: no <level>_<side>.json in {side_vol_dir}; cbt skipped')
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return None, 0
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ct_path, lb_path, ap_flip = find_native_paths(volume_id)
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ct = sitk.ReadImage(ct_path)
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n_xyz = np.array(ct.GetSize(), int) # (x,y,z)
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n_zyx = n_xyz[::-1].copy() # 輸出 (z,y,x)
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sn = np.array(ct.GetSpacing(), float)
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N05 = np.maximum(1, np.ceil(n_xyz.astype(float) * sn / 0.5 - 1e-6).astype(int))
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# 主路徑：transform.json 記錄的正向鏈（仿射），逆向 o = M^-1 (s - t)
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meta = None
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try:
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meta = load_transform(os.path.join(standardized_dir, volume_id))
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except FileNotFoundError:
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logger.warning(f'{volume_id}: no transform.json '
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f'({transform_path(os.path.join(standardized_dir, volume_id))}); '
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f'全部 level 退回重算路徑（近似）')
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if meta is not None and not np.array_equal(
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np.asarray(meta['original']['size'], int), n_xyz):
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logger.warning(f'{volume_id}: transform.json original size '
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f'{meta["original"]["size"]} != CT {list(n_xyz)}; '
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f'忽略 transform.json，退回重算路徑')
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meta = None
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out_arr = np.zeros(n_zyx, np.uint8)
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lb_img = lb_arr = None # fallback 才需要讀 native label
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geom_cache = {} # fallback：每 level 的 (R, c, fstart, bbox2s, wx, wy)
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aff_cache = {} # 主路徑：每 level 的 (M^-1, t)
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n_screws, skipped = 0, []
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n_tf = n_fb = 0
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for li, level in enumerate(LEVELS):
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for side in ('L', 'R'):
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jp = os.path.join(side_vol_dir, f'{level}_{side}.json')
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if not os.path.isfile(jp):
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continue
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pos = json.load(open(jp))['position']
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try:
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cyl = screw_voxel_xyz(pos)
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lv = meta['levels'].get(level) if meta is not None else None
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if lv is not None and 'rotated' in lv:
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if level not in aff_cache:
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M, t = original_to_source(meta, level, 'rotated')
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aff_cache[level] = (np.linalg.inv(M), t)
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Mi, t = aff_cache[level]
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nat = (cyl - t) @ Mi.T # (N,3) 原 CT 連續 index
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n_tf += 1
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else:
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if lb_arr is None:
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lb_img = sitk.ReadImage(lb_path)
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lb_arr = sitk.GetArrayFromImage(lb_img)
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if level not in geom_cache:
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geom_cache[level] = level_geometry(volume_id, level, lb_img, lb_arr)
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nat = rotated_to_native(cyl, geom_cache[level], N05, sn, ap_flip)
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n_fb += 1
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ni = np.rint(nat).astype(int)
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valid = (ni >= 0).all(1) & (ni < n_xyz).all(1)
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idx = ni[valid]
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if idx.shape[0] == 0:
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raise ValueError('all screw voxels out of original CT bounds')
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val = li * 2 + 1 + (1 if side == 'R' else 0)
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out_arr[idx[:, 2], idx[:, 1], idx[:, 0]] = val
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n_screws += 1
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except Exception as e:
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logger.error(f'{volume_id} {level}_{side}: {e}')
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skipped.append(f'{level}_{side} ({e})')
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if n_screws == 0:
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raise ValueError(f'{volume_id}: no screw could be written (skipped: {skipped or "none read"})')
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out_dir = os.path.join(output_root, date, volume_id)
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os.makedirs(out_dir, exist_ok=True)
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out_img = sitk.GetImageFromArray(out_arr)
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out_img.CopyInformation(ct)
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out_path = os.path.join(out_dir, 'cbt.nii.gz')
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sitk.WriteImage(out_img, out_path)
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if skipped:
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logger.warning(f'{volume_id}: failed sides: {", ".join(skipped)}')
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logger.info(f'{volume_id}: {n_screws}/10 screws -> {out_path} '
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f'(transform.json={n_tf}, re-est={n_fb}, ap_flip={ap_flip})')
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return out_path, n_screws
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def main():
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parser = argparse.ArgumentParser(
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description='Write <Output_dir>/<date>/<volume_id>/cbt.nii.gz (screws mapped to native space) '
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'from a side_results run')
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parser.add_argument('run_id', help='e.g. 20260907_230652')
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parser.add_argument('volumes', nargs='*',
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help='volume ids (full or trailing digits); default: all in the run')
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parser.add_argument('--date', default=None, help='output date dir (default: run_id[:8])')
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args = parser.parse_args()
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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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run_dir = os.path.join(SIDE_RESULT_DIR, args.run_id)
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if not os.path.isdir(run_dir):
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sys.exit(f'side results dir not found: {run_dir}')
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run_vols = sorted(d for d in os.listdir(run_dir) if os.path.isdir(os.path.join(run_dir, d)))
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if args.volumes:
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vols = [v for v in run_vols
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if v in args.volumes or v.rsplit('.', 1)[-1] in args.volumes]
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if not vols:
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sys.exit(f'none of {args.volumes} found in run {args.run_id}')
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else:
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vols = run_vols
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ok, fail = 0, 0
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for vid in vols:
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try:
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write_volume_cbt(vid, args.run_id, date=args.date)
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ok += 1
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except Exception as e:
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fail += 1
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logger.error(f'{vid}: {e}')
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print(f'done: {ok} written, {fail} failed / {len(vols)} volume(s)')
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if __name__ == '__main__':
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main() |