feat(core): implement vertebral body rewards and enhanced segmentation logic

Introduces a new scoring component for vertebral body (VBODY) rewards
to improve optimization accuracy. The update includes:

- Added `vbody_tensor` to `OptimizationContext` and scoring functions
  to reward screw placement within the vertebral body.
- Enhanced `segment_spinous_process` with diagnostic capabilities to
  detect spinous process absence (e.g., post-laminectomy).
- Improved `resample_img` to prevent physical boundary clipping and
  handle interpolation more robustly for CT and label data.
- Implemented a metadata cache using TinyDB in the preprocessing
  pipeline to skip low-resolution or insufficient scans efficiently.
- Added robust error handling for NFS-based file operations and
  directory creation.
- Added new visualization tools for bone figures and level plotting.

refactor(imaging): improve segmentation and resampling precision

- Refactored `seg_bone` to support original resolution binary masks and
  Signed Maurer Distance Maps (SMD) for more accurate boundary handling.
- Updated `resample_img` to use `ceil` for output size calculation to
  ensure full physical coverage.
- Optimized `process_single_image` to utilize metadata for skipping
  processing of invalid or low-quality scans.

.gitignore

@@ -217,4 +217,6 @@ __marimo__/
 
 .kilo/
 logs/
+results/
 progress.json
+xfr_image_metadata*

core/objective.py

@@ -34,6 +34,8 @@ class OptimizationContext:
     Optional:
         grid:            precomputed coordinate grid (z_t, y_t, x_t)
         use_tip_penalty: add the tip-cylinder penalty to the loss
+        vbody_tensor:    VBODY (vertebral body) mask 0/1 — adds the VBODY
+                         voxel rewards in cl_score_torch_xfr
         The *_array / spine_roi_tensor / diameter / length fields are kept
         for compatibility and debugging; the loss itself does not use them.
     """
@@ -44,6 +46,7 @@ class OptimizationContext:
     device: torch.device
     grid: Optional[tuple] = None
     use_tip_penalty: bool = False
+    vbody_tensor: Optional[torch.Tensor] = None
     spine_roi_tensor: Optional[torch.Tensor] = None
     image1_array: Optional[np.ndarray] = None
     image2_array: Optional[np.ndarray] = None
@@ -121,7 +124,8 @@ def cylinder_circle_line_intersection_loss_deductions_torch(
     loss_value = cl_score_torch_xfr(
         ctx.cortical_tensor, ctx.spine_tensor,
         cyl_fwd, cyl_opp, intersections,
-        cylinder_tip_torch=cyl_tip
+        cylinder_tip_torch=cyl_tip,
+        vbody_tensor=ctx.vbody_tensor
     )
 
     return loss_value

core/optimizer.py

@@ -1,10 +1,12 @@
+import json
+import os
 import time
 from datetime import datetime
 import SimpleITK as sitk
 import torch
 from imaging.orientation import (azimuth_rotation, analyze_vertebral_tilt_contour,
                                   best_symmetry_plane, best_upper_endplate_plane,
-                                  segment_spinous_process)
+                                  segment_spinous_process, segment_vertebral_body)
 from config.constant import ALLOWED_DIAMETERS, ALLOWED_LENGTHS
 from core.objective import OptimizationContext, make_objective_function, make_objective_function_xfr
 from pyswarm import pso
@@ -16,12 +18,30 @@ from visualization.res_plot_3d import res_plt_2_torch
 
 LATERAL_REFINE_MIN_IN_BONE = 0.97
 
+# 入口柱向前（+y，椎體方向）幾個 voxel 內進入 VBODY 即視為「入口在椎體上」：
+# 涵蓋椎體後側皮質邊緣（mask 外 1~2 voxel 的分割界線帶）；
+# 真正的後側要素與椎體間隔（椎間孔）大於此值，不受影響。
+VBODY_ENTRY_EDGE = 4
+
+
+def _makedirs_retry(path, retries=5, delay=0.5):
+    """NFS 上建目錄重試（同 res_plot_3d._retry_robust 處理的瞬時錯誤）"""
+    for i in range(retries):
+        try:
+            os.makedirs(path, exist_ok=True)
+            return
+        except OSError:
+            if i == retries - 1:
+                raise
+            time.sleep(delay)
+
 
 def refine_lateral_longer(
     z, x, azimuth, altitude, diameter_raw, length_raw,
     side, az_bounds, x_bounds, y_indices,
     image_shape, spacing, device, grid,
     cortical_tensor, spine_tensor,
+    vbody_tensor=None,
 ):
     """
     Deterministic local refinement after PSO: try aiming more laterally and
@@ -43,8 +63,9 @@ def refine_lateral_longer(
         if cyl.sum().item() == 0:
             return None
         inter, _ = center_line_intersections_torch(z_c, y_c, x_c, az_c, alt_c,
-                                                   L_c, spine_tensor, spacing, device)
+                                                    L_c, spine_tensor, spacing, device)
-        loss = cl_score_torch_xfr(cortical_tensor, spine_tensor, cyl, cyl_o, inter)
+        loss = cl_score_torch_xfr(cortical_tensor, spine_tensor, cyl, cyl_o, inter,
+                                  vbody_tensor=vbody_tensor)
         in_bone = ((spine_tensor == 1) & (cyl == 1)).sum().item() / cyl.sum().item()
         return {'pos': cand, 'loss': loss, 'in_bone': in_bone}
 
@@ -86,7 +107,20 @@ def _validate_bounds(lb, ub, name):
             raise ValueError(f'PSO bounds invalid for {name}: dim {i} lower {lo} >= upper {hi}')
 
 
-def get_first_nonzero_y(arr):
+def get_first_nonzero_y(arr, endplate_plane=None, vbody_mask=None):
+    """每個 (z, x) 柱的第一個 bone voxel 的 y（voxel index）。
+
+    endplate_plane 為 {'plane': (a, b, c, d), ...}（法線朝上，c > 0）時，
+    入口點 (x, y, z) 落在終板面之上的柱也設 OUTSIDE_VALUE，
+    避免從終板上方的柱選入射點。
+
+    vbody_mask（(z, y, x) 0/1，VBODY 椎體 mask）提供時，
+    入口點落在椎體上的柱設 OUTSIDE_VALUE，避免螺絲入口點放在椎體上：
+    入口 voxel 本身在 VBODY 內、或往前（+y，椎體方向） VBODY_ENTRY_EDGE
+    個 voxel 內進入 VBODY（椎體後側皮質邊緣，mask 外 0.5~2mm 的交界帶）
+    都算。真正的後側要素（椎弓根/椎板/關節突）厚度遠大於該邊緣，
+    且與椎體之間有椎間孔間隔，不會被誤排。
+    """
     OUTSIDE_VALUE = -100
 
     # 1. Create a boolean mask where elements are non-zero
@@ -104,7 +138,35 @@ def get_first_nonzero_y(arr):
     
     y_indices = np.where(y_indices < arr.shape[1] * .1, OUTSIDE_VALUE, y_indices)
     y_indices = np.where(y_indices > arr.shape[1] * .4, OUTSIDE_VALUE, y_indices)
-    
+
+    # 5. 入口點在終板面上方（a*x + b*y + c*z - d > 0）的柱設 OUTSIDE_VALUE
+    if endplate_plane is not None and y_indices.max() >= 0:
+        a, b, c, d = endplate_plane['plane']
+        z_grid, x_grid = np.meshgrid(np.arange(arr.shape[0]), np.arange(arr.shape[2]),
+                                     indexing='ij')
+        above = (y_indices >= 0) & (a * x_grid + b * y_indices + c * z_grid > d)
+        y_indices = np.where(above, OUTSIDE_VALUE, y_indices)
+
+    # 6. 入口點落在椎體上的柱設 OUTSIDE_VALUE（入口不放椎體）：
+    #    入口 voxel 本身在 VBODY 內，或往前 VBODY_ENTRY_EDGE 個 voxel 內進入
+    #    VBODY（椎體後側皮質邊緣，mask 外 0.5~2mm 的分割界線帶）都排除。
+    if vbody_mask is not None:
+        vb = np.asarray(vbody_mask) > 0
+        valid = y_indices >= 0
+        y_i = np.where(valid, y_indices, 0).astype(np.int64)
+        z_grid, x_grid = np.meshgrid(np.arange(arr.shape[0]), np.arange(arr.shape[2]),
+                                     indexing='ij')
+        on_vbody = np.zeros(y_indices.shape, dtype=bool)
+        for k in range(VBODY_ENTRY_EDGE + 1):
+            y_k = np.minimum(y_i + k, arr.shape[1] - 1)
+            on_vbody |= valid & vb[z_grid, y_k, x_grid]
+        n_vb = int(on_vbody.sum())
+        if n_vb:
+            y_indices = np.where(on_vbody, OUTSIDE_VALUE, y_indices)
+            print(f"[Y-INDEX] VBODY entry excluded: {n_vb} columns whose entry "
+                  f"is on/within {VBODY_ENTRY_EDGE} vox of VBODY removed from "
+                  f"entry surface")
+
     return y_indices.astype(np.float32)
 
 def constraint_y(x, y_indices):
@@ -125,6 +187,11 @@ def run_pso_torch_xfr(
     grid=None,
     debug=False,
     omega = 0.9,
+    side: str = 'both',
+    level: str = None,
+    patient_id: str = None,
+    side_dir: str = None,
+    run_id: str = None,
 ):
     """
     Main function to run PSO. 
@@ -169,19 +236,19 @@ def run_pso_torch_xfr(
         length=length if not optimize_size else None,
     )
 
-    azi = azimuth_rotation(image2_path)
+    if not CBT:
-    res = analyze_vertebral_tilt_contour(image2_path, edge_type='superior', show_plot=False, debug=False)
+        azi = azimuth_rotation(image2_path)
-    alt = res['superior']['tilt_angle_deg']
+        res = analyze_vertebral_tilt_contour(image2_path, edge_type='superior', show_plot=False, debug=False)
+        alt = res['superior']['tilt_angle_deg']
 
-    # ===== az/alt 搜尋範圍錨點：以椎體自身座標系取代 2D 近似 =====
+    # ===== 平面：影像已由 xfr_preprocess 對齊旋轉到椎體基準系 =====
-    # 鏡稱對稱面（最佳 mirror plane）：法線 (s_nx, s_ny, s_nz)，s_nx>0 固定符號
+    # （鏡稱面法線 -> +x、上終板 normal y=0 / z>0），az/alt 範圍改用固定
-    #   theta_v = atan2(s_ny, s_nx) 是椎體真實左右軸相對 +x 的旋轉角，
+    # 約束（見下方 CBT bounds），不再逐椎以 theta_v / tau 重新錨定。
-    #   取代舊 2D 輪廓前點角 azi（舊式 az 中心 90-azi == 新式 90+theta_v）。
+    # 此處平面仅供：
-    # 上終板面（normal 朝上, e_nz>0）：
+    #   - 棘突移除（segment_spinous_process，sym）
-    #   tau_y = atan2(e_ny, e_nz)：終板 AP 面傾斜；負 = 面向 +y（終板側）升高，
+    #   - 入口面終板上方剪除（get_first_nonzero_y，endplate）
-    #       軌跡需爬得更陡 → altitude 中心減小（舊式 65-alt 的 3D 版）。
+    #   - VBODY 椎體分割（segment_vertebral_body，sym + endplate）
-    #   tau_x = atan2(e_nx, e_nz)：終板 LR 面傾斜；正 = 面向小 x（L 側）升高，
+    #   - 對齊健全性檢查：基準系下 theta_v ≈ 0、tau_y ≈ 0（偏大 = 預處理失效）
-    #       L 側需更陡（-tau_x）、R 側較平（+tau_x）。
     sym_plane = best_symmetry_plane(image2_array)
 
     # 入口面 y_indices 取「每個 (z,x) 柱第一個 bone voxel（最後側）」，
@@ -189,19 +256,51 @@ def run_pso_torch_xfr(
     # 見 segment_spinous_process）從 image2_array 移除再取 surface，
     # 讓 y_indices 永不落在棘突上（loss 用 spine_tensor，不受影響）。
     sp_mask, sp_th, sp_info = segment_spinous_process(image2_array, sym_plane)
-    if sp_mask is not None and sp_mask.any():
+
+    # 上終板面與椎體都在「完整 mask（SP 移除前）」上計算：
+    #   - 終板面由前側頂面擬合，SP 移除不改變平面；
+    #   - 椎體與 res_plt_2_torch 的 gold 顯示完全同 input / 同參數，
+    #     確保顯示出來的椎體就是 loss 裡 VBODY 獎勵的區域。
+    # 棘突缺如（laminectomy，mode='no_spinous'）時不該把殘留後側要素
+    # 當「棘突」移除（會鏟進椎體後側），入口面維持完整 mask。
+    endplate_plane = best_upper_endplate_plane(image2_array)
+
+    # VBODY 評分獎勵：兩平面（鏡稱面 + 上終板）切出的椎體 mask
+    vb_mask_np, vb_th, vb_info = segment_vertebral_body(image2_array, sym_plane,
+                                                        endplate_plane, sp_th, sp_info['mode'])
+    vbody_tensor = None
+    if vb_mask_np is not None and vb_mask_np.any():
+        vbody_tensor = torch.from_numpy(vb_mask_np.astype(np.uint8)).to(device=device)
+        print(f"[VBODY-SCORE] n={vb_info['n_vb']} "
+              f"({100.0 * vb_info['n_vb'] / max(int(image2_array.sum()), 1):.1f}% of bone) "
+              f"AP<{vb_info['ap_thresh']:.1f} mode={vb_info['mode']} -> added to loss")
+        if vb_info['mode'] == 'quantile':
+            print(f"[VBODY-SCORE] WARNING: 未找到體/弓後側谷底，閾值退回 55 百分位 "
+                  f"（可能切進椎體內），建議人工核對該 level 的椎體邊界")
+    else:
+        print(f"[VBODY-SCORE] skipped: {vb_info['mode']}")
+    ctx.vbody_tensor = vbody_tensor
+
+    if sp_info['mode'] == 'no_spinous':
+        top_off = f"{sp_info['top_off']:.1f}" if sp_info.get('top_off') is not None else 'n/a'
+        print(f"[NO-SP] 中線後側缺如（先前 laminectomy / 棘突切除）: "
+              f"deficit={sp_info['deficit']:.1f} vox ({sp_info['deficit'] * 0.5:.1f} mm), "
+              f"rear3={sp_info['rear3']} vox, top_off={top_off} vox "
+              f"-> 不移除 SP（完整 mask 取入口面），椎體用放寬後側谷底切分")
+    elif sp_mask is not None and sp_mask.any():
         n_sp = int(sp_mask.sum())
         image2_array[sp_mask] = 0
         print(f"[Y-INDEX] spinous process removed from entry surface: {n_sp} vox "
               f"(band=+/-{sp_info['band_w']:.1f} voxel, AP>={sp_info['ap_thresh']:.1f}, "
               f"mode={sp_info['mode']})")
 
-    y_indices = get_first_nonzero_y(image2_array)
+    y_indices = get_first_nonzero_y(image2_array, endplate_plane, vb_mask_np)
+
     objective_fn = make_objective_function_xfr(ctx, y_indices)
 
+    # 對齊健全性檢查（基準系下 theta_v ≈ 0、tau_y ≈ 0；不參與 bounds 計算）
     s_nx, s_ny, s_nz = sym_plane['normal']
     theta_v = float(np.degrees(np.arctan2(s_ny, s_nx)))
-    endplate_plane = best_upper_endplate_plane(image2_array)
     if endplate_plane is not None:
         e_nx, e_ny, e_nz = endplate_plane['normal']
         tau_y = float(np.degrees(np.arctan2(e_ny, e_nz)))
@@ -217,7 +316,7 @@ def run_pso_torch_xfr(
               f"  (tau_y={tau_y:+.2f} deg, tau_x={tau_x:+.2f} deg, "
               f"inlier={endplate_plane['inlier_ratio']:.2f})")
     else:
-        print("[PLANE] endplate: 資料不足，altitude 錨點退回 tau_y=tau_x=0")
+        print("[PLANE] endplate: 資料不足，終板入口剪除停用")
 
     # flat_min_index = np.argmin(y_indices)
     # z_border, x_border = np.unravel_index(flat_min_index, y_indices.shape)
@@ -282,18 +381,21 @@ def run_pso_torch_xfr(
         if x_bounds_right[0] >= x_bounds_right[1]:
             x_bounds_right = (x_bounds_right[1] - min_band, x_bounds_right[1])
 
+        # 固定約束（影像已由 xfr_preprocess 對齊旋轉到椎體基準系：鏡稱面法線 +x、
+        # 終板 normal y=0 / z>0；基準系下 theta_v≈0、tau_y≈0，舊式逐椎錨定
+        # (98+theta_v, 105+theta_v) / (60+tau_y∓tau_x*sin_mid, 70+tau_y∓tau_x*sin_mid)
+        # 不再需要）：
+        #   azimuth (Lateral)：az=90° 為 AP 直向，每側向外發散 8~20°
+        #            L = 90 + (8~20) = 98~110、R = 90 - (8~20) = 70~82
+        #   altitude (Cephalad)：相對終板面 25~30°（+z 極角 90 - 25~30）= 60~65
         # 舊 2D 版本（以輪廓角 azi / 矢狀面傾斜 alt 平移固定範圍），保留供對照：
         # azimuth_bounds_l = ((98-azi), (120-azi))
         # azimuth_bounds_r = ((60-azi), (82-azi))
         # altitude_bounds = ((60-alt), (70-alt))
-        # 新：範圍以「椎體自身座標系」為中心 —— 椎體系中 az=90° 是 AP 直向、
+        azimuth_bounds_l = (98, 110)
-        # L 帶 = AP 後退 8~30°（偏 -x）、R 帶 = AP 前進 8~30°（偏 +x）、
+        azimuth_bounds_r = (70, 82)
-        # altitude 60~70。再換算回影像系：az 整體加 theta_v（鏡稱面），
+        altitude_bounds_l = (60, 65)
-        # altitude 加 tau_y（終板 AP 傾斜）並逐側加 -/+tau_x（終板 LR 傾斜）。
+        altitude_bounds_r = (60, 65)
-        azimuth_bounds_l = ((98+theta_v), (120+theta_v))
-        azimuth_bounds_r = ((60+theta_v), (82+theta_v))
-        altitude_bounds_l = ((60+tau_y-tau_x), (70+tau_y-tau_x))
-        altitude_bounds_r = ((60+tau_y+tau_x), (70+tau_y+tau_x))
 
     else:      
         z_bounds = (0, image_shape[0] - 1)   
@@ -340,7 +442,8 @@ def run_pso_torch_xfr(
         diameter_bounds = (min(ALLOWED_DIAMETERS), max(ALLOWED_DIAMETERS)*1.01)
         length_bounds = (min(ALLOWED_LENGTHS), max(ALLOWED_LENGTHS)*1.01)
         
-        # bounds 現在有 7 個參數（altitude 分 L/R 兩側，由終板面 tau_x 決定）
+        # bounds 現在有 6 個參數 [z, x, az, alt, d, L]（y 由 y_indices 取）；
+        # az/alt 兩側用同一組固定約束，x 帶依 L/R 分開
         lb_l = [z_bounds[0], x_bounds_left[0], azimuth_bounds_l[0], 
                 altitude_bounds_l[0], diameter_bounds[0], length_bounds[0]]
         ub_l = [z_bounds[1], x_bounds_left[1], azimuth_bounds_l[1], 
@@ -365,220 +468,200 @@ def run_pso_torch_xfr(
         ub_r = [z_bounds[1], y_bounds[1], x_bounds_right[1], azimuth_bounds_r[1], altitude_bounds_r[1]]
 
     if True or debug:
-        print(lb_l)
+        for b in (lb_l, ub_l, lb_r, ub_r):
-        print(ub_l)
+            print('[' + ', '.join(f'{v:10.2f}' for v in b) + ']')
-        print(lb_r)
-        print(ub_r)
 
     best_loss_l = float('inf')
     best_loss_r = float('inf')
     best_position_l = None
     best_position_r = None
 
-    # Left side optimization
+    # L/R 是兩次獨立 PSO（bounds 不同、目標函數共用），互不依賴：
-    print(f"\n=== {label_str} 左側 ===")
+    # side='both' 維持原行為（同一次呼叫先 L 後 R）；
-    _validate_bounds(lb_l, ub_l, f'{label_str} L')
+    # side='L'/'R' 只跑該側，讓兩側可排到不同 GPU worker。
-    position_l, loss_l = pso(objective_fn, lb_l, ub_l,
+    # 單側模式的合併輸出（3D 圖 + CSV）由「較晚完成」的一側在
-        # ieqcons=[constraint_y],
+    # 下方「單側收尾」段觸發。
-        swarmsize=swarm_size,
+    def _side_bounds(s_i):
-        omega = omega,
+        if s_i == 'L':
-        maxiter=max_iter, debug=debug)
+            return lb_l, ub_l, azimuth_bounds_l, x_bounds_left
+        return lb_r, ub_r, azimuth_bounds_r, x_bounds_right
 
-    z, x, azimuth, altitude, diameter, length = position_l
+    def _run_one_side(s_i):
-    az_pso, x_pso, L_pso = azimuth, x, length
+        lb_s, ub_s, az_bounds_s, x_bounds_s = _side_bounds(s_i)
-    y = y_indices[round(z), round(x)]
+        tag_cn = '左側' if s_i == 'L' else '右側'
+        tag = 'LEFT' if s_i == 'L' else 'RIGHT'
+        print(f"\n=== {label_str} {tag_cn} ===")
+        _validate_bounds(lb_s, ub_s, f'{label_str} {s_i}')
+        position, loss = pso(objective_fn, lb_s, ub_s,
+            # ieqcons=[constraint_y],
+            swarmsize=swarm_size,
+            omega=omega,
+            maxiter=max_iter, debug=debug)
 
-    z, x, azimuth, altitude, diameter, length, adopted_l, ref_l = refine_lateral_longer(
+        # 如果需要 retry（loss > 0）：重跑 PSO 取較好者
-        z, x, azimuth, altitude, diameter, length,
+        # （原 L/R 各一份註解版 retry，此處合併為一式）
-        "L", azimuth_bounds_l, x_bounds_left, y_indices,
+        # max_retries = 0
-        image_shape, spacing, device, grid,
+        # retries = 0
-        cortical_tensor, spine_tensor,
+        # while loss > 0 and retries < max_retries:
-    )
+        #     position, loss = pso(objective_fn, lb_s, ub_s,
-    y = y_indices[round(z), round(x)]
+        #                          swarmsize=swarm_size, maxiter=max_iter)
-    if adopted_l:
+        #     retries += 1
-        loss_l = ref_l['loss']
-        print(f"[LEFT] lateral-refine: az {az_pso:.2f} -> {azimuth:.2f}, x {x_pso:.2f} -> {x:.2f}, "
-              f"L {L_pso:.2f} -> {length:.2f}, in-bone {ref_l['in_bone']*100:.1f}%")
-    else:
-        print("[LEFT] lateral-refine: no improvement")
 
-    position_l = z, y, x, azimuth, altitude, diameter, length
+        z, x, azimuth, altitude, diameter, length = position
+        az_pso, x_pso, L_pso = azimuth, x, length
+        y = y_indices[round(z), round(x)]
 
-    overlap_l, diameter_l, length_l = eval_overlap_from_position(
+        z, x, azimuth, altitude, diameter, length, adopted, ref = refine_lateral_longer(
-        position_l, "L", optimize_size, spine_tensor, image_shape, spacing
+            z, x, azimuth, altitude, diameter, length,
-    )
+            s_i, az_bounds_s, x_bounds_s, y_indices,
-    print(f"[LEFT] overlap: {overlap_l*100:.1f}%")
+            image_shape, spacing, device, grid,
+            cortical_tensor, spine_tensor,
+            vbody_tensor,
+        )
+        y = y_indices[round(z), round(x)]
+        if adopted:
+            loss = ref['loss']
+            print(f"[{tag}] lateral-refine: az {az_pso:.2f} -> {azimuth:.2f}, x {x_pso:.2f} -> {x:.2f}, "
+                  f"L {L_pso:.2f} -> {length:.2f}, in-bone {ref['in_bone']*100:.1f}%")
+        else:
+            print(f"[{tag}] lateral-refine: no improvement")
 
-    if optimize_size:
+        position = z, y, x, azimuth, altitude, diameter, length
-        print(f"[LEFT] Position: {position_l[:5]}")
-        print(f"[LEFT] Diameter: {diameter_l} mm (raw: {position_l[5]:.2f})")
-        print(f"[LEFT] Length: {length_l} mm (raw: {position_l[6]:.2f})")
-        print(f"[LEFT] Loss: {loss_l}\n")
-        best_position_l = list(position_l[:5]) + [diameter_l, length_l]
-    else:
-        print(f"[LEFT] Position: {position_l}")
-        best_position_l = position_l
 
-    best_loss_l = loss_l
+        overlap_s, d_snap, L_snap = eval_overlap_from_position(
-    best_overlap_l = overlap_l   # 新增
+            position, s_i, optimize_size, spine_tensor, image_shape, spacing
-    
+        )
-    # max_retries = 0
+        print(f"[{tag}] overlap: {overlap_s*100:.1f}%")
-    # retries = 0
 
-    # 左側 retry：loss 要 <=0 且 overlap >= 0.5 才算過關
+        if optimize_size:
-    # while (best_loss_l > 0 or best_overlap_l < OVERLAP_THRESH) and retries < max_retries:
+            print(f"[{tag}] Position: {position[:5]}")
-        # position_l, loss_l = pso(objective_fn, lb_l, ub_l, swarmsize=swarm_size, maxiter=max_iter)
+            print(f"[{tag}] Diameter: {d_snap} mm (raw: {position[5]:.2f})")
-        # overlap_l, diameter_l, length_l = eval_overlap_from_position(
+            print(f"[{tag}] Length: {L_snap} mm (raw: {position[6]:.2f})")
-            # position_l, "L", optimize_size, spine_tensor, image_shape, spacing
+            print(f"[{tag}] Loss: {loss}\n")
-        # )
+            best_pos = list(position[:5]) + [d_snap, L_snap]
+        else:
+            print(f"[{tag}] Position: {position}")
+            best_pos = position
+        return best_pos, loss, overlap_s
 
-    # 只要找到更好的 loss（或你想用 loss+overlap 綜合排序也行）就更新 best
+    sides = ('L', 'R') if side == 'both' else (side,)
-    # 安全版本：優先選「合格解」；沒有合格解時才用 loss 最小的當備案
+    side_time = {}
-        # candidate_pos = (list(position_l[:5]) + [diameter_l, length_l]) if optimize_size else position_l
+    for s_i in sides:
+        t0 = time.time()
+        pos_s, loss_s, _ = _run_one_side(s_i)
+        side_time[s_i] = time.time() - t0
+        if s_i == 'L':
+            best_position_l, best_loss_l = pos_s, loss_s
+        else:
+            best_position_r, best_loss_r = pos_s, loss_s
 
-        # candidate_ok = is_solution_ok(loss_l, overlap_l, OVERLAP_THRESH)
-        # best_ok = is_solution_ok(best_loss_l, best_overlap_l, OVERLAP_THRESH)
-
-        # if candidate_ok and (not best_ok or loss_l < best_loss_l):
-            # best_position_l = candidate_pos
-            # best_loss_l = loss_l
-            # best_overlap_l = overlap_l
-            # print(f"[LEFT][retry {retries+1}] ✅ ok | loss={loss_l:.4f}, overlap={overlap_l*100:.1f}%")
-        # elif (not best_ok) and (loss_l < best_loss_l):
-            # best 還不合格時，先用更小 loss 的當暫存（至少越來越好）
-            # best_position_l = candidate_pos
-            # best_loss_l = loss_l
-            # best_overlap_l = overlap_l
-            # print(f"[LEFT][retry {retries+1}] ⚠️ not ok | loss improved={loss_l:.4f}, overlap={overlap_l*100:.1f}%")
-        # else:
-            # print(f"[LEFT][retry {retries+1}] ❌ no improve | loss={loss_l:.4f}, overlap={overlap_l*100:.1f}%")
-
-        # retries += 1
-    
-    # Right side optimization
-    print(f"\n=== {label_str} 右側 ===")
-    _validate_bounds(lb_r, ub_r, f'{label_str} R')
-    position_r, loss_r = pso(objective_fn, lb_r, ub_r,
-        # ieqcons=[constraint_y],
-        swarmsize=swarm_size,
-        omega = omega,
-        maxiter=max_iter, debug=debug)
-
-    z, x, azimuth, altitude, diameter, length = position_r
-    az_pso, x_pso, L_pso = azimuth, x, length
-    y = y_indices[round(z), round(x)]
-
-    z, x, azimuth, altitude, diameter, length, adopted_r, ref_r = refine_lateral_longer(
-        z, x, azimuth, altitude, diameter, length,
-        "R", azimuth_bounds_r, x_bounds_right, y_indices,
-        image_shape, spacing, device, grid,
-        cortical_tensor, spine_tensor,
-    )
-    y = y_indices[round(z), round(x)]
-    if adopted_r:
-        loss_r = ref_r['loss']
-        print(f"[RIGHT] lateral-refine: az {az_pso:.2f} -> {azimuth:.2f}, x {x_pso:.2f} -> {x:.2f}, "
-              f"L {L_pso:.2f} -> {length:.2f}, in-bone {ref_r['in_bone']*100:.1f}%")
-    else:
-        print("[RIGHT] lateral-refine: no improvement")
-
-    position_r = z, y, x, azimuth, altitude, diameter, length
-
-    overlap_r, diameter_r, length_r = eval_overlap_from_position(
-        position_r, "R", optimize_size, spine_tensor, image_shape, spacing
-    )
-    print(f"[RIGHT] overlap: {overlap_r*100:.1f}%")
-
-    if optimize_size:
-        # diameter_r, length_r = snap_to_discrete_values(position_r[5], position_r[6])
-        diameter_r, length_r = snap_to_discrete_values_xfr(position_r[5], position_r[6])
-        print(f"[RIGHT] Position: {position_r[:5]}")
-        print(f"[RIGHT] Diameter: {diameter_r} mm (raw: {position_r[5]:.2f})")
-        print(f"[RIGHT] Length: {length_r} mm (raw: {position_r[6]:.2f})")
-        print(f"[RIGHT] Loss: {loss_r}\n")
-        
-        best_position_r = list(position_r[:5]) + [diameter_r, length_r]
-    else:
-        print(f"[RIGHT] Position: {position_r}")
-        print(f"[RIGHT] Loss: {loss_r}\n")
-        best_position_r = position_r
-    
-    best_loss_r = loss_r
-    best_overlap_r = overlap_r 
-    
-    # 如果需要 retry（loss > 0）
-    # max_retries = 10
-    # retries = 0
-
-    # while (best_loss_r > 0 or best_overlap_r < OVERLAP_THRESH) and retries < max_retries:
-        # position_r, loss_r = pso(objective_fn, lb_r, ub_r, swarmsize=swarm_size, maxiter=max_iter)
-        # overlap_r, diameter_r, length_r = eval_overlap_from_position(
-            # position_r, "R", optimize_size, spine_tensor, image_shape, spacing
-        # )
-
-        # 只要找到更好的 loss（或你想用 loss+overlap 綜合排序也行）就更新 best
-        # 這裡給你一個更安全的版本：優先選「合格解」；沒有合格解時才用 loss 最小的當備案
-        # candidate_pos = (list(position_r[:5]) + [diameter_r, length_r]) if optimize_size else position_r
-
-        # candidate_ok = is_solution_ok(loss_r, overlap_r, OVERLAP_THRESH)
-        # best_ok = is_solution_ok(best_loss_r, best_overlap_r, OVERLAP_THRESH)
-
-        # if candidate_ok and (not best_ok or loss_r < best_loss_r):
-            # best_position_r = candidate_pos
-            # best_loss_r = loss_r
-            # best_overlap_r = overlap_r
-            # print(f"[RIGHT][retry {retries+1}] ✅ ok | loss={loss_r:.4f}, overlap={overlap_r*100:.1f}%")
-        # elif (not best_ok) and (loss_r < best_loss_r):
-            # best 還不合格時，先用更小 loss 的當暫存（至少越來越好）
-            # best_position_r = candidate_pos
-            # best_loss_r = loss_r
-            # best_overlap_r = overlap_r
-            # print(f"[RIGHT][retry {retries+1}] ⚠️ not ok | loss improved={loss_r:.4f}, overlap={overlap_r*100:.1f}%")
-        # else:
-            # print(f"[RIGHT][retry {retries+1}] ❌ no improve | loss={loss_r:.4f}, overlap={overlap_r*100:.1f}%")
-
-        # retries += 1
-    
     end_time = time.time()
     total_time = end_time - start_time
 
     # 提取最終的 diameter 和 length
     if optimize_size:
-        final_diameter_l = best_position_l[5]
+        final_diameter_l = best_position_l[5] if best_position_l is not None else float('nan')
-        final_length_l = best_position_l[6]
+        final_length_l = best_position_l[6] if best_position_l is not None else float('nan')
-        final_diameter_r = best_position_r[5]
+        final_diameter_r = best_position_r[5] if best_position_r is not None else float('nan')
-        final_length_r = best_position_r[6]
+        final_length_r = best_position_r[6] if best_position_r is not None else float('nan')
-        
-        print(f"\n=== {label_str} 最終結果 ===")
-        print(f"Left - Diameter: {final_diameter_l} mm, Length: {final_length_l} mm")
-        print(f"Right - Diameter: {final_diameter_r} mm, Length: {final_length_r} mm")
     else:
         final_diameter_l = diameter
         final_length_l = length
         final_diameter_r = diameter
         final_length_r = length
 
-    res_plt_2_torch(
+    def _plot_combined(d_l, l_l, d_r, l_r, pos_l, pos_r, total_t):
-    spine_tensor,
+        res_plt_2_torch(
-    cortical_tensor,
+            spine_tensor,
-    image_shape,
+            cortical_tensor,
-    image2_path,
+            image_shape,
-    folder,
+            image2_path,
-    label_str,
+            folder,
-    final_diameter_l,
+            label_str,
-    final_length_l,
+            d_l,
-    final_diameter_r,
+            l_l,
-    final_length_r,
+            d_r,
-    best_position_l,
+            l_r,
-    best_position_r,
+            pos_l,
-    swarm_size,
+            pos_r,
-    max_iter,
+            swarm_size,
-    total_time,
+            max_iter,
-    spacing,
+            total_t,
-    CBT,
+            spacing,
-    device,
+            CBT,
-    grid)
+            device,
-    
+            grid,
+        )
+
+    if side == 'both':
+        print(f"\n=== {label_str} 最終結果 ===")
+        print(f"Left - Diameter: {final_diameter_l} mm, Length: {final_length_l} mm")
+        print(f"Right - Diameter: {final_diameter_r} mm, Length: {final_length_r} mm")
+        _plot_combined(final_diameter_l, final_length_l,
+                       final_diameter_r, final_length_r,
+                       best_position_l, best_position_r, total_time)
+        return best_position_l, best_loss_l, best_position_r, best_loss_r, total_time
+
+    # ---- 單側收尾：寫該側結果檔；兩側都完成時由較晚的一側觸發合併輸出 ----
+    # 兩側可能在不同 GPU worker：各自把結果寫 <level>_<side>.json
+    # （先寫 tmp 再 os.replace，對端讀到的一定是完整檔）。先完成者看不到
+    # 對端檔就跳過；後完成者看到兩側齊了、搶到 plot lock（O_EXCL，
+    # 確保合併輸出只跑一次）才載入對端結果跑 res_plt_2_torch
+    # （3D 圖 + CSV 兩行，與 'both' 模式相同）。json / lock 保留供事後
+    # 檢查；若該側流程死在 plotting 中段，該 (volume, level) 重跑即可
+    # （run_id 是新的一次，不會互相干擾）。
+    other = 'R' if side == 'L' else 'L'
+    own_pos = best_position_l if side == 'L' else best_position_r
+    own_d = final_diameter_l if side == 'L' else final_diameter_r
+    own_L = final_length_l if side == 'L' else final_length_r
+    own_cn = 'Left' if side == 'L' else 'Right'
+    side_cn = '左' if side == 'L' else '右'
+    print(f"\n=== {label_str} 最終結果（{side_cn}側） ===")
+    print(f"{own_cn} - Diameter: {own_d} mm, Length: {own_L} mm")
+
+    missing_pair = [n for n, v in (('level', level), ('patient_id', patient_id),
+                                   ('side_dir', side_dir), ('run_id', run_id)) if not v]
+    if missing_pair:
+        print(f"[SIDE] 合併輸出跳過（未提供 {', '.join(missing_pair)}）")
+    else:
+        patient_dir = os.path.join(side_dir, run_id, patient_id)
+        own_path = os.path.join(patient_dir, f'{level}_{side}.json')
+        other_path = os.path.join(patient_dir, f'{level}_{other}.json')
+        _makedirs_retry(patient_dir)
+        own = {'position': [float(v) for v in own_pos],
+               'diameter': float(own_d),
+               'length': float(own_L),
+               'time': float(side_time[side])}
+        tmp_path = f'{own_path}.{os.getpid()}.tmp'
+        with open(tmp_path, 'w') as f:
+            json.dump(own, f)
+        os.replace(tmp_path, own_path)
+
+        if not os.path.isfile(other_path):
+            print(f"[SIDE] {other} 側尚未完成，合併輸出（圖 + CSV）待該側完成時觸發")
+        else:
+            lock_path = os.path.join(patient_dir, f'{level}.plot.lock')
+            try:
+                fd = os.open(lock_path, os.O_CREAT | os.O_EXCL | os.O_WRONLY)
+                os.close(fd)
+            except FileExistsError:
+                print(f'[SIDE] 合併輸出已由 {other} 側觸發，跳過')
+            else:
+                with open(other_path) as f:
+                    other_res = json.load(f)
+                pos_other = [float(v) for v in other_res['position']]
+                if side == 'L':
+                    d_l, l_l, pos_l = own_d, own_L, list(own_pos)
+                    d_r, l_r, pos_r = other_res['diameter'], other_res['length'], pos_other
+                else:
+                    d_r, l_r, pos_r = own_d, own_L, list(own_pos)
+                    d_l, l_l, pos_l = other_res['diameter'], other_res['length'], pos_other
+                print(f"[SIDE] {side} + {other} 兩側完成 -> 合併輸出（圖 + CSV）")
+                # total_time 用兩側各自耗時相加（各含一次影像載入/平面計算，
+                # 比原同流程 wall time 略大，僅影響 CSV 的時間欄）
+                _plot_combined(d_l, l_l, d_r, l_r, pos_l, pos_r,
+                               side_time[side] + other_res['time'])
+
     return best_position_l, best_loss_l, best_position_r, best_loss_r, total_time
 
 

core/scoring.py

@@ -10,13 +10,23 @@ def cl_score_torch_xfr(
     intersections: int,
     diameter: float = None,
     length: float = None,
-    cylinder_tip_torch: torch.Tensor = None  # 新增：尖端 mask
+    cylinder_tip_torch: torch.Tensor = None,  # 新增：尖端 mask
+    vbody_tensor: torch.Tensor = None  # VBODY（椎體）mask (z,y,x) 0/1，None = 不計 VBODY 獎勵
 ) -> float:
     """
     漸進式評分：優先確保找到骨頭，再改善細節
     """
     cyl_total = cylinder_torch.sum().item()
     overlap = ((cortical_tensor == 1) & (cylinder_torch == 1)).sum().item()
+    # VBODY 獎勵：螺絲落在 (cortical + VBODY) 內的 voxel 每個 100 分
+    # （100 分項由純 cortical 擴展到 cortical∪VBODY；cortical voxel 分數不變），
+    # 其中落在 VBODY 的 voxel 每個再加 10 分
+    if vbody_tensor is not None:
+        in_vbody = ((vbody_tensor == 1) & (cylinder_torch == 1)).sum().item()
+        in_corti_vb = (((cortical_tensor == 1) | (vbody_tensor == 1)) & (cylinder_torch == 1)).sum().item()
+    else:
+        in_vbody = 0
+        in_corti_vb = overlap
     null_vox = ((cortical_tensor == 0) & (cylinder_torch == 1)).sum().item()
     null_vox2 = ((spine_tensor == 1) & (cylinder_o_torch == 1)).sum().item()
 
@@ -38,10 +48,12 @@ def cl_score_torch_xfr(
 
     score += 20   * in_bone # 10 實在太低
     score += 100  * overlap
+    score += 100  * in_corti_vb # (cortical + VBODY) 每 voxel 100 分
+    score += 50   * in_vbody # VBODY 每 voxel 再加 10 分
     # score -= 2000 * max(0, not_in_bone-10)
     # score -= 1000 * max(0, null_vox2-10)
     score -= 1000 * not_in_bone
-    score -= 1000 * null_vox2
+    score -= 2000 * null_vox2
 
     return float(-score)
     

imaging/orientation.py

@@ -1,8 +1,15 @@
 import numpy as np
 import SimpleITK as sitk
-from scipy.ndimage import center_of_mass, rotate
+from scipy.ndimage import center_of_mass, rotate, distance_transform_edt, gaussian_filter
 import matplotlib.pyplot as plt
 
+# 鏡稱面法線的左右（LR，=x 軸）分量大下。正常左右鏡稱面法線幾乎沿 x；
+# 若 |a| < 0.7，代表搜尋掉進前後（coronal）面局部極大（椎體是厚實塊狀，
+# 易自鏡射拿高分，例：0019 L3/L4），以該平面定義的「中線帶」變成斜切
+# 板層，其後側中線缺如判定不可信 → diagnose 回 bad_mirror_plane、
+# 不判 no_spinous（避免假 [NO-SP] 誤改椎體切分）。
+MIRROR_MIN_LR = 0.7
+
 def _best_vertical_split(mask2d):
     """
     binary 2D 陣列（最後一軸 = x）：找讓 mask 與其鏡射重疊最大的垂直線 x = t。
@@ -158,8 +165,83 @@ def best_symmetry_plane(mask_zyx, phi_max=45.0, subsample=7,
         'v': (float(v[0]), float(v[1]), float(v[2])),
     }
 
+def diagnose_spinous_process(mask_zyx, sym, band_frac=0.06, min_band=6.0,
+                             deficit_min=4.0, rear_margin=3.0, rear3_max=20,
+                             narrow_frac=0.4):
+    """
+    診斷該椎體的棘突（中線後側構造）是否缺如
+    （先前手術如 laminectomy / 棘突切除所造成）。
+
+    棘突完整時，其尖端是全椎體最後側的骨構造且位於中線，因此：
+      deficit = 全骨最後側 AP - 中線帶最後側 AP ~= 0，
+      且中線窄帶 |s| <= narrow_frac*w 在最後側骨 rear_margin 內有充足骨 voxel。
+    切除後，中線帶的後側止於殘留後側要素，最後側骨偏到側方的
+    殘餘結構（椎板/關節突）→ deficit 大 + 後側中線空洞。
+    判定：no_spinous = deficit >= deficit_min 且 rear3 <= rear3_max。
+
+    回傳 dict：
+      n_bone     : 骨 voxel 總數
+      band_w     : 中線帶半寬 w（voxel）
+      deficit    : 後側中線缺如量（voxel，0.5 mm/vox）
+      rear3      : 最後側 3 voxel 內、中線窄帶的骨 voxel 數
+      rear6      : 最後側 6 voxel 內、中線窄帶的骨 voxel 數
+      top_off    : axial 投影（y,x）最後側一行相對鏡稱中線的偏移（voxel）
+      no_spinous : True = 後側中線缺如（棘突已切除）
+      reason     : 'ok' / 'no_spinous' / 'too_few_bone' / 'too_few_midline'
+                   / 'bad_mirror_plane'
+    """
+    m = np.asarray(mask_zyx) > 0
+    zz, yy, xx = np.nonzero(m)
+    out = {'n_bone': int(zz.size), 'band_w': None, 'deficit': 0.0,
+           'rear3': None, 'rear6': None, 'top_off': None,
+           'no_spinous': False, 'reason': 'ok'}
+    if zz.size < 100:
+        out['reason'] = 'too_few_bone'
+        return out
+    a, b, c, d = sym['plane']
+    if abs(a) < MIRROR_MIN_LR:
+        # 鏡稱面非左右為主（前後 coronal 局部極大）→ 缺如判定不可信，
+        # 按 ok 回傳（寧可漏報，不可假切除）
+        out['reason'] = 'bad_mirror_plane'
+        return out
+    X = xx.astype(np.float64)
+    Y = yy.astype(np.float64)
+    Z = zz.astype(np.float64)
+    s = X * a + Y * b + Z * c - d
+    u_ap = _ap_axis(sym)                                # +AP = 後側（y 小側）
+    ap = X * u_ap[0] + Y * u_ap[1] + Z * u_ap[2]
+    w = max(float(min_band), float(band_frac) * float(s.max() - s.min()))
+    mid = np.abs(s) <= w
+    aps = ap[mid]
+    out['band_w'] = float(w)
+    if aps.size < 50:
+        out['reason'] = 'too_few_midline'
+        return out
+    narrow = np.abs(s) <= w * float(narrow_frac)
+    ap_max_all = float(ap.max())
+    deficit = ap_max_all - float(aps.max())
+    rear3 = int(((ap >= ap_max_all - rear_margin) & narrow).sum())
+    rear6 = int(((ap >= ap_max_all - 2.0 * rear_margin) & narrow).sum())
+    out['deficit'] = float(deficit)
+    out['rear3'] = rear3
+    out['rear6'] = rear6
+    proj = m.max(axis=0)                                # (y, x)
+    ys_p, xs_p = np.where(proj > 0)
+    # 只在鏡稱面 x 分量主導時才算 top_off（最後側一行對中線的 x 偏移）；
+    # 脊椎在面內大角度旋轉時 |a| 小，(d-b*y-c*z)/a 會放大成無意義的巨值。
+    if ys_p.size and abs(a) >= 0.5 * max(abs(b), abs(c)):
+        y_min = int(ys_p.min())
+        zc = (m.shape[0] - 1) / 2.0
+        x_mid = (d - b * y_min - c * zc) / a
+        out['top_off'] = float(abs(xs_p[ys_p == y_min].mean() - x_mid))
+    if deficit >= float(deficit_min) and rear3 <= int(rear3_max):
+        out['no_spinous'] = True
+        out['reason'] = 'no_spinous'
+    return out
+
+
 def segment_spinous_process(mask_zyx, sym, band_frac=0.06, min_band=6.0,
-                            min_mass_frac=0.05):
+                            min_mass_frac=0.05, expand_cap=5):
     """
     以 best_symmetry_plane 的結果 sym 從 3D bone mask (z, y, x) 切出棘突。
     棘突是中線後側構造，利用鏡稱面 a·x+b·y+c·z=d 定義：
@@ -170,8 +252,14 @@ def segment_spinous_process(mask_zyx, sym, band_frac=0.06, min_band=6.0,
       3) 中線帶的 AP 分佈呈兩大叢（椎體在前、椎弓/棘突在後），
          以兩叢間的 AP 谷底為界，AP >= 谷底 的中線帶 voxel = 棘突（含中線椎弓）；
          無明顯谷底（如骨橋）fallback 取中線帶後側 15%。
+       4) 中線帶側緣補回（_expand_spinous_runs，expand_cap）：帶由鏡稱面定義，
+          棘突楔若略偏中線，側緣薄條會留在帶外成為 other bone；每條 (y, z)
+          線把棘突 run 向左右各補至多 expand_cap 個 bone voxel。
+    先做後側中線缺如判定（diagnose_spinous_process，laminectomy/棘突切除）；
+    缺如、或谷底後側叢只剩 <5% 殘片時 mode='no_spinous'、sp_mask=None，
+    由呼叫端（入口面 / 椎體）改用對應策略。
     回傳 (sp_mask (z,y,x) bool, ap_thresh, info dict)；
-    資料過少時 sp_mask = None（info['mode'] 說明原因）。
+    資料過少或棘突缺如時 sp_mask = None（info['mode'] 說明原因）。
     """
     m = np.asarray(mask_zyx) > 0
     zz, yy, xx = np.nonzero(m)
@@ -197,6 +285,19 @@ def segment_spinous_process(mask_zyx, sym, band_frac=0.06, min_band=6.0,
     if aps.size < 50:
         info['mode'] = 'too_few_midline'
         return None, None, info
+
+    # 後側中線缺如（laminectomy / 棘突切除）：最後側骨偏到側方殘餘、
+    # 中線帶後側無質量，谷底搜尋沒有意義 → no_spinous，
+    # 呼叫端（y_indices 入口面 / segment_vertebral_body）改用對應策略。
+    diag = diagnose_spinous_process(mask_zyx, sym, band_frac=band_frac, min_band=min_band)
+    info['deficit'] = diag['deficit']
+    info['rear3'] = diag['rear3']
+    info['rear6'] = diag['rear6']
+    if diag['no_spinous']:
+        info['mode'] = 'no_spinous'
+        info['top_off'] = diag['top_off']
+        return None, None, info
+
     lo = int(np.floor(aps.min()))
     hi = int(np.ceil(aps.max()))
     th = None
@@ -216,6 +317,14 @@ def segment_spinous_process(mask_zyx, sym, band_frac=0.06, min_band=6.0,
             if score > best_score:
                 best_score, best_i = score, i
         if best_i is not None:
+            post_frac = (total - csum[best_i + 1]) / total
+            if post_frac < 0.05 and abs(a) >= MIRROR_MIN_LR:
+                # 谷底後側叢只剩小殘片（<5% 中線帶質量）＝棘突幾乎全除
+                # （部分切除殘餘）：當作缺如，椎體切分不採用此閾值。
+                # 僅在鏡稱面左右為主時才算數（斜板層時 post_frac 不可信）
+                info['mode'] = 'no_spinous'
+                info['post_frac'] = float(post_frac)
+                return None, None, info
             th = float(0.5 * (edges[best_i] + edges[best_i + 1]))
             mode = 'gap'
     if th is None:
@@ -223,19 +332,247 @@ def segment_spinous_process(mask_zyx, sym, band_frac=0.06, min_band=6.0,
     sp_mask = np.zeros(m.shape, dtype=bool)
     sel = mid & (ap >= th)
     sp_mask[zz[sel], yy[sel], xx[sel]] = True
-    info.update(n_sp=int(sel.sum()), ap_thresh=th, mode=mode)
+    sp_mask = _expand_spinous_runs(sp_mask, m, cap=expand_cap)
+    info.update(n_sp=int(sp_mask.sum()), ap_thresh=th, mode=mode)
     return sp_mask, th, info
 
-def best_upper_endplate_plane(mask_zyx, angle_max=45.0, thresh=3.0,
+
+def _expand_spinous_runs(sp_mask, bone, cap=5):
+    """對每條 (y, z) 水平線（x = 左右方向），把既有棘突 run 向左右兩側各延伸
+    至多 cap 個 bone voxel：補回落在中線帶 |s|<=w 之外的棘突楔側緣薄條
+    （帶由鏡稱面定義，楔略偏中線時側緣會被漏成 other bone）。
+    遇到非 bone、既有棘突 voxel 或達 cap 即停；只延伸既有 run，不新建
+    run（該線無棘突時絕不標記）。椎弓厚處最多少數 cap 個「棘突基部」
+    相鄰 bone 一併補入，屬棘突連續結構。"""
+    out = sp_mask.copy()
+    if not out.any():
+        return out
+    nz, ny, nx = out.shape
+    for y in range(ny):
+        sp_y = out[:, y, :]
+        if not sp_y.any():
+            continue
+        bone_y = bone[:, y, :]
+        for z in np.flatnonzero(sp_y.any(axis=1)):
+            idx = np.flatnonzero(sp_y[z])
+            runs = np.split(idx, np.flatnonzero(np.diff(idx) > 1) + 1)
+            for r in runs:
+                lo, hi = int(r[0]), int(r[-1])
+                x = lo - 1
+                added = 0
+                while x >= 0 and added < cap and bone_y[z, x] and not out[z, y, x]:
+                    out[z, y, x] = True
+                    x -= 1
+                    added += 1
+                x = hi + 1
+                added = 0
+                while x < nx and added < cap and bone_y[z, x] and not out[z, y, x]:
+                    out[z, y, x] = True
+                    x += 1
+                    added += 1
+    return out
+
+def smooth_mask_sdf(mask_zyx, sigma=1.5):
+    """對 3D boolean mask 做有號距離場（SDF）高斯平滑：
+    把表面沿法線做近似平均曲率流（mean curvature flow），圓化凸出的
+    鋸齒/尖刺、填進凹陷的缺口，但不會均勻收縮整體形状（與直接對 mask
+    做高斯Blur再 thresh 不同——後者會把薄結構一起磨細、體積明顯縮小）。
+    這是消除「三线性旋轉 > 0.5 之後仍剩餘的 voxel 級鋸齒」最有效的方法。
+
+    參數：
+      mask_zyx : (z, y, x) boolean / 0-1 陣列
+      sigma    : 平滑強度（voxel）。1.5 ≈ 表面積 -4%、體積 -0.6%；
+                 越大越圓，但薄結構（棘突尖）會被磨損越多。
+    回傳同 shape 的 boolean mask。
+    """
+    m = np.asarray(mask_zyx) > 0
+    if not m.any() or m.all():
+        return m.copy()
+    d_in = distance_transform_edt(m)
+    d_out = distance_transform_edt(~m)
+    sdf = d_in - d_out
+    return gaussian_filter(sdf, sigma=float(sigma)) > 0.0
+
+def shape_based_smooth(vol01, sigma=1.5):
+    """Shape-based interpolation（SBI）平滑：以 0..1 體積的 0.5 等值面為
+    物件形狀（shape），計算有號距離場（SDF，內正外負），在距離域做高斯
+    插值（interpolation），再於 0 重新閾值，得到圓滑的 smooth mask。
+    與 smooth_mask_sdf 的差異：邊界層（0 < v < 1）內三线性場值滿足
+    v ≈ 0.5 + d（d = 以 voxel 為單位的有號距離），故直接以 v - 0.5 替換
+    EDT 量值，得到次體素精確的 SDF（層外仍由 distance_transform_edt 給出
+    精確距離）；表面梯度連續，不再是被 EDT 量化成 ±1 的硬階梯，平滑後
+    的邊界更貼合 soft boundary 的真實位置。
+    參數：
+      vol01 : (z, y, x) 0..1 浮點體積（例如旋轉後的 _binary_linear）
+      sigma : 高斯平滑強度（voxel），意義與 smooth_mask_sdf 相同。
+    回傳：同 shape 的 boolean mask。
+    """
+    v = np.clip(np.asarray(vol01, dtype=np.float32), 0.0, 1.0)
+    b = v > 0.5
+    if not b.any() or b.all():
+        return b.copy()
+    d_in = distance_transform_edt(b)
+    d_out = distance_transform_edt(~b)
+    sdf = d_in - d_out
+    band = (v > 0) & (v < 1)
+    sdf[band] = v[band] - 0.5
+    return gaussian_filter(sdf, sigma=float(sigma)) > 0.0
+
+def _ap_axis(sym):
+    """鏡稱面內的前後（AP）軸：(u,v) 中 |y| 分量大者，正規化成 +AP = 後側（y 小側）
+    （本資料系 y 往前遞增，與 segment_spinous_process 同慣例）。"""
+    u = np.array(sym['u'])
+    v = np.array(sym['v'])
+    u_ap = u if abs(u[1]) >= abs(v[1]) else v
+    if u_ap[1] > 0:
+        u_ap = -u_ap
+    return u_ap
+
+
+def _full_ap_valley(aps, min_side_frac=0.15, max_ratio=0.85, smooth=3):
+    """終板下骨體 AP 分佈的平滑谷底：最深相對谷底（sm[i] 對鄰近峰的最小比值），
+    要求兩側各有 >= min_side_frac 的質量（拒絕對小尾巴的偽谷底）。
+    回傳 (th 或 None, ratio 或 None)。"""
+    lo = int(np.floor(aps.min()))
+    hi = int(np.ceil(aps.max()))
+    if hi - lo < 10:
+        return None, None
+    hist, edges = np.histogram(aps, bins=range(lo, hi + 1))
+    sm = np.convolve(hist, np.ones(smooth) / float(smooth), mode='same')
+    csum = np.concatenate([[0], np.cumsum(hist)])
+    total = csum[-1]
+    best_i, best_ratio = None, 1.0
+    for i in range(1, len(hist) - 1):
+        if not (sm[i] <= sm[i - 1] and sm[i] <= sm[i + 1]):
+            continue
+        if csum[i] < min_side_frac * total or (total - csum[i + 1]) < min_side_frac * total:
+            continue
+        flank = min(float(sm[:i].max()), float(sm[i + 1:].max()))
+        if flank <= 0:
+            continue
+        ratio = float(sm[i]) / flank
+        if ratio <= max_ratio and ratio < best_ratio:
+            best_ratio, best_i = ratio, i
+    if best_i is None:
+        return None, None
+    return float(0.5 * (edges[best_i] + edges[best_i + 1])), best_ratio
+
+
+def _posterior_min_threshold(aps, rear_frac=0.40, min_side_frac=0.08, smooth=3):
+    """AP 分佈後側 `rear_frac` 區間內、平滑直方圖的最小值位置（該處後側質量
+    比例需 >= min_side_frac）：棘突缺如椎體中 _full_ap_valley 失敗時的
+    「椎體後側末端 = 體/弓最薄處」備援。
+    回傳 th 或 None。"""
+    lo = int(np.floor(aps.min()))
+    hi = int(np.ceil(aps.max()))
+    if hi - lo < 10:
+        return None
+    hist, edges = np.histogram(aps, bins=range(lo, hi + 1))
+    sm = np.convolve(hist, np.ones(smooth) / float(smooth), mode='same')
+    csum = np.concatenate([[0], np.cumsum(hist)])
+    total = csum[-1]
+    i0 = int(len(hist) * (1.0 - rear_frac))
+    best_i, best_val = None, np.inf
+    for i in range(i0, len(hist)):
+        if (total - csum[i + 1]) < min_side_frac * total:
+            continue
+        if sm[i] < best_val:
+            best_val, best_i = float(sm[i]), i
+    if best_i is None:
+        return None
+    return float(0.5 * (edges[best_i] + edges[best_i + 1]))
+
+
+def segment_vertebral_body(mask_zyx, sym, endplate, ap_thresh, sp_mode, margin=2.0):
+    """
+    以兩平面從 3D bone mask (z, y, x) 切出椎體（前側中央主體塊）：
+      1) best_upper_endplate_plane 的上終板面（法線朝上 a·x+b·y+c·z=d）：
+         只保留終板下側（身體側，e·p-d <= margin）的 bone voxel，
+         排除跨在終板上方的後側構造（椎板/棘突）。
+      2) best_symmetry_plane 的鏡稱面：提供平面內 AP 軸（_ap_axis，
+         +AP = 後側，與 segment_spinous_process 同慣例）；AP 切點取三層優先：
+         a) sp_mode == 'gap'：中線帶（椎管）的體/弓谷底 ap_thresh
+            （segment_spinous_process 回傳值，最可靠）；
+         b) sp_mode == 'no_spinous'（棘突已切除）：中線帶沒有空的體/弓谷底
+            可用；椎體後側末端 = 終板下整體 AP 分佈的局部最小（體/弓最薄處）。
+            切除後殘留後側要素會部分填滿椎管、谷底比正常椎體淺，
+            因此放寬 _full_ap_valley 條件（min_side_frac 0.15->0.10、
+            max_ratio 0.85->0.95）；再失敗則取後側 40% 區間的平滑谷底
+            （_posterior_min_threshold）。
+         c) 否則：終板下整體 AP 分佈的平滑谷底（_full_ap_valley，
+            處理中線骨橋等中線搜尋 fallback 的情形）；
+         d) 最後 fallback：AP 分佈 55 百分位（可能切進椎體內，會打 WARNING）。
+         椎體 = AP < 切點（切點之前側）且終板下側的 bone。
+    回傳 (vb_mask (z,y,x) bool, ap_thresh, info dict)；
+    資料不足或上終板面缺位時 vb_mask = None（info['mode'] 說明原因）。
+    """
+    m = np.asarray(mask_zyx) > 0
+    zz, yy, xx = np.nonzero(m)
+    info = {'n_bone': int(zz.size), 'n_vb': 0, 'ap_thresh': None, 'mode': 'empty'}
+    if zz.size < 50:
+        return None, None, info
+    if endplate is None:
+        info['mode'] = 'no_endplate'
+        return None, None, info
+    a, b, c, d = endplate['plane']
+    X = xx.astype(np.float64)
+    Y = yy.astype(np.float64)
+    Z = zz.astype(np.float64)
+    below = (X * a + Y * b + Z * c - d) <= float(margin)
+    u_ap = _ap_axis(sym)
+    ap = X * u_ap[0] + Y * u_ap[1] + Z * u_ap[2]
+    aps = ap[below]
+    if aps.size < 50:
+        info['mode'] = 'too_few_below'
+        return None, None, info
+    th, mode = None, 'quantile'
+    if sp_mode == 'gap' and ap_thresh is not None:
+        th, mode = float(ap_thresh), 'midline_gap'
+    elif sp_mode == 'no_spinous':
+        # 棘突已切除：用放寬條件的整體谷底（見 docstring b）
+        th, _ = _full_ap_valley(aps, min_side_frac=0.10, max_ratio=0.95)
+        if th is not None:
+            mode = 'nosp_gap'
+        else:
+            th = _posterior_min_threshold(aps)
+            if th is not None:
+                mode = 'nosp_post_min'
+    else:
+        th, _ = _full_ap_valley(aps)
+        if th is not None:
+            mode = 'full_gap'
+    if th is None:
+        th = float(np.quantile(aps, 0.55))
+    sel = below & (ap < th)
+    if not sel.any():
+        info['mode'] = 'no_body_voxels'
+        return None, None, info
+    vb_mask = np.zeros(m.shape, dtype=bool)
+    vb_mask[zz[sel], yy[sel], xx[sel]] = True
+    info.update(n_vb=int(sel.sum()), ap_thresh=th, mode=mode)
+    return vb_mask, th, info
+
+def best_upper_endplate_plane(mask_zyx, angle_max=45.0, thresh=4.0,
                               n_iter=500, seed=42):
     """
     3D bone mask (z, y, x) 的最佳「上終板」近似平面 a·x + b·y + c·z = d
     （voxel index 座標；(a,b,c) 為朝上的單位法線）。
-    1) 每個 (y, x) 欄位取最上方 bone voxel 作為頂面點（僅前側半邊，
+
-       y >= COM_y，避開後方元素，與 2D superior endplate 定義一致）
+    區域：只用該 level 的前側半邊（y 為 AP 方向，anterior = y 較大側）：
-    2) RANSAC 三點擬平面：法線限制在與 +z 軸 ≤ angle_max° 內，
+    切點 = bone 的 y 範圍中點（y >= (y_min+y_max)//2），避開後方
-       計數 ±thresh voxel 內的頂面點為 inlier，取 inlier 最多者
+    棘突 / 弓根 / 椎管結構，與 2D superior endplate 定義一致。
-    3) SVD 最小二乘微調
+
+    兩階段穩健擬合（舊式單次 3D RANSAC 會被側旁結構 / 上層椎體侵入
+    的頂面污染擬出過陡平面，例：L1 擬到 21°）：
+    1) Stage A（矢狀線）：每個 (y, x) 欄位取最上方 bone voxel 作為頂面點，
+       再收斂成 per-y 最上 z，RANSAC 擬合矢狀 (y-z) 線 z = s·y + i，
+       取得穩健的矢狀斜率 s；
+    2) Stage B（側向線）：先把頂面點筛到矢狀線 ±max(2·thresh, 5) 帶內
+       （移除離帶的高/低污染點），再 RANSAC 擬合 (z − s·y − i) = c·x + k，
+       取得側向斜率 c；
+    3) 平面 z = s·y + c·x + (i+k) → 單位法線 (−c,−s,1)/√(1+s²+c²)、
+       d = (i+k)/√(1+s²+c²)、tilt_deg = 法線與 +z 軸夾角；
+       inlier_ratio = 全部前側半頂面點落在平面 ±thresh 的比例。
     回傳 dict（資料不足時回傳 None）：
       plane : (a, b, c, d)
       normal / offset
@@ -244,51 +581,67 @@ def best_upper_endplate_plane(mask_zyx, angle_max=45.0, thresh=3.0,
       n_points / n_inliers
       u, v : 平面內正交方向（供繪製用）
     """
+    from sklearn.linear_model import RANSACRegressor
+
     m = np.asarray(mask_zyx) > 0
     nz, ny, nx = m.shape
+    if not m.any():
+        return None
     idx = np.where(m, np.arange(nz)[:, None, None], -1)
     ztop = idx.max(axis=0)                                # (y, x) 每欄最上 z
-    y_split = int(round(center_of_mass(m)[1])) if m.sum() else 0
+    # 前側半邊：bone y 範圍中點為切點（前側 = y >= 切點）
+    y_present = np.where(np.any(m, axis=(0, 2)))[0]
+    y_split = int((y_present[0] + y_present[-1]) // 2)
     # ztop 是 (y, x)：條件作用在 y 軸（axis 0）
     sel = (ztop >= 0) & (np.arange(ny)[:, None] >= y_split)
     yy, xx = np.where(sel)
-    if xx.size < 8:
+    if xx.size < 20:
         return None
-    P = np.stack((xx, yy, ztop[yy, xx]), axis=1).astype(np.float64)
+    xa = xx.astype(np.float64)
-    n = P.shape[0]
+    ya = yy.astype(np.float64)
+    za = ztop[yy, xx].astype(np.float64)
+    n = za.size
 
-    rng = np.random.default_rng(seed)
+    def _line1d(x1, y1, residual):
-    cos_min = np.cos(np.deg2rad(angle_max))
+        """RANSAC 擬線 y = k·x + b；失敗時退回普通最小二乘。"""
-    best_cnt, best_nv, best_d = -1, None, 0.0
+        try:
-    for _ in range(n_iter):
+            fit = RANSACRegressor(residual_threshold=float(residual),
-        i, j, k = rng.choice(n, 3, replace=False)
+                                  max_trials=int(n_iter),
-        cr = np.cross(P[j] - P[i], P[k] - P[i])
+                                  random_state=int(seed)).fit(x1.reshape(-1, 1), y1)
-        ln = np.linalg.norm(cr)
+            return float(fit.estimator_.coef_[0]), float(fit.estimator_.intercept_)
-        if ln < 1e-6:
+        except Exception:
-            continue
+            k, b = np.polyfit(x1, y1, 1)
-        nv = cr / ln
+            return float(k), float(b)
-        if nv[2] < 0:
+
-            nv = -nv
+    # ---- Stage A：矢狀 (y-z) 線 → 穩健矢狀斜率 s ----
-        if nv[2] < cos_min:                               # 法線必須朝上
+    zt = np.full(ny, -1.0)
-            continue
+    np.maximum.at(zt, yy, za)
-        d = float(nv @ P[i])
+    yv = np.where(zt >= 0)[0]
-        cnt = int(np.count_nonzero(np.abs(P @ nv - d) <= thresh))
+    if yv.size < 10:
-        if cnt > best_cnt:
-            best_cnt, best_nv, best_d = cnt, nv, d
-    if best_nv is None:
         return None
-    # SVD 微調
+    s, i = _line1d(yv.astype(np.float64), zt[yv], 5.0)
-    inl = P[np.abs(P @ best_nv - best_d) <= thresh]
+    if abs(float(np.degrees(np.arctan(s)))) > angle_max:
-    if inl.shape[0] < 3:
         return None
-    mean = inl.mean(axis=0)
+
-    _, _, Vt = np.linalg.svd(inl - mean, full_matrices=False)
+    # ---- Stage B：固定 s，擬側向 (x) 線 (z − s·y − i) = c·x + k ----
-    nv = Vt[2]
+    # 合起來 z = s·y + c·x + (i + k) → n0·p = d0，n0 = (−c, −s, 1), d0 = i + k
-    if nv[2] < 0:
+    res_sag = za - s * ya - i
-        nv = -nv
+    band = np.abs(res_sag) <= max(2.0 * float(thresh), 5.0)
-    d = float(nv @ mean)
+    if int(band.sum()) < 20:
-    dist = np.abs(P @ nv - d)
+        band = np.ones(n, dtype=bool)
-    inl = P[dist <= thresh]
+    c, k = _line1d(xa[band], res_sag[band], float(thresh))
+    d0 = i + k
+
+    n0 = np.array([-c, -s, 1.0])
+    norm0 = float(np.linalg.norm(n0))
+    nv = n0 / norm0
+    d = float(d0 / norm0)
+    tilt_deg = float(np.degrees(np.arccos(np.clip(nv[2], -1.0, 1.0))))
+    if tilt_deg > angle_max:
+        return None
+
+    dist = np.abs(-c * xa - s * ya + za - d0) / norm0
+    n_in = int(np.count_nonzero(dist <= float(thresh)))
     u = np.cross(nv, [1.0, 0.0, 0.0])
     u = u / np.linalg.norm(u)
     v = np.cross(nv, u)
@@ -296,10 +649,10 @@ def best_upper_endplate_plane(mask_zyx, angle_max=45.0, thresh=3.0,
         'plane': (float(nv[0]), float(nv[1]), float(nv[2]), d),
         'normal': (float(nv[0]), float(nv[1]), float(nv[2])),
         'offset': d,
-        'tilt_deg': float(np.degrees(np.arccos(np.clip(nv[2], -1.0, 1.0)))),
+        'tilt_deg': tilt_deg,
-        'inlier_ratio': float(inl.shape[0] / n),
+        'inlier_ratio': float(n_in / n),
         'n_points': int(n),
-        'n_inliers': int(inl.shape[0]),
+        'n_inliers': n_in,
         'u': (float(u[0]), float(u[1]), float(u[2])),
         'v': (float(v[0]), float(v[1]), float(v[2])),
     }

imaging/preprocessing.py

@@ -20,13 +20,89 @@ def save_progress(progress, PROGRESS_FILE):
     with open(PROGRESS_FILE, "w") as f:
         json.dump(progress, f, indent=2)
         
-def process_single_image(image_path, label_path, output_dir_base=None):
+def process_single_image(image_path, label_path, output_dir_base=None, max_z_spacing=None, allowed_levels=None, min_levels=None, metadata_cache=None):
+    """metadata_cache：可選，需提供 get(name) -> dict|None 與
+    put(name, dict)。dict 可含 spacing=[x,y,z]、labels=[label id]。
+    兩者都在 db 裡時整支跳過判定不需讀影像 / label 檔。"""
 
-    image = sitk.ReadImage(image_path)
-    label = sitk.ReadImage(label_path)
     file_name = os.path.basename(image_path)
     name = file_name.replace(".nii.gz", "")
 
+    # pixel spacing / labels 優先用 metadata db，避免每次 run 都讀檔
+    meta = metadata_cache.get(name) if metadata_cache is not None else None
+    image = None
+    label = None
+    spacing = meta.get("spacing") if meta is not None else None
+    existing_labels = meta.get("labels") if meta is not None else None
+
+    if spacing is None:
+        image = sitk.ReadImage(image_path)
+        spacing = [float(v) for v in image.GetSpacing()]
+        if metadata_cache is not None:
+            metadata_cache.put(name, {"spacing": spacing})
+
+    # z spacing 過大（低解析度掃描）跳過整支 pipeline
+    if max_z_spacing is not None and spacing[2] > max_z_spacing:
+        z_spacing = spacing[2]
+        print(f"z spacing {z_spacing:.2f} mm > {max_z_spacing} mm, "
+              f"skipping pipeline for {name}")
+        return {
+            "processed_labels": [],
+            "missing_labels": [],
+            "skipped": True,
+            "skip_reason": f"z spacing {z_spacing:.2f} mm > {max_z_spacing} mm"
+        }
+
+    if existing_labels is None:
+        label = sitk.ReadImage(label_path)
+        # 取得現有 label
+        lssif = sitk.LabelShapeStatisticsImageFilter()
+        lssif.Execute(label)
+        existing_labels = [int(v) for v in lssif.GetLabels()]  # 例如 [1,2,3,20,21]
+        if metadata_cache is not None:
+            metadata_cache.put(name, {"labels": existing_labels})
+    else:
+        print(f"Metadata db hit for {name} (spacing={spacing}, labels={existing_labels})")
+
+    print(f"Existing labels in {os.path.basename(label_path)}: {existing_labels}")
+
+    allowed_label_list = [n for n in existing_labels
+                          if n in LABEL_MAP and (allowed_levels is None
+                                                 or LABEL_MAP[n] in allowed_levels)]
+
+    # 沒有任何符合 allowed levels（如 lumbar）的 label：不建立輸出資料夾、
+    # 不做重取樣，整檔跳過（不計入 max_images）
+    if not allowed_label_list:
+        print(f"No label matches allowed levels {allowed_levels} in {name}, "
+              f"skipping (no output folder)")
+        return {
+            "processed_labels": [],
+            "missing_labels": [],
+            "skipped": True,
+            "skip_reason": f"no label in allowed levels {allowed_levels}"
+        }
+
+    # 符合 allowed levels 的 label 少於 min_levels（如 lumbar < 2 層）：
+    # 整支 pipeline 跳過，不建立輸出資料夾（不計入 max_images）
+    if min_levels is not None and len(allowed_label_list) < min_levels:
+        have = ", ".join(f"{n} ({LABEL_MAP[n]})" for n in allowed_label_list)
+        print(f"Only {len(allowed_label_list)} allowed-level label(s) [{have}] in {name} "
+              f"< {min_levels}, skipping pipeline (no output folder)")
+        return {
+            "processed_labels": [],
+            "missing_labels": [],
+            "skipped": True,
+            "skip_reason": (f"only {len(allowed_label_list)} label(s) in allowed "
+                            f"levels < {min_levels}")
+        }
+
+    # 進入 pipeline：若上面的 spacing / labels 來自 metadata db，
+    # 影像與 label 檔還沒讀，這裡補讀
+    if image is None:
+        image = sitk.ReadImage(image_path)
+    if label is None:
+        label = sitk.ReadImage(label_path)
+
     # LabelStatisticsImageFilter computes statistics (e.g., mean, minimum, maximum, median) of pixel values in an image, segmented by labels in a corresponding label image.
     lsif = sitk.LabelStatisticsImageFilter()
     lsif.Execute(image, label)
@@ -34,14 +110,7 @@ def process_single_image(image_path, label_path, output_dir_base=None):
     # Assume to have some sitk image (itk_image) and label (itk_label)
     resampled_sitk_img = resample_img(image, out_spacing=[0.5, 0.5, 0.5], is_label=False)
     resampled_sitk_lbl = resample_img(label, out_spacing=[0.5, 0.5, 0.5], is_label=True)
-    
+
-    # 取得現有 label
-    lssif = sitk.LabelShapeStatisticsImageFilter()
-    lssif.Execute(label)
-    existing_labels = lssif.GetLabels()  # 這會回傳 list，例如 [1,2,3,20,21]
-    
-    print(f"Existing labels in {os.path.basename(label_path)}: {existing_labels}")
-    
     # 建立每個檔案的輸出資料夾
     file_name = os.path.basename(image_path)
     name = file_name.replace(".nii.gz", "")
@@ -54,21 +123,47 @@ def process_single_image(image_path, label_path, output_dir_base=None):
         for lab in existing_labels:
             f.write(f"{lab}\t{LABEL_MAP.get(lab, 'Unknown')}\n")
     
-    # 遍歷現有 label 做分割
+    # 遍歷現有 label 做分割；個別 label 失敗（label_map 缺該 label、
+    # 或 seg_bone 報錯）只跳過該 label，不中斷整檔處理
+    processed = []
+    skipped = []
     for n in existing_labels:
+        if n not in LABEL_MAP:
+            print(f"Label {n} not found in label_map, skipping this label (file continues).")
+            skipped.append(n)
+            continue
+        if allowed_levels is not None and LABEL_MAP[n] not in allowed_levels:
+            print(f"Label {n} ({LABEL_MAP[n]}) not in allowed levels, "
+                  f"skipping this label (file continues).")
+            skipped.append(n)
+            continue
         try:
-            roi_path, binary_path, roi2_path, cortical_path = seg_bone(n, name, resampled_sitk_img, resampled_sitk_lbl, output_dir, label_map=LABEL_MAP)
+            res = seg_bone(n, name, resampled_sitk_img, resampled_sitk_lbl, output_dir,
-            for path in [roi_path, binary_path, roi2_path, cortical_path]:
+                           label_map=LABEL_MAP, original_label=label)
-                standardize_affine(path, output_dir)
+            if res is None:
+                print(f"Label {n}: empty after largest-CC extraction, skipping this label.")
+                skipped.append(n)
+                continue
+            (roi_path, binary_path, roi2_path, cortical_path, binary_nn_path,
+             binary_linear_path, smd_path, resampled_path, binary_sdf_path,
+             binary_erode_path) = res
+            for path in [roi_path, binary_path, roi2_path, cortical_path,
+                         binary_nn_path, binary_linear_path,
+                         smd_path, resampled_path, binary_sdf_path,
+                         binary_erode_path]:
+                if path is not None:
+                    standardize_affine(path, output_dir)
+            processed.append(n)
         except RuntimeError as e:
             print(f"Label {n} could not be processed, skipping. Error: {e}")
+            skipped.append(n)
 
     return {
-        "processed_labels": [lab for lab in existing_labels],
+        "processed_labels": processed,
-        "missing_labels": []
+        "missing_labels": skipped
     }
 
-def process_dataset(image_dir, label_dir, output_dir, labels_to_process=None):
+def process_dataset(image_dir, label_dir, output_dir, labels_to_process=None, max_images=None, post_process=None, max_z_spacing=None, allowed_levels=None, min_levels=None, metadata_cache=None):
     image_files = sorted(glob.glob(os.path.join(image_dir, "*.nii.gz")))
     total_files = len(image_files)
     print(f"Total files: {total_files}")
@@ -77,8 +172,15 @@ def process_dataset(image_dir, label_dir, output_dir, labels_to_process=None):
 
     progress = load_progress(PROGRESS_FILE)
     all_file_summary = []
+    # max_images 統計「實際進入 pipeline 的檔數」：
+    # z spacing 超標被跳過的檔不計入配額，繼續掃描後續檔案
+    processed_count = 0
 
     for idx, image_path in enumerate(image_files, 1):
+        if max_images is not None and processed_count >= max_images:
+            print(f"Reached max_images={max_images}, stopping early.")
+            break
+
         file_name = os.path.basename(image_path)
         name = file_name.replace(".nii.gz", "")
         label_path = os.path.join(label_dir, file_name.replace(".nii.gz", "_seg.nii.gz"))
@@ -93,25 +195,40 @@ def process_dataset(image_dir, label_dir, output_dir, labels_to_process=None):
             print(f"[{idx}/{total_files}] Already finished: {file_name}")
             file_summary["current_labels"] = progress[name].get("processed_labels", [])
             file_summary["missing_labels"] = progress[name].get("missing_labels", [])
+            processed_count += 1
             all_file_summary.append(file_summary)
             continue
 
         if not os.path.exists(label_path):
             print(f"[{idx}/{total_files}] Warning: label not found for {file_name}")
             file_summary["note"] = "Label file not found"
+            processed_count += 1
             all_file_summary.append(file_summary)
             continue
 
         try:
-            result = process_single_image(image_path, label_path, output_dir_base=output_dir)
+            result = process_single_image(image_path, label_path, output_dir_base=output_dir,
+                                           max_z_spacing=max_z_spacing,
+                                           allowed_levels=allowed_levels,
+                                           min_levels=min_levels,
+                                           metadata_cache=metadata_cache)
             # print(result)
             # exit()
         except Exception as e:
             print(f"[{idx}/{total_files}] Error processing {file_name}: {e}")
             file_summary["note"] = f"Error: {e}"
+            processed_count += 1
             all_file_summary.append(file_summary)
             continue
 
+        if result.get("skipped"):
+            # z spacing 超標：不計入 max_images 配額，繼續掃描後續檔案
+            print(f"[{idx}/{total_files}] Skipped ({result['skip_reason']}): {file_name}")
+            file_summary["note"] = result["skip_reason"]
+            all_file_summary.append(file_summary)
+            continue
+
+        processed_count += 1
         file_summary["current_labels"] = result["processed_labels"]
         file_summary["missing_labels"] = result["missing_labels"]
         all_file_summary.append(file_summary)
@@ -123,7 +240,15 @@ def process_dataset(image_dir, label_dir, output_dir, labels_to_process=None):
         }
         save_progress(progress, PROGRESS_FILE)
 
-        print(f"[{idx}/{total_files}] Finished: {file_name} | Missing labels: {result['missing_labels'] or 'None'}")
+        count_msg = f" | processed {processed_count}/{max_images}" if max_images is not None else ""
+        print(f"[{idx}/{total_files}] Finished: {file_name} | "
+              f"Missing labels: {result['missing_labels'] or 'None'}{count_msg}")
+
+        if post_process is not None:
+            try:
+                post_process(os.path.join(output_dir, name), result["processed_labels"])
+            except Exception as e:
+                print(f"[{idx}/{total_files}] post_process error for {name}: {e}")
 
     # --- Summary ---
     summary_path = os.path.join(output_dir, "all_files_label_summary.txt")

imaging/resample.py

@@ -2,28 +2,49 @@ import numpy as np
 import SimpleITK as sitk
 from config.constant import LABEL_MAP
 
-def resample_img(sitk_image, out_spacing=[0.5, 0.5, 0.5], is_label=False):
+def resample_img(sitk_image, out_spacing=[0.5, 0.5, 0.5], is_label=False,
-    
+                 interpolator=None, cval=None):
-    # Resample images to 2mm spacing with SimpleITK
+    """重採樣到 out_spacing，完整保留物理範圍（邊界 margin 不裁剪）：
-    original_spacing = sitk_image.GetSpacing()
+      - CT（is_label=False）：线性插值。本流程是上採樣（~0.75-1mm -> 0.5mm），
-    original_size = sitk_image.GetSize()
+        线性即無漣波的理想重建；B-spline 會在身體 margin 等強邊界產生
-
+        非物理的 undershoot/overshoot（量測：~0.5% 體素低於 air floor
-    out_size = [
+        -1024 HU，最低 -1274，沿體輪廓形成黑暈）。
-        int(np.round(original_size[0] * (original_spacing[0] / out_spacing[0]))),
+      - 預設填充值 = 影像最小值（air），而非 GetPixelIDValue()
-        int(np.round(original_size[1] * (original_spacing[1] / out_spacing[1]))),
+        （對 int16 CT 回傳佔位值 2 ≈ 軟組織，會把 margin 填成軟組織）。
-        int(np.round(original_size[2] * (original_spacing[2] / out_spacing[2])))]
+      - 輸出尺寸用 ceil 覆蓋原物理尺寸（round 會讓遠端端點被裁 ≤0.25mm）。
+    label（is_label=True）：最近邻、填充 0。
+    interpolator：明確指定插值器（None = 依 is_label 取 Linear / NearestNeighbor；
+      例如 SMD 等 piecewise-linear 場用 sitk.sitkBSpline，三阶 B 样条对分段
+      线性场为精确重建、無漣波）。
+    cval：明確指定填充值（None = 上述預設）。
+    """
+    original_spacing = np.array(sitk_image.GetSpacing(), dtype=float)
+    original_size = np.array(sitk_image.GetSize())
+    out_spacing = np.array(out_spacing, dtype=float)
+    physical = original_size * original_spacing
+    out_size = [max(1, int(np.ceil(physical[i] / out_spacing[i] - 1e-6)))
+                for i in range(3)]
 
     resample = sitk.ResampleImageFilter()
-    resample.SetOutputSpacing(out_spacing)
+    resample.SetOutputSpacing(out_spacing.tolist())
     resample.SetSize(out_size)
     resample.SetOutputDirection(sitk_image.GetDirection())
     resample.SetOutputOrigin(sitk_image.GetOrigin())
     resample.SetTransform(sitk.Transform())
-    resample.SetDefaultPixelValue(sitk_image.GetPixelIDValue())
 
     if is_label:
-        resample.SetInterpolator(sitk.sitkNearestNeighbor)
+        resample.SetInterpolator(interpolator or sitk.sitkNearestNeighbor)
+        resample.SetDefaultPixelValue(cval if cval is not None else 0)
+    elif interpolator is not None:
+        resample.SetInterpolator(interpolator)
+        # SMD 等 signed 場的填充：預設 0 = 表面層值（比影像 min/max 安全，
+        # 不會製造假的零穿越環）；可用品值可用 cval 覆蓋
+        resample.SetDefaultPixelValue(float(cval) if cval is not None else 0.0)
     else:
-        resample.SetInterpolator(sitk.sitkBSpline)
+        resample.SetInterpolator(sitk.sitkLinear)
+        # air 值 = 影像最小 HU（statistics 濾波器 streaming 計算，不載入整張 array）
+        stats = sitk.StatisticsImageFilter()
+        stats.Execute(sitk_image)
+        resample.SetDefaultPixelValue(float(stats.GetMinimum()))
 
     return resample.Execute(sitk_image)

imaging/segmentation.py

@@ -1,6 +1,7 @@
 import os
 import SimpleITK as sitk
 from config.constant import LABEL_MAP
+from imaging.resample import resample_img
 import numpy as np
 
 """
@@ -12,7 +13,28 @@ my_map = {1: "L1", 2: "L2", 3: "L3"}
 seg_bone(n, name, img, lbl, label_map=my_map)
 """
 
-def seg_bone(n, name, resampled_sitk_img, resampled_sitk_lbl, output_base=None, label_map=LABEL_MAP):
+def _largest_cc_bbox(mask_img):
+    """26-連通的最大连通區域 + 其 bbox（RelabelComponent 依大小排序，最大者=1）。
+    回傳 (largest_mask, bbox2)；沒有任何組件時回傳 None。
+    bbox2 格式：[x_start, y_start, z_start, x_size, y_size, z_size]。"""
+    cc_image = sitk.ConnectedComponent(mask_img, True)  # fullyConnected
+    relabeled_cc = sitk.RelabelComponent(cc_image, sortByObjectSize=True)
+    shape_stats = sitk.LabelShapeStatisticsImageFilter()
+    shape_stats.Execute(relabeled_cc)
+    if shape_stats.GetNumberOfLabels() < 1:
+        return None
+    return (relabeled_cc == 1), shape_stats.GetBoundingBox(1)
+
+def _bbox_roi(img, bbox, margin=0):
+    """裁 bbox（對稱外擴 margin 個 voxel，clamp 到影像邊界）。
+    bbox 格式：[x_start, y_start, z_start, x_size, y_size, z_size]。"""
+    n = img.GetSize()  # (x, y, z)
+    index = [max(0, int(bbox[i]) - margin) for i in range(3)]
+    size = [min(n[i] - index[i], int(bbox[i + 3]) + 2 * margin) for i in range(3)]
+    return sitk.RegionOfInterest(img, size, index)
+
+def seg_bone(n, name, resampled_sitk_img, resampled_sitk_lbl, output_base=None, label_map=LABEL_MAP,
+             original_label=None):
 
     if output_base==None:
         output_base=='Dataset'
@@ -22,87 +44,118 @@ def seg_bone(n, name, resampled_sitk_img, resampled_sitk_lbl, output_base=None,
 
     label_name = label_map[n]
 
-    # lssif = sitk.LabelShapeStatisticsImageFilter()
+    # ============ 原解析度（未插值）chain ============
-    # lssif.Execute(resampled_sitk_lbl)
+    # 1. 提取標籤 n 的二值遮罩 (將標籤 n 設為 1，其餘為 0)，最大連通區域
+    smd_path = resampled_path = binary_sdf_path = binary_erode_path = None
+    binary_linear_path = binary_nn_path = None
+    if original_label is not None:
+        bin_orig = sitk.BinaryThreshold(original_label, n, n, 1, 0)
+        cc_orig = _largest_cc_bbox(bin_orig)
+        if cc_orig is None:
+            return None
+        largest_orig, bbox_orig = cc_orig
 
-    # if not lssif.HasLabel(n):
+        # _binary.nii.gz：原解析度【未插值】遮罩（最大连通區域、裁到物件 bbox，
-    #     raise RuntimeError(f"Label {n} not found")
+        # 不重取樣、不插值 —— 原始 label 的忠實二值版本）
+        binary_path = os.path.join(output_base, f"{label_name}_binary.nii.gz")
+        sitk.WriteImage(_bbox_roi(largest_orig, bbox_orig), binary_path)
 
-    # bbox2 = lssif.GetBoundingBox(n)
+        # _smd.nii.gz：SignedMaurerDistanceMap（ITK 慣例：物件內負 / 外正；
+        # 距離以原始 index（pixel）單位、不隨各向异性 spacing 縮放——
+        # _binary_sdf 的 0.5 閾值（mid-gap）正是依賴這個 index 單位慣例）。
+        # 裁 bbox_orig 外擴 4 voxel 的背景輪：
+        # 沒有背景輪時填充值直接貼着物件邊緣，重取樣會在裁切邊界產生
+        # 假的閾值穿越。
+        # 這個 SimpleITK build 的 3D SignedMaurerDistanceMap 只支援整數輸入，
+        # 先 Cast 到 uint8 再回傳 float32 輸出
+        smd_full = sitk.SignedMaurerDistanceMap(sitk.Cast(largest_orig, sitk.sitkUInt8))
+        smd_full = sitk.Cast(smd_full, sitk.sitkFloat32)
+        smd_margined = _bbox_roi(smd_full, bbox_orig, margin=4)
+        smd_path = os.path.join(output_base, f"{label_name}_smd.nii.gz")
+        sitk.WriteImage(smd_margined, smd_path)
 
-    # 1. 提取標籤 n 的二值遮罩 (將標籤 n 設為 1，其餘為 0)
+        # SMD 體積【线性插值】重取樣到 0.5mm（reference = 0.5mm CT，與
-    binary_mask = sitk.BinaryThreshold(resampled_sitk_lbl,  n, n, 1, 0)
+        # resampled_sitk_img 同 grid，之後可直接用 0.5mm bbox 裁切）。
-    
+        # SMD 在每個 input voxel 內分段線性，线性重取樣近似精確、無漣波，
-    # 2. 獲取所有連通區域
+        # 各等值面（物件邊界等）不變。填充值 = 裁切角落（背景側，正值）；
-    # 連通區域濾波器會將 binary_mask 中的不同物體標記為 1, 2, 3...
+        # 若為負（物件貼影像邊界的病態情況）用 0。
-    cc_image = sitk.ConnectedComponent(binary_mask, True) #fullyConnected
+        corner = float(sitk.GetArrayViewFromImage(smd_margined).flat[0])
-    
+        rs = sitk.ResampleImageFilter()
-    # 3. 根據區域大小（像素/體積）重新標記
+        rs.SetReferenceImage(resampled_sitk_img)
-    # RelabelComponent 會按大小排序，最大的物體標籤會被設為 1
+        rs.SetInterpolator(sitk.sitkLinear)
-    relabeled_cc = sitk.RelabelComponent(cc_image, sortByObjectSize=True)
+        rs.SetDefaultPixelValue(corner if corner > 0 else 0.0)
-    largest_mask = relabeled_cc == 1
+        smd_res_full = rs.Execute(smd_margined)
-    
+
-    # 4. 計算形狀統計信息
+        # 0.5mm linear 二值化 mask（full extent，與 resampled_sitk_img 同 grid）：
-    shape_stats = sitk.LabelShapeStatisticsImageFilter()
+        # 原數據 5mm 切片上採樣 10x 到 0.5mm，最近邻會在邊界產生 10 體素厚的
-    shape_stats.Execute(relabeled_cc)
+        # 階梯鋸齒；线性插值使邊界落在次體素位置（rotation 前的邊界更平滑）。
-    
+        bin_lin = resample_img(sitk.Cast(bin_orig, sitk.sitkFloat32))
-    # 檢查是否有找到任何組件
+        arr = (sitk.GetArrayFromImage(bin_lin) > 0.5).astype(np.uint8)
-    if shape_stats.GetNumberOfLabels() < 1:
+        if arr.shape != resampled_sitk_img.GetSize()[::-1]:
+            raise RuntimeError(
+                f"linear binary resample shape mismatch: {arr.shape} vs {resampled_sitk_img.GetSize()}")
+        binary_mask = sitk.GetImageFromArray(arr)
+        binary_mask.CopyInformation(resampled_sitk_img)
+    else:
+        # 無原始 label：舊版路徑（0.5mm label 閾值），不產生 SMD/SDF chain
+        binary_mask = sitk.BinaryThreshold(resampled_sitk_lbl, n, n, 1, 0)
+        binary_path = None
+
+    # 2. 0.5mm 最大連通區域（26-連通）+ 邊界框；所有 0.5mm 輸出裁到同一 bbox
+    cc_res = _largest_cc_bbox(binary_mask)
+    if cc_res is None:
         return None
-        
+    largest_mask, bbox2 = cc_res
-    # 5. 獲取最大組件（標籤為 1）的邊界框
-    # 格式通常為 [x_start, y_start, z_start, x_size, y_size, z_size]
-    bbox2 = shape_stats.GetBoundingBox(1)
 
+    if binary_path is None:
+        binary_path = os.path.join(output_base, f"{label_name}_binary.nii.gz")
+        sitk.WriteImage(sitk.RegionOfInterest(largest_mask, bbox2[3:], bbox2[:3]), binary_path)
+
+    if smd_path is not None:
+        # _smd_resampled.nii.gz：线性重取樣到 0.5mm 的 SMD（浮點，裁 bbox2）
+        resampled_path = os.path.join(output_base, f"{label_name}_smd_resampled.nii.gz")
+        sitk.WriteImage(sitk.RegionOfInterest(smd_res_full, bbox2[3:], bbox2[:3]), resampled_path)
+
+        # _binary_sdf.nii.gz：_smd_resampled 於 0.5 閾值 -> 0.5mm 平滑 mask
+        # （SMD 內負/外正；0.5 介於內殼 ≈0 與外殼 ≈+1 之間，即原解析度
+        #  label 邊界的 mid-gap 位置，physical volume 與 _binary/_binary_nn
+        #  一致，sub-voxel 表面、無 NN 階梯）
+        bin_sdf_full = sitk.GetImageFromArray(
+            (sitk.GetArrayFromImage(smd_res_full) < 0.5).astype(np.uint8))
+        bin_sdf_full.CopyInformation(resampled_sitk_img)
+        binary_sdf_path = os.path.join(output_base, f"{label_name}_binary_sdf.nii.gz")
+        sitk.WriteImage(sitk.RegionOfInterest(bin_sdf_full, bbox2[3:], bbox2[:3]), binary_sdf_path)
+
+        # _binary_nn.nii.gz：0.5mm label 最近邻（舊版），裁自己的 bbox，僅供對比
+        nn_mask = sitk.BinaryThreshold(resampled_sitk_lbl, n, n, 1, 0)
+        nn_res = _largest_cc_bbox(nn_mask)
+        if nn_res is not None:
+            nn_largest, nn_bbox = nn_res
+            binary_nn_path = os.path.join(output_base, f"{label_name}_binary_nn.nii.gz")
+            sitk.WriteImage(sitk.RegionOfInterest(nn_largest, nn_bbox[3:], nn_bbox[:3]),
+                            binary_nn_path)
+
+    # 3. roi（0.5mm）
+    # _roi2 不再存檔；_cortical 改由 xfr_preprocess 的旋轉後處理產出
+    # （rotated/{level}_cortical.nii.gz，定義不變：門檻 = 骨頭 mask 內 median HU）
     roi    = sitk.RegionOfInterest(resampled_sitk_img, bbox2[3:], bbox2[:3])
     roi_path = os.path.join(output_base, f"{label_name}_roi.nii.gz")
     sitk.WriteImage(roi, roi_path)
 
-    # label2 = sitk.RegionOfInterest(resampled_sitk_lbl, bbox2[3:], bbox2[:3])
+    return roi_path, binary_path, None, None, binary_nn_path, \
-    # binary = sitk.BinaryThreshold(label2, lowerThreshold=n, upperThreshold=n, outsideValue=0, insideValue=1)
+        binary_linear_path, smd_path, resampled_path, binary_sdf_path, binary_erode_path
-    binary = sitk.RegionOfInterest(largest_mask, bbox2[3:], bbox2[:3])
-    binary_path = os.path.join(output_base, f"{label_name}_binary.nii.gz")
-    sitk.WriteImage(binary, binary_path)
-
-    # roi_pixel_type = roi.GetPixelID()
-    # binary_cast = sitk.Cast(binary, roi_pixel_type)
-    # roi2 = roi * binary_cast
-    roi2 = sitk.Mask(roi, binary)
-    roi2_path = os.path.join(output_base, f"{label_name}_roi2.nii.gz")
-    sitk.WriteImage(roi2, roi2_path)
-
-    # lsif = sitk.LabelStatisticsImageFilter()
-    # label2_int = sitk.Cast(label2, sitk.sitkUInt16)
-    # lsif.Execute(roi2, label2_int)
-    # labels_in_roi = lsif.GetLabels()
-    # if n in labels_in_roi:
-    #     roi_hu = sitk.GetArrayFromImage(roi2)
-    #     threshold = np.percentile(roi_hu, 60)
-    # else:
-    #     threshold = lsif.GetMedian(labels_in_roi[0])
-
-    stats = sitk.LabelStatisticsImageFilter()
-    stats.UseHistogramsOn() # Required for median calculation
-    stats.Execute(roi, binary)
-
-    # Get the median for the region where mask == 1
-    threshold = stats.GetMedian(1)
-
-    cortical = sitk.BinaryThreshold(roi2, lowerThreshold=threshold, upperThreshold=10000, outsideValue=0, insideValue=1)
-    cortical_path = os.path.join(output_base, f"{label_name}_cortical.nii.gz")
-    sitk.WriteImage(cortical, cortical_path)
-
-    return roi_path, binary_path, roi2_path, cortical_path
 
 """
 Dataset/
 └── standardized/
     └── subject001/
+        ├── L1_binary.nii.gz          # 原解析度【未插值】遮罩（最大连通區域、裁物件 bbox）
+        ├── L1_smd.nii.gz             # SignedMaurerDistanceMap（內負/外正，原始 index 單位；
+        │                             #   bbox 外扩 4 voxel 背景輪，供重取樣插值用）
+        ├── L1_smd_resampled.nii.gz   # _smd 經线性插值重取樣到 0.5mm（浮點，裁 0.5mm bbox）
+        ├── L1_binary_sdf.nii.gz      # _smd_resampled 於 0.5 閾值 -> 0.5mm 平滑 mask（0/1，裁同 bbox）
+        ├── L1_binary_nn.nii.gz       # 最近邻版 0/1（對比用，各自 bbox）
         ├── L1_roi.nii.gz
-        ├── L1_binary.nii.gz
-        ├── L1_roi2.nii.gz
-        ├── L1_cortical.nii.gz
-        ├── L2_roi.nii.gz
         ├── L2_binary.nii.gz
         ...
 """

visualization/res_bone_figure.py

@@ -0,0 +1,451 @@
+import os
+from datetime import datetime
+
+import matplotlib
+matplotlib.use("Agg")
+import matplotlib.pyplot as plt
+from matplotlib.colors import to_rgba
+from matplotlib.lines import Line2D
+
+import numpy as np
+import SimpleITK as sitk
+from scipy.ndimage import map_coordinates
+
+from imaging.orientation import (best_symmetry_plane, best_upper_endplate_plane,
+                                 segment_spinous_process, segment_vertebral_body)
+from utils.helpers import get_unique_filepath
+
+
+# 體積吸收渲染（Beer-Lambert），與 res_plot_3d 相同：
+# 每 voxel 不透明度 = 1 - exp(-mu * voxel_width)
+BONE_MU_CORTICAL = 0.02     # 1/mm
+BONE_MU_TRABECULAR = 0.005  # 1/mm
+BONE_MARKER_SIZE = 3.0      # 骨散點點面積 (pt^2)
+BONE_SUBSAMPLE = 1          # 抽稀（1 = 全畫）
+
+
+def set_axes_equal_3d(ax):
+    """讓 3D 座標軸等比例，球/立方不變形（同 res_plot_3d）。"""
+    x_limits = ax.get_xlim3d()
+    y_limits = ax.get_ylim3d()
+    z_limits = ax.get_zlim3d()
+
+    x_range = abs(x_limits[1] - x_limits[0])
+    x_middle = np.mean(x_limits)
+    y_range = abs(y_limits[1] - y_limits[0])
+    y_middle = np.mean(y_limits)
+    z_range = abs(z_limits[1] - z_limits[0])
+    z_middle = np.mean(z_limits)
+
+    plot_radius = 0.5 * max([x_range, y_range, z_range])
+
+    ax.set_xlim3d([x_middle - plot_radius, x_middle + plot_radius])
+    ax.set_ylim3d([y_middle - plot_radius, y_middle + plot_radius])
+    ax.set_zlim3d([z_middle - plot_radius, z_middle + plot_radius])
+    try:
+        ax.set_box_aspect([1, 1, 1])
+    except AttributeError:
+        pass
+
+
+def _load_mask(path):
+    """讀取 nifti 二值遮罩 -> (z,y,x) bool；缺檔/讀取失敗/空 -> None。"""
+    if path is None or not os.path.exists(path):
+        return None
+    try:
+        arr = sitk.GetArrayFromImage(sitk.ReadImage(path, sitk.sitkUInt8))
+    except Exception as e:
+        print(f"[warn] 讀取失敗 {path}: {e}")
+        return None
+    m = arr > 0
+    if int(m.sum()) == 0:
+        return None
+    return m
+
+
+def _rgba_block(n, color, a):
+    arr = np.empty((n, 4))
+    arr[:] = to_rgba(color)
+    arr[:, 3] = a
+    return arr
+
+
+# ======================================================================
+# 旋轉對齊（index space）：
+#   1) 最佳鏡稱面 normal -> +X（使鏡稱面平行 x=0）
+#   2) 再繞 X 旋轉，使上終板面 normal 的 y 分量为 0（與 y 無關）
+# 所有向量採 (x, y, z) 順序；array 為 (z, y, x)。
+# ======================================================================
+def _unit(v):
+    v = np.asarray(v, dtype=float)
+    n = np.linalg.norm(v)
+    return v / n if n > 0 else v
+
+
+def _skew(ax):
+    ax = np.asarray(ax, dtype=float)
+    return np.array([[0.0, -ax[2], ax[1]],
+                     [ax[2], 0.0, -ax[0]],
+                     [-ax[1], ax[0], 0.0]])
+
+
+def rotation_from_to(u, v):
+    """3x3 旋轉矩陣，把單位向量 u 映射到單位向量 v（最小角旋转）。"""
+    u = _unit(u)
+    v = _unit(v)
+    c = float(np.clip(np.dot(u, v), -1.0, 1.0))
+    if c > 1.0 - 1e-12:
+        return np.eye(3)
+    if c < -1.0 + 1e-12:            # 反平行：繞任一垂直軸轉 180 度
+        if abs(u[0]) < 0.9:
+            ax = np.cross([1.0, 0.0, 0.0], u)
+        else:
+            ax = np.cross([0.0, 1.0, 0.0], u)
+        ax = ax / np.linalg.norm(ax)
+        K = _skew(ax)
+        return np.eye(3) + 2.0 * (K @ K)
+    ax = np.cross(u, v)
+    s = np.linalg.norm(ax)
+    ax = ax / s
+    K = _skew(ax)
+    ang = np.arccos(c)
+    return np.eye(3) + np.sin(ang) * K + (1.0 - np.cos(ang)) * (K @ K)
+
+
+def rotation_about_x(theta):
+    ct, st = np.cos(theta), np.sin(theta)
+    return np.array([[1.0, 0.0, 0.0],
+                     [0.0, ct, -st],
+                     [0.0, st, ct]])
+
+
+def compute_normalizing_rotation(mask, sym, symp):
+    """回傳 (R, c_xyz)。
+    R：使鏡稱面 normal -> +X、上終板面 normal 的 y 分量 -> 0（z 分量保持 >0）。
+       若 symp 為 None，只做鏡稱面對齊。
+    c_xyz：旋轉中心（array 中心），(x, y, z) 順序。
+    """
+    nz, ny, nx = mask.shape
+    c_xyz = np.array([(nx - 1) / 2.0, (ny - 1) / 2.0, (nz - 1) / 2.0])
+    n_sym = _unit(sym["normal"])
+    R1 = rotation_from_to(n_sym, np.array([1.0, 0.0, 0.0]))
+    if symp is None:
+        return R1, c_xyz
+    n_end = _unit(symp["normal"])
+    w = R1 @ n_end
+    if abs(w[1]) + abs(w[2]) < 1e-12:
+        return R1, c_xyz
+    theta = float(np.arctan2(w[1], w[2]))
+    R2 = rotation_about_x(theta)
+    return R2 @ R1, c_xyz
+
+
+def rotate_volume(arr, R, c_xyz, order=1, cval=0.0):
+    """以 R（作用於 (x,y,z) 向量）在 index space 旋轉 (z,y,x) 體積，
+    繞 c_xyz 中心。用逆向映射 + 多項式插值（order=0 最近邻 / 1 三线性）。"""
+    nz, ny, nx = arr.shape
+    idx = np.indices((nz, ny, nx), dtype=np.float64)
+    xx, yy, zz = idx[2], idx[1], idx[0]
+    V = np.stack([xx, yy, zz], axis=0)                    # (3, nz,ny,nx) = (x,y,z)
+    c = c_xyz[:, None, None, None]
+    W = np.tensordot(R.T, V - c, axes=([1], [0])) + c     # (3, nz,ny,nx) = (in_x,in_y,in_z)
+    return map_coordinates(arr, [W[2], W[1], W[0]], order=order, cval=cval, mode="constant")
+
+
+def rotated_sitk_image(src_image, arr):
+    """以相同幾何（origin/spacing/direction）包裝旋轉後的 array。"""
+    out = sitk.GetImageFromArray(arr)
+    out.CopyInformation(src_image)
+    return out
+
+
+def rotated_grid(box_size_zyx, R, c_xyz, margin=4):
+    """未旋轉（緊密裁切）grid 的 8 角點經 (R, c_xyz) 剛性旋轉（forward
+    dest = R(src - c) + c）後取最小包圍軸對齊盒，外擴 margin。
+    回傳 (start, size)，皆為 (x, y, z) 序、模板 index 系；size 含旋轉
+    擴張，旋轉後整顆骨頭保留、不被裁切（同尺寸旋轉會切掉角落）。"""
+    nz, ny, nx = box_size_zyx
+    c = np.asarray(c_xyz, dtype=np.float64)
+    Rf = np.asarray(R, dtype=np.float64)
+    corners = np.array([[x, y, z]
+                        for x in (0.0, float(nx))
+                        for y in (0.0, float(ny))
+                        for z in (0.0, float(nz))], dtype=np.float64)
+    pts = (corners - c) @ Rf.T + c
+    lo = np.floor(pts.min(axis=0)).astype(int) - int(margin)
+    hi = np.ceil(pts.max(axis=0)).astype(int) + int(margin)
+    return lo, hi - lo + 1
+
+
+def rotate_volume_to(arr, R, c_xyz, start, size, order=1, cval=0.0):
+    """以 R（作用於 (x,y,z)）逆向映射旋轉 (z,y,x) 體積，繞 c_xyz（模板
+    index 系），輸出到指定 grid (start, size)（模板 index 系，(x, y, z)
+    序）；arr 外區域以 cval 填充。回傳 (size_z, size_y, size_x) 陣列。"""
+    sx, sy, sz = (int(v) for v in start)
+    nx, ny, nz = (int(v) for v in size)
+    idx = np.indices((nz, ny, nx), dtype=np.float64)
+    V = np.stack([idx[2] + sx, idx[1] + sy, idx[0] + sz], axis=0)
+    c = np.asarray(c_xyz, dtype=np.float64)[:, None, None, None]
+    Rf = np.asarray(R, dtype=np.float64)
+    W = np.tensordot(Rf.T, V - c, axes=([1], [0])) + c
+    return map_coordinates(arr, [W[2], W[1], W[0]], order=order, cval=cval,
+                           mode="constant")
+
+
+def rotated_sitk_image_at(src_image, arr, start):
+    """包裝 arr（size 可不同於 src_image）：spacing/direction 同 src_image；
+    origin = start（(x, y, z)，src_image index 系）對應的實體座標。"""
+    out = sitk.GetImageFromArray(arr)
+    out.SetSpacing(src_image.GetSpacing())
+    d = src_image.GetDirection()
+    out.SetDirection([d[i * 3 + j] for i in range(3) for j in range(3)])
+    out.SetOrigin(src_image.TransformIndexToPhysicalPoint(
+        (int(start[0]), int(start[1]), int(start[2]))))
+    return out
+
+
+def _shift_plane_params(plane, start):
+    """平面（與模板同原點系，n·x = d）換到陣列原點 = 模板原點 + start 的
+    局部系：x = v + start -> n·v = d - n·start（方向 u, v 不變）。"""
+    n = np.asarray(plane["plane"][:3], dtype=float)
+    d = float(plane["plane"][3]) - float(n @ np.asarray(start, dtype=float))
+    out = dict(plane)
+    out["plane"] = (float(n[0]), float(n[1]), float(n[2]), d)
+    return out
+
+
+def _rotate_plane_params(plane, R, c_xyz):
+    """把平面 (a,b,c,d) 與 in-plane 方向 u,v 一併旋轉；回傳同結構 dict。"""
+    n = np.array(plane["plane"][:3], dtype=float)
+    d = float(plane["plane"][3])
+    n_rot = R @ n
+    d_rot = float(n_rot @ c_xyz) + d - float(n @ c_xyz)
+    u_rot = R @ np.array(plane["u"], dtype=float)
+    v_rot = R @ np.array(plane["v"], dtype=float)
+    out = {
+        "plane": (n_rot[0], n_rot[1], n_rot[2], d_rot),
+        "normal": (n_rot[0], n_rot[1], n_rot[2]),
+        "offset": d_rot,
+        "u": (u_rot[0], u_rot[1], u_rot[2]),
+        "v": (v_rot[0], v_rot[1], v_rot[2]),
+    }
+    for k in ("ratio", "inlier_ratio", "tilt_deg", "theta_deg", "phi_deg"):
+        if k in plane:
+            out[k] = plane[k]
+    return out
+
+
+def render_bone_figure(volume_id, level, binary_path, cortical_path,
+                      base_folder="/mnt/1248/open2/cyrou/Output",
+                      spacing=(0.5, 0.5, 0.5), way="CBT",
+                      planes_only=False, output_path=None, rotation=None):
+    """繪製單一 (volume, level) 骨頭 X-ray 圖（不畫螺絲）。
+
+    四視角：預設/axial/coronal/sagittal。
+    內容：皮質 vs 鬆質吸收骨、椎體(gold)、棘突(purple)、
+          中矢狀鏡稱面(orange)、上終板面(green)。無圓柱/中心線。
+
+    planes_only=True：只畫骨頭 + 中矢狀鏡稱面 + 上終板面，
+                     不做棘突 / 椎體（VBODY）分割。
+    output_path：若給定，直接存到該路徑（含自動加 _1/_2 防覆蓋）；
+                 否則存到 base_folder/{date}/{volume_id}/{volume_id} {level}_{way}.png。
+    rotation：(R, c_xyz)。給定時，把骨頭點雲與兩個平面都依 R 旋轉（繞 c_xyz），
+              用於畫「對齊後（rotated）」的平面圖；R 作用於 (x,y,z) 向量。
+    cortical_path：皮質遮罩路徑，或 (z,y,x) 0/1 陣列（須與 binary_path 同 grid）；
+                  None / 缺檔時全部視為鬆質骨。
+    回傳存檔路徑；無有效骨頭遮罩時回傳 None。
+    """
+    spine = _load_mask(binary_path)
+    if spine is None:
+        print(f"[skip] {volume_id} {level}: 無/空骨頭遮罩 {binary_path}")
+        return None
+
+    if isinstance(cortical_path, np.ndarray):
+        cortical = cortical_path > 0
+    else:
+        cortical = _load_mask(cortical_path)
+    if cortical is None:
+        cortical = np.zeros_like(spine)
+
+    voxel_mm = float(spacing[0])
+    alpha_cortical = 1.0 - np.exp(-BONE_MU_CORTICAL * voxel_mm)
+    alpha_trabecular = 1.0 - np.exp(-BONE_MU_TRABECULAR * voxel_mm)
+
+    # 骨頭 voxel 拆成皮質 / 鬆質兩組（同 res_plt_2_torch）
+    z_corti, y_corti, x_corti = np.where((spine) & (cortical))
+    z_trab, y_trab, x_trab = np.where((spine) & (~cortical))
+
+    # ---- 方向 / 解剖分割 ----
+    sym = best_symmetry_plane(spine)
+    symp = best_upper_endplate_plane(spine)
+
+    if planes_only:
+        # 只做方向平面，不做棘突 / 椎體分割
+        sp_corti = sp_trab = None
+        vb_corti = vb_trab = None
+        sp_info = {}
+        vb_info = {}
+    else:
+        sp_mask, sp_th, sp_info = segment_spinous_process(spine, sym)
+        if sp_mask is not None and sp_mask.any():
+            sp_corti = sp_mask[z_corti, y_corti, x_corti]
+            sp_trab = sp_mask[z_trab, y_trab, x_trab]
+        else:
+            sp_corti = sp_trab = None
+
+        vb_mask, vb_th, vb_info = segment_vertebral_body(spine, sym, symp, sp_th, sp_info["mode"])
+        if vb_mask is not None and vb_mask.any():
+            vb_corti = vb_mask[z_corti, y_corti, x_corti]
+            vb_trab = vb_mask[z_trab, y_trab, x_trab]
+        else:
+            vb_corti = vb_trab = None
+
+    # ---- 骨頭點雲（體積吸收）----
+    x_bone = np.concatenate([x_corti, x_trab])
+    y_bone = np.concatenate([y_corti, y_trab])
+    z_bone = np.concatenate([z_corti, z_trab])
+    bone_rgba = np.concatenate([
+        _rgba_block(len(x_corti), "lightblue", float(alpha_cortical)),
+        _rgba_block(len(x_trab), "lightblue", float(alpha_trabecular)),
+    ])
+    bone_size = np.full(len(x_bone), BONE_MARKER_SIZE)
+
+    if BONE_SUBSAMPLE > 1:
+        x_bone = x_bone[::BONE_SUBSAMPLE]
+        y_bone = y_bone[::BONE_SUBSAMPLE]
+        z_bone = z_bone[::BONE_SUBSAMPLE]
+        bone_rgba = bone_rgba[::BONE_SUBSAMPLE]
+        bone_size = bone_size[::BONE_SUBSAMPLE]
+
+    if vb_corti is not None:
+        vb_flag = np.concatenate([vb_corti, vb_trab])
+        if BONE_SUBSAMPLE > 1:
+            vb_flag = vb_flag[::BONE_SUBSAMPLE]
+        bone_rgba[vb_flag] = to_rgba("gold", 0.95)
+    if sp_corti is not None:
+        sp_flag = np.concatenate([sp_corti, sp_trab])
+        if BONE_SUBSAMPLE > 1:
+            sp_flag = sp_flag[::BONE_SUBSAMPLE]
+        bone_rgba[sp_flag] = to_rgba("purple", 0.95)
+
+    # ---- 旋轉對齊（若給定）：骨頭點雲與平面同旋轉 ----
+    if rotation is not None:
+        R, c_xyz = rotation
+        P = np.stack([x_bone - c_xyz[0], y_bone - c_xyz[1], z_bone - c_xyz[2]], axis=0)
+        P = R @ P
+        x_bone = P[0] + c_xyz[0]
+        y_bone = P[1] + c_xyz[1]
+        z_bone = P[2] + c_xyz[2]
+        sym = _rotate_plane_params(sym, R, c_xyz)
+        if symp is not None:
+            symp = _rotate_plane_params(symp, R, c_xyz)
+
+    # ---- 中矢狀（鏡稱）平面 ----
+    _a, _b, _c, _d = sym["plane"]
+    _n = np.array([_a, _b, _c])
+    _u = np.array(sym["u"])
+    _v = np.array(sym["v"])
+    _p0 = _d * _n
+    xyz_bone = np.stack([x_bone - _p0[0], y_bone - _p0[1], z_bone - _p0[2]], axis=1)
+    _pu = xyz_bone @ _u
+    _pv = xyz_bone @ _v
+    _U_, _V_ = np.meshgrid(np.linspace(_pu.min(), _pu.max(), 8),
+                           np.linspace(_pv.min(), _pv.max(), 8))
+    _Xp = _p0[0] + _U_ * _u[0] + _V_ * _v[0]
+    _Yp = _p0[1] + _U_ * _u[1] + _V_ * _v[1]
+    _Zp = _p0[2] + _U_ * _u[2] + _V_ * _v[2]
+
+    # ---- 上終板平面 ----
+    _EX = _EY = _EZ = None
+    if symp is not None:
+        _ea, _eb, _ec, _ed = symp["plane"]
+        _en = np.array([_ea, _eb, _ec])
+        _eu = np.array(symp["u"])
+        _ev = np.array(symp["v"])
+        _ep0 = _ed * _en
+        xz_ep = np.stack([x_bone - _ep0[0], y_bone - _ep0[1], z_bone - _ep0[2]], axis=1)
+        _pu_ep = xz_ep @ _eu
+        _pv_ep = xz_ep @ _ev
+        _EU, _EV = np.meshgrid(np.linspace(_pu_ep.min(), _pu_ep.max(), 8),
+                               np.linspace(_pv_ep.min(), _pv_ep.max(), 8))
+        _EX = _ep0[0] + _EU * _eu[0] + _EV * _ev[0]
+        _EY = _ep0[1] + _EU * _eu[1] + _EV * _ev[1]
+        _EZ = _ep0[2] + _EU * _eu[2] + _EV * _ev[2]
+
+    # ---- 圖 ----
+    fig = plt.figure(figsize=(12, 12))
+
+    legend_handles = []
+    if vb_corti is not None:
+        legend_handles.append(Line2D([], [], marker="o", ls="", ms=6, color="gold", label="VertebralBody"))
+    if sp_corti is not None:
+        legend_handles.append(Line2D([], [], marker="o", ls="", ms=6, color="purple", label="Spinous"))
+
+    def _fill_ax(ax):
+        ax.computed_zorder = False
+        sc_bone = ax.scatter(x_bone, y_bone, z_bone, c=bone_rgba, s=bone_size, marker="o")
+        sc_bone.set_zorder(5)
+        plane = ax.plot_surface(_Xp, _Yp, _Zp, color="orange", alpha=0.30,
+                                linewidth=1.0, edgecolor="orange", rstride=1, cstride=1)
+        plane.set_zorder(8)
+        if _EX is not None:
+            ep = ax.plot_surface(_EX, _EY, _EZ, color="green", alpha=0.35,
+                                 linewidth=1.0, edgecolor="green", rstride=1, cstride=1)
+            ep.set_zorder(7)
+
+    ax1 = fig.add_subplot(221, projection="3d")
+    _fill_ax(ax1)
+    ax1.set_xlabel("X-axis"); ax1.set_ylabel("Y-axis"); ax1.set_zlabel("Z-axis")
+    set_axes_equal_3d(ax1)
+
+    ax2 = fig.add_subplot(222, projection="3d")
+    ax2.view_init(elev=90, azim=-90, roll=0)
+    _fill_ax(ax2)
+    ax2.set_xlabel("X-axis"); ax2.set_ylabel("Y-axis"); ax2.set_zlabel("Z-axis")
+    set_axes_equal_3d(ax2)
+    if legend_handles:
+        ax2.legend(handles=legend_handles)
+
+    ax3 = fig.add_subplot(223, projection="3d")
+    ax3.view_init(elev=0, azim=90, roll=0)
+    _fill_ax(ax3)
+    ax3.set_xlabel("X-axis"); ax3.set_ylabel("Y-axis"); ax3.set_zlabel("Z-axis")
+    set_axes_equal_3d(ax3)
+
+    ax4 = fig.add_subplot(224, projection="3d")
+    ax4.view_init(elev=0, azim=0, roll=0)
+    _fill_ax(ax4)
+    ax4.set_xlabel("X-axis"); ax4.set_ylabel("Y-axis"); ax4.set_zlabel("Z-axis")
+    set_axes_equal_3d(ax4)
+
+    label_str = f"{volume_id} {level}"
+    base_tag = "planes only" if planes_only else "no screws"
+    if rotation is not None:
+        base_tag += ", rotated"
+    fig.text(0.5, 0.98, f"{label_str}  ({base_tag})", ha="center", fontsize=15)
+
+    ratio = float(sym.get("ratio", float("nan")))
+    if planes_only:
+        ep_ratio = float(symp.get("inlier_ratio", float("nan"))) if symp is not None else float("nan")
+        info = (f"sym_ratio={ratio:.3f}   "
+                f"endplane_ratio={ep_ratio:.3f}   "
+                f"endplate={'yes' if symp is not None else 'no'}")
+    else:
+        info = (f"sym_ratio={ratio:.3f}   "
+                f"spinous={sp_info.get('n_sp', 0)} ({sp_info.get('mode', '?')})   "
+                f"vertebral_body={vb_info.get('n_vb', 0)} ({vb_info.get('mode', '?')})")
+    fig.text(0.5, 0.03, info, ha="center", fontsize=8)
+
+    fig.tight_layout()
+
+    if output_path is not None:
+        path = get_unique_filepath(output_path)
+    else:
+        date_str = datetime.now().strftime("%Y%m%d")
+        output_folder = os.path.join(base_folder, date_str, volume_id)
+        output_file = os.path.join(output_folder, f"{volume_id} {level}_{way}.png")
+        path = get_unique_filepath(output_file)
+    os.makedirs(os.path.dirname(path) or ".", exist_ok=True)
+    fig.savefig(path, dpi=200, bbox_inches="tight")
+    plt.close(fig)
+    return path

visualization/res_plot_3d.py

@@ -5,6 +5,8 @@ from matplotlib.colors import to_rgba
 from matplotlib.lines import Line2D
 from mpl_toolkits.mplot3d.art3d import Poly3DCollection
 import os
+import errno
+import time
 from datetime import datetime
 import csv
 
@@ -13,7 +15,7 @@ from core.intersection import center_line_intersections_torch
 from core.scoring import cl_score_torch, compute_overlap_ratio_from_cylinder_mask, cl_score_torch_xfr
 from imaging.orientation import (azimuth_rotation, analyze_vertebral_tilt_contour,
                                   best_symmetry_plane, best_upper_endplate_plane,
-                                  segment_spinous_process)
+                                  segment_spinous_process, segment_vertebral_body)
 from utils.helpers import save_with_unique_name
 
 # Volume absorption 渲染（Beer-Lambert）：每 voxel 不透明度 = 1 - exp(-mu * voxel_width)
@@ -25,6 +27,17 @@ BONE_MU_TRABECULAR = 0.005 # 1/mm  → 每 voxel = 1-exp(-0.005*0.5) ~ 0.0025
 BONE_MARKER_SIZE = 3.0     # 骨骼散點點面積 (pt^2)；略大以補償抽稀後的顆粒感
 BONE_SUBSAMPLE = 1         # 每 10 個骨 voxel 畫 1 個，降低堆疊不透明度（1=全畫）
 
+def _retry_robust(fn, *args, retries=20, delay=0.5, **kwargs):
+    """對 ENOENT/EEXIST 重試：NFS 上輸出樹被外部刪除（或多 worker 併發建同一
+    output 目錄）會有短暫的 ENOENT 窗口，重試可恢復；其他錯誤直接丟出。"""
+    for i in range(retries):
+        try:
+            return fn(*args, **kwargs)
+        except OSError as e:
+            if e.errno not in (errno.ENOENT, errno.EEXIST) or i == retries - 1:
+                raise
+            time.sleep(delay)
+
 def set_axes_equal_3d(ax):
     """
     Make axes of 3D plot have equal scale so that spheres appear as spheres,
@@ -156,11 +169,15 @@ def res_plt_2_torch(
         device
     )
     # loss_r = cl_score_torch(cortical_tensor, spine_tensor, cyl_r, cyl_ro, intersections_r)
-    loss_r = cl_score_torch_xfr(cortical_tensor, spine_tensor, cyl_r, cyl_ro, intersections_r)
+    # loss_r 放在下方 VBODY mask 計算之後：計入與 PSO 目標函數相同的 VBODY voxel 獎勵
 
-    azi = azimuth_rotation(image2_path)
+    if CBT:
-    res = analyze_vertebral_tilt_contour(image2_path, edge_type='superior', show_plot=False, debug=False)
+        azi = float('nan')
-    alt = res['superior']['tilt_angle_deg']
+        alt = float('nan')
+    else:
+        azi = azimuth_rotation(image2_path)
+        res = analyze_vertebral_tilt_contour(image2_path, edge_type='superior', show_plot=False, debug=False)
+        alt = res['superior']['tilt_angle_deg']
 
     # Move data to CPU for plotting
     line_mask_l_cpu = line_mask_l.cpu().numpy()
@@ -191,8 +208,16 @@ def res_plt_2_torch(
     sym = best_symmetry_plane(spine_cpu)
 
     # 棘突：鏡稱面中線帶（|s|<=w）且在 AP 谷底之後側的骨 voxel，換不同顏色標示
+    # 棘突缺如（先前 laminectomy / 棘突切除）時 sp_mask=None，不標示。
     sp_mask, sp_th, sp_info = segment_spinous_process(spine_cpu, sym)
-    if sp_mask is not None and sp_mask.any():
+    if sp_info['mode'] == 'no_spinous':
+        top_off = f"{sp_info['top_off']:.1f}" if sp_info.get('top_off') is not None else 'n/a'
+        print(f"[NO-SP] 中線後側缺如（先前 laminectomy / 棘突切除）: "
+              f"deficit={sp_info['deficit']:.1f} voxel ({sp_info['deficit'] * 0.5:.1f} mm), "
+              f"rear3={sp_info['rear3']} voxel, top_off={top_off} voxel "
+              f"-> 不標示棘突；椎體用放寬後側谷底切分")
+        sp_corti = sp_trab = None
+    elif sp_mask is not None and sp_mask.any():
         sp_corti = sp_mask[z_corti, y_corti, x_corti]
         sp_trab = sp_mask[z_trab, y_trab, x_trab]
         sp_n_bone = max(int(spine_cpu.sum()), 1)
@@ -203,6 +228,34 @@ def res_plt_2_torch(
     else:
         sp_corti = sp_trab = None
 
+    # 上終板平面：RANSAC 擬合骨頭頂面（前側）的最佳 a·x + b·y + c·z = d
+    symp = best_upper_endplate_plane(spine_cpu)
+
+    # 椎體：上終板之下（排除跨終板的後側構造）且中線 AP 谷底之前側的骨 voxel，
+    # 換不同顏色標示（見 segment_vertebral_body；谷底優先取中線帶，
+    # 中線搜尋 fallback 時退回終板下整體 AP 分佈谷底）
+    vb_mask, vb_th, vb_info = segment_vertebral_body(spine_cpu, sym, symp,
+                                                     sp_th, sp_info['mode'])
+    if vb_mask is not None and vb_mask.any():
+        vb_corti = vb_mask[z_corti, y_corti, x_corti]
+        vb_trab = vb_mask[z_trab, y_trab, x_trab]
+        print(f"[VBODY] n={vb_info['n_vb']} "
+              f"({100.0 * vb_info['n_vb'] / max(int(spine_cpu.sum()), 1):.1f}% of bone) "
+              f"AP<{vb_info['ap_thresh']:.1f} mode={vb_info['mode']}")
+        if vb_info['mode'] == 'quantile':
+            print(f"[VBODY] WARNING: 未找到體/弓後側谷底，閾值退回 55 百分位 "
+                  f"（可能切進椎體內），建議人工核對該 level 的椎體邊界")
+    else:
+        vb_corti = vb_trab = None
+        print(f"[VBODY] skipped: {vb_info['mode']}")
+
+    # loss_r 使用與 PSO 目標函數相同的 VBODY 獎勵（回報分數與優化一致）
+    vbody_tensor = None
+    if vb_mask is not None and vb_mask.any():
+        vbody_tensor = torch.from_numpy(vb_mask.astype(np.uint8)).to(device=device)
+    loss_r = cl_score_torch_xfr(cortical_tensor, spine_tensor, cyl_r, cyl_ro, intersections_r,
+                                vbody_tensor=vbody_tensor)
+
     # X-ray 外觀：骨頭合成一個半透明體積吸收點雲（下方）；
     # 螺絲（中心線 + 圓柱 + 入口軌跡延长）合成一個全不透明點雲，永遠畫在骨頭之上
     def _rgba_block(n, color, a):
@@ -227,11 +280,41 @@ def res_plt_2_torch(
         z_bone = z_bone[::BONE_SUBSAMPLE]
         bone_rgba = bone_rgba[::BONE_SUBSAMPLE]
         bone_size = bone_size[::BONE_SUBSAMPLE]
-    if sp_corti is not None:
+    # 平面 patch 的範圍用「完整骨頭」（含 VBODY / SP）算：
-        sp_flag = np.concatenate([sp_corti, sp_trab])
+    # VBODY 前側是整顆骨最前緣，剔除後綠色終板 patch 會縮小
+    x_bone_all, y_bone_all, z_bone_all = x_bone, y_bone, z_bone
+    # VBODY / 棘突拆成獨立上層（在 _fill_ax 內畫）：
+    # 繪製順序 基底骨(5) < VBODY gold(6) < SP purple(6.5) < 終板(7) < 鏡稱面(8) < 螺絲(10)
+    # axial 視角（ax3）相機在 +y 前側，椎體 physically 擋在棘突與相機之間，
+    # 棘突最後畫 -> 紫色不被 gold 遮住
+    vb_flag = np.zeros(x_bone.shape, dtype=bool)
+    sp_flag = np.zeros(x_bone.shape, dtype=bool)
+    if vb_corti is not None:
+        f = np.concatenate([vb_corti, vb_trab]).astype(bool)
         if BONE_SUBSAMPLE > 1:
-            sp_flag = sp_flag[::BONE_SUBSAMPLE]
+            f = f[::BONE_SUBSAMPLE]
-        bone_rgba[sp_flag] = to_rgba('purple', 0.95)
+        vb_flag |= f
+    if sp_corti is not None:
+        f = np.concatenate([sp_corti, sp_trab]).astype(bool)
+        if BONE_SUBSAMPLE > 1:
+            f = f[::BONE_SUBSAMPLE]
+        sp_flag |= f
+
+    vbody_pts = None
+    vbody_mask = vb_flag & ~sp_flag
+    if vbody_mask.any():
+        vbody_pts = (x_bone[vbody_mask], y_bone[vbody_mask], z_bone[vbody_mask])
+    sp_pts = None
+    if sp_flag.any():
+        sp_pts = (x_bone[sp_flag], y_bone[sp_flag], z_bone[sp_flag])
+
+    # 基底骨層去掉 VBODY / SP voxel（由上面的專屬圖層畫）
+    base_mask = ~(vb_flag | sp_flag)
+    x_bone = x_bone[base_mask]
+    y_bone = y_bone[base_mask]
+    z_bone = z_bone[base_mask]
+    bone_rgba = bone_rgba[base_mask]
+    bone_size = bone_size[base_mask]
 
     x_screw = np.concatenate([x_lin1, x_lin2, x_cyl_l1, x_cyl_l2, x_cyl_r1, x_cyl_r2])
     y_screw = np.concatenate([y_lin1, y_lin2, y_cyl_l1, y_cyl_l2, y_cyl_r1, y_cyl_r2])
@@ -242,7 +325,7 @@ def res_plt_2_torch(
     _u = np.array(sym['u'])
     _v = np.array(sym['v'])
     _p0 = _d * _n                                # 平面上最接近原點的點
-    xyz_bone = np.stack([x_bone - _p0[0], y_bone - _p0[1], z_bone - _p0[2]], axis=1)
+    xyz_bone = np.stack([x_bone_all - _p0[0], y_bone_all - _p0[1], z_bone_all - _p0[2]], axis=1)
     _pu = xyz_bone @ _u
     _pv = xyz_bone @ _v
     _U_, _V_ = np.meshgrid(np.linspace(_pu.min(), _pu.max(), 8),
@@ -251,8 +334,6 @@ def res_plt_2_torch(
     _Yp = _p0[1] + _U_ * _u[1] + _V_ * _v[1]
     _Zp = _p0[2] + _U_ * _u[2] + _V_ * _v[2]
 
-    # 上終板平面：RANSAC 擬合骨頭頂面（前側）的最佳 a·x + b·y + c·z = d
-    symp = best_upper_endplate_plane(spine_cpu)
     _EX = _EY = _EZ = None
     if symp is not None:
         _ea, _eb, _ec, _ed = symp['plane']
@@ -260,7 +341,7 @@ def res_plt_2_torch(
         _eu = np.array(symp['u'])
         _ev = np.array(symp['v'])
         _ep0 = _ed * _en
-        xz_ep = np.stack([x_bone - _ep0[0], y_bone - _ep0[1], z_bone - _ep0[2]], axis=1)
+        xz_ep = np.stack([x_bone_all - _ep0[0], y_bone_all - _ep0[1], z_bone_all - _ep0[2]], axis=1)
         _pu_ep = xz_ep @ _eu
         _pv_ep = xz_ep @ _ev
         _EU, _EV = np.meshgrid(np.linspace(_pu_ep.min(), _pu_ep.max(), 8),
@@ -284,32 +365,32 @@ def res_plt_2_torch(
 
     fig = plt.figure(figsize=(12, 12))
 
-    # 圖例色塊提高到可讀不透明度（實際渲染仍用真實吸收 alpha）
-    _leg_alpha_c = max(float(alpha_cortical), 0.35)
-    _leg_alpha_t = max(float(alpha_trabecular), 0.2)
     legend_handles = [
-        Line2D([], [], marker='o', ls='', ms=5, color=to_rgba('lightblue', _leg_alpha_c), label='Spine (cortical)'),
-        Line2D([], [], marker='o', ls='', ms=5, color=to_rgba('lightblue', _leg_alpha_t), label='Spine (trabecular)'),
-        Line2D([], [], marker='o', ls='', ms=2, color='r', label='Centerline'),
         Line2D([], [], marker='o', ls='', ms=6, color='darkcyan', label='Cylinder(L)'),
         Line2D([], [], marker='o', ls='', ms=6, color='blue', label='Cylinder(R)'),
-        Line2D([], [], marker='o', ls='', ms=6, color='pink', label='Entry track (outer)'),
-Line2D([], [], color='orange', lw=2, alpha=0.6,
-        label=f"Mirror plane {sym['plane'][0]:+.2f}x {sym['plane'][1]:+.2f}y {sym['plane'][2]:+.2f}z = {sym['plane'][3]:.1f}"),
     ]
+    if vb_corti is not None:
+        legend_handles.append(
+            Line2D([], [], marker='o', ls='', ms=6, color='gold', label='VertebralBody'))
     if sp_corti is not None:
-        legend_handles.append(Line2D([], [], marker='o', ls='', ms=6, color='purple',
+        legend_handles.append(
-                              label=f"Spinous process (mirror-plane midline, {sp_info['n_sp']} vox)"))
+            Line2D([], [], marker='o', ls='', ms=6, color='purple', label='SpinousProcess'))
-    if symp is not None:
-        legend_handles.append(Line2D([], [], color='green', lw=2, alpha=0.7,
-                              label=f"Upper endplate plane tilt {symp['tilt_deg']:.1f} deg"))
 
     def _fill_ax(ax):
         # X-ray 外觀：關閉 mplot3d 依深度自動排序 zorder（否則半透明骨頭會被重繪到
-        # 螺絲上方）；改為固定分層：吸收骨頭 zorder=5，全不透明螺絲 zorder=10
+        # 螺絲上方）；改為固定分層：
+        # 基底骨 zorder=5 < VBODY 6 < SP 6.5 < 終板 7 < 鏡稱面 8 < 螺絲 10
         ax.computed_zorder = False
         sc_bone = ax.scatter(x_bone, y_bone, z_bone, c=bone_rgba, s=bone_size, marker='o')
         sc_bone.set_zorder(5)
+        if vbody_pts is not None:
+            sc_vb = ax.scatter(vbody_pts[0], vbody_pts[1], vbody_pts[2],
+                               c=to_rgba('gold', 0.95), s=BONE_MARKER_SIZE, marker='o')
+            sc_vb.set_zorder(6)
+        if sp_pts is not None:
+            sc_sp = ax.scatter(sp_pts[0], sp_pts[1], sp_pts[2],
+                               c=to_rgba('purple', 0.95), s=BONE_MARKER_SIZE, marker='o')
+            sc_sp.set_zorder(6.5)
         sc_screw = ax.scatter(x_screw, y_screw, z_screw, c=screw_rgba, s=screw_size, marker='o')
         sc_screw.set_zorder(10)
         # 中矢狀面（理論左右對稱切分面）：半透明橘色平面 x = x_mid
@@ -366,28 +447,90 @@ Line2D([], [], color='orange', lw=2, alpha=0.6,
     user_azimuth_l = 90 - best_position_l[3] - azi
     user_azimuth_r = 90 - best_position_r[3] - azi
 
+    # 螺絲方向向量（與 generate_cylinder_n_torch 同慣例）：
+    # d = (cos(az)·sin(alt), sin(az)·sin(alt), cos(alt))，alt = 相对 +z 的極角
+    # Azimuth 相对鏡稱面（法線 s，theta_v = atan2(sy, sx)）：
+    #   Azimuth_Lateral = az - theta_v - 90 （面內 AP 軸起的帶號發散角，+ = L 側往外，− = R 側）
+    # Altitude 相對上終板面（法線 e，朝上）：
+    #   Altitude_Cephalad_Endplate = 90 - (d 與 e 的夾角)
+    sym_n = np.asarray(sym['normal'], dtype=float)
+    theta_v = float(np.degrees(np.arctan2(sym_n[1], sym_n[0])))
+    if symp is not None:
+        e_n = np.asarray(symp['normal'], dtype=float)
+        e_n = e_n / np.linalg.norm(e_n)
+        tau_y = float(np.degrees(np.arctan2(e_n[1], e_n[2])))
+        tau_x = float(np.degrees(np.arctan2(e_n[0], e_n[2])))
+    else:
+        e_n = None
+        tau_y = float('nan')
+        tau_x = float('nan')
+
+    def _rel_angles(az_deg, alt_deg):
+        az_r = np.radians(az_deg)
+        alt_r = np.radians(alt_deg)
+        d_v = np.array([np.cos(az_r) * np.sin(alt_r),
+                        np.sin(az_r) * np.sin(alt_r),
+                        np.cos(alt_r)])
+        az_lateral = az_deg - theta_v - 90.0
+        if e_n is not None:
+            ang_norm = float(np.degrees(np.arccos(np.clip(d_v @ e_n, -1.0, 1.0))))
+            alt_cep = 90.0 - ang_norm
+        else:
+            alt_cep = float('nan')
+        return az_lateral, alt_cep
+
+    azlat_l, acep_l = _rel_angles(best_position_l[3], best_position_l[4])
+    azlat_r, acep_r = _rel_angles(best_position_r[3], best_position_r[4])
+
     date_str = datetime.now().strftime("%Y%m%d")
-    patient_id = os.path.basename(os.path.dirname(image2_path))
+    # 旋轉後影像存在 <volume_id>/rotated/ 下：parent 是 'rotated'，
+    # 再上一層才是 volume id（未旋轉路徑不受影響）
+    img_parent = os.path.dirname(image2_path)
+    patient_id = os.path.basename(os.path.dirname(img_parent)) \
+        if os.path.basename(img_parent) == 'rotated' else os.path.basename(img_parent)
     output_folder = os.path.join(base_folder, date_str, patient_id)
-    os.makedirs(output_folder, exist_ok=True)
+    _retry_robust(os.makedirs, output_folder, exist_ok=True)
     csv_path = os.path.join(output_folder, 'output.csv')
     
-    # 檢查檔案是否存在 (決定是否寫入標題)
+    # 欄位標題 (Header)。CBT 模式下恆為 nan 的 2D 參考欄
-    file_exists = os.path.isfile(csv_path)
+    # (Azimuth_Diff / Altitude_Diff / User_Azimuth / User_Altitude) 不寫入 CSV。
-
-    # 欄位標題 (Header)
     headers = [
-        'Label', 'Side', 'Diameter', 'Length', 'Swarm_Size', 'Max_Iter', 
+        'Label', 'Side', 'Diameter', 'Length', 'Swarm_Size', 'Max_Iter',
-        'Position_XYZ', 'Raw_Azimuth', 'Azimuth_Diff', 'Raw_Altitude', 'Altitude_Diff',
+        'Position_XYZ', 'Raw_Azimuth', 'Raw_Altitude',
-        'Intersections', 'Best_Loss', 'cyl_points', 'Overlap_Cortical', 'Overlap_Bone', 
+        'Intersections', 'Best_Loss', 'cyl_points', 'Overlap_Cortical', 'Overlap_Bone',
-        'Cortical_Bone_Ratio', 'User_Azimuth', 'User_Altitude', 'Total_Time'
+        'Cortical_Bone_Ratio',
+        'Sym_Theta_v_deg', 'Endplate_Tau_y_deg', 'Endplate_Tau_x_deg',
+        'Azimuth_Lateral_deg',
+        'Altitude_Cephalad_Endplate_deg',
+        'Total_Time'
     ]
 
+    def _fmt(v):
+        return '' if not np.isfinite(v) else f"{float(v):.2f}"
+
+    # 檢查檔案是否存在 (決定是否寫入標題)；舊 schema 的檔案按欄位名稱重映射後
+    # 改以新 Header 重寫（舊檔多出的欄位捨去、缺的欄位補空白），避免 append 欄位錯位
+    file_exists = os.path.isfile(csv_path)
+    if file_exists:
+        with _retry_robust(open, csv_path, newline='') as f:
+            old_rows = [row for row in csv.reader(f) if any(c.strip() for c in row)]
+        if not old_rows or old_rows[0] != headers:
+            old_h = old_rows[0] if old_rows else None
+            with _retry_robust(open, csv_path, 'w', newline='') as f:
+                w = csv.writer(f)
+                w.writerow(headers)
+                for r in (old_rows[1:] if old_rows else []):
+                    if old_h:
+                        d = dict(zip(old_h, r))
+                        w.writerow([d.get(h, '') for h in headers])
+                    else:
+                        w.writerow(r + [''] * max(0, len(headers) - len(r)))
+
     try:
-        with open(csv_path, 'a', newline='') as csvfile:
+        with _retry_robust(open, csv_path, 'a', newline='') as csvfile:
             writer = csv.writer(csvfile)
-            
+
-            # 如果是新檔案，寫入 Header
+            # 新檔案寫入 Header
             if not file_exists:
                 writer.writerow(headers)
 
@@ -402,17 +545,18 @@ Line2D([], [], color='orange', lw=2, alpha=0.6,
                 # f"({best_position_l[0]:.2f}, {best_position_l[1]:.2f}, {best_position_l[2]:.2f})",
                 f"({best_position_l[2]:.2f}, {best_position_l[1]:.2f}, {best_position_l[0]:.2f})",
                 f"{best_position_l[3]:.2f}",
-                f"{best_position_l[3]-azi:.2f}",
                 f"{best_position_l[4]:.2f}",
-                f"{best_position_l[4]-alt:.2f}",
                 intersections_l,
                 f"{loss_l:.2f}",
                 cyl_points_l,
                 f"{overlap_cortical_l:.2f}",
                 f"{overlap_vertebral_l:.2f}",
                 f"{(overlap_cortical_l/overlap_vertebral_l if overlap_vertebral_l!=0 else 0):.2f}",
-                f"{user_azimuth_l:.2f}",
+                _fmt(theta_v),
-                f"{user_altitude_l:.2f}",
+                _fmt(tau_y),
+                _fmt(tau_x),
+                _fmt(azlat_l),
+                _fmt(acep_l),
                 f"{total_time:.2f}"
             ])
             
@@ -427,17 +571,18 @@ Line2D([], [], color='orange', lw=2, alpha=0.6,
                 # f"({best_position_r[0]:.2f}, {best_position_r[1]:.2f}, {best_position_r[2]:.2f})",
                 f"({best_position_r[2]:.2f}, {best_position_r[1]:.2f}, {best_position_r[0]:.2f})",
                 f"{best_position_r[3]:.2f}",
-                f"{best_position_r[3]-azi:.2f}",
                 f"{best_position_r[4]:.2f}",
-                f"{best_position_r[4]-alt:.2f}",
                 intersections_r,
                 f"{loss_r:.2f}",
                 cyl_points_r,
                 f"{overlap_cortical_r:.2f}",
                 f"{overlap_vertebral_r:.2f}",
                 f"{(overlap_cortical_r/overlap_vertebral_r if overlap_vertebral_r!=0 else 0):.2f}",
-                f"{user_azimuth_r:.2f}",
+                _fmt(theta_v),
-                f"{user_altitude_r:.2f}",
+                _fmt(tau_y),
+                _fmt(tau_x),
+                _fmt(azlat_r),
+                _fmt(acep_r),
                 f"{total_time:.2f}"
             ])
         print(f"[CSV Saved] {csv_path}")
@@ -453,21 +598,41 @@ Line2D([], [], color='orange', lw=2, alpha=0.6,
         f'Swarm size = {swarm_size}, Iteration = {max_iter}, Total time = {total_time:.2f} s',
         ha='center', fontsize=12
     )
+
+    # 角度註記：CBT 沒有 2D 參考面（user az/alt 為 nan），Azimuth/Altitude 直接顯示
+    # 最佳化出的原始角（＝CSV 的 Raw_Azimuth / Raw_Altitude）；TPS 沿用 2D 參考之相對角。
+    # 另補上相對骨骼的角度（與 CSV 同參數）：
+    #   Azimuth_Lateral  = 螺絲在鏡稱面內相對 AP 軸的發散角（+ = L 側往外，− = R 側）
+    #   Altitude_Endplate = 螺絲相對上終板面的仰角
+    # 終板面擬合失敗（nan）時該段自動略過。
+    def _fig_angle_segs(az, alt, azlat, acep):
+        segs = [f'Azimuth = {az:.2f}', f'Altitude = {alt:.2f}']
+        if np.isfinite(azlat):
+            segs.append(f'Azimuth_Lateral = {azlat:.2f}')
+        if np.isfinite(acep):
+            segs.append(f'Altitude_Endplate = {acep:.2f}')
+        return ', '.join(segs)
+
+    if CBT:
+        _ang_l = _fig_angle_segs(float(best_position_l[3]), float(best_position_l[4]), azlat_l, acep_l)
+        _ang_r = _fig_angle_segs(float(best_position_r[3]), float(best_position_r[4]), azlat_r, acep_r)
+    else:
+        _ang_l = _fig_angle_segs(user_azimuth_l, user_altitude_l, azlat_l, acep_l)
+        _ang_r = _fig_angle_segs(user_azimuth_r, user_altitude_r, azlat_r, acep_r)
+
     fig.text(
         0.5, 0.03,
-        # f'Left : Position = ({best_position_l[0]:.2f}, {best_position_l[1]:.2f}, {best_position_l[2]:.2f}), '
         f'Left : Position = ({best_position_l[2]:.2f}, {best_position_l[1]:.2f}, {best_position_l[0]:.2f}), '
-        f'Azimuth = {user_azimuth_l:.2f}, Altitude = {user_altitude_l:.2f}, '
+        f'{_ang_l}, '
         f'Intersection = {intersections_l}, Score = {overlap_cortical_l:.2f} / {overlap_vertebral_l:.2f} / {cb_ratio_l:.2f}',
-        ha='center', fontsize=9
+        ha='center', fontsize=8
     )
     fig.text(
         0.5, 0.01,
-        # f'Right : Position = ({best_position_r[0]:.2f}, {best_position_r[1]:.2f}, {best_position_r[2]:.2f}), '
         f'Right : Position = ({best_position_r[2]:.2f}, {best_position_r[1]:.2f}, {best_position_r[0]:.2f}), '
-        f'Azimuth = {user_azimuth_r:.2f}, Altitude = {user_altitude_r:.2f}, '
+        f'{_ang_r}, '
         f'Intersection = {intersections_r}, Score = {overlap_cortical_r:.2f} / {overlap_vertebral_r:.2f} / {cb_ratio_r:.2f}',
-        ha='center', fontsize=9
+        ha='center', fontsize=8
     )
 
     fig.tight_layout()
@@ -476,7 +641,6 @@ Line2D([], [], color='orange', lw=2, alpha=0.6,
     file_name = os.path.basename(image2_path) 
     level = file_name.split('_')[0]
     output_folder = os.path.join(base_folder, date_str, patient_id)
-    os.makedirs(output_folder, exist_ok=True)
 
     if CBT == True:
         way = 'CBT'
@@ -484,11 +648,18 @@ Line2D([], [], color='orange', lw=2, alpha=0.6,
     else:
         way = 'TPS'
 
-    path = save_with_unique_name(output_folder, label_str, way,
+    # 建目錄 + 存檔一起重試：輸出樹被外部刪除（NFS 刪除競態）時，重試會重建目錄
-                                 diameter_l, length_l, diameter_r, length_r,
+    path = None
-                                 swarm_size, max_iter)
+    def _save_fig_once():
+        nonlocal path
+        _retry_robust(os.makedirs, output_folder, exist_ok=True)
+        # 檔名只用 level（volume id 已在資料夾名裡，不重複）
+        path = save_with_unique_name(output_folder, level, way,
+                                     diameter_l, length_l, diameter_r, length_r,
+                                     swarm_size, max_iter)
+        fig.savefig(path, dpi=200, bbox_inches="tight")
 
-    fig.savefig(path, dpi=200, bbox_inches="tight")
+    _retry_robust(_save_fig_once)
     print("[Saved figure]", path)
     plt.close(fig)
 

xfr_check_spinous.py

@@ -0,0 +1,310 @@
+#!/home/xfr/.conda/envs/cbt/bin/python
+"""
+檢查各 (volume, level) 的棘突（midline 後側構造）是否缺如
+（先前手術如 laminectomy / 棘突切除，例：0005 L5、0770 L5）。
+
+判定原理（見 imaging.orientation.diagnose_spinous_process）：
+  棘突完整時，尖端是全椎體最後側的骨且位於中線 →
+    deficit（全骨最後側 - 中線帶最後側）≈ 0，後側中線窄帶有骨。
+  切除後，最後側骨偏到側方殘餘、後側中線空洞 → deficit 大 + rear3 ≈ 0。
+  no_spinous = deficit >= 4 vox 且 rear3 <= 20 vox（正常 level deficit 恒為 0）。
+
+兩種模式：
+  quick（預設，掃全資料集用）→ 兩段式：
+    stage 1：axial 投影快速篩檢（~0.5s/level）。用「寬行（椎體行）」擬合
+          中線軌跡（對傾斜/旋轉穩健，不受後側殘片污染），找出「缺棘突候選」。
+          高召回（幾乎不漏）、但因純投影在傾斜脊椎上仍會有少數假候補。
+    stage 2：僅對候選跑 full（鏡稱面）驗證（~3s/候選），以 full 為準給出
+          最終判定（confirmed / false alarm）。全資料集 ~25min + 候數×3s。
+  full（指定單一 volume+level 時預設）：跑鏡稱面 + 棘突/椎體完整分割，
+          另回報 VBODY 分割 mode（nosp_gap / nosp_post_min / quantile...），
+          確認該 level 的椎體切分落在「椎體後側末端（體/弓最薄處）」。
+
+識別出的 no_spinous level 在 xfr_debug.py 執行時會打 [NO-SP] 標記，
+並自動改用放寬後側谷底的椎體切分（不再把殘留後側要素當棘突移除）。
+
+Usage:
+  python xfr_check_spinous.py                    # quick，全部 volume L1~L5
+  python xfr_check_spinous.py 0005               # quick，該 volume L1~L5
+  python xfr_check_spinous.py 0005 L5            # full（精確）單一 level
+  python xfr_check_spinous.py --full 0005 L5     # 強制 full
+  python xfr_check_spinous.py --quick            # 強制 quick（全資料集掃）
+"""
+
+import csv
+import os
+import sys
+import time
+
+import numpy as np
+import SimpleITK as sitk
+
+from imaging.orientation import (best_symmetry_plane, segment_spinous_process,
+                                 best_upper_endplate_plane, segment_vertebral_body,
+                                 diagnose_spinous_process)
+
+standardized_dir = '/mnt/1248/open2/cyrou/CBT/Seg/Resample/standardized-xfr/'
+
+LEVELS = ('L1', 'L2', 'L3', 'L4', 'L5')
+
+LOG_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'results')
+
+# 與 diagnose_spinous_process 相同的判定閾值
+DEFICIT_MIN = 4.0
+REAR3_MAX = 20
+# quick：中線帶內一行的最小 bone voxel 數（< 此值視為殘片游離 voxel，不算「尖端在」）
+MIN_MID_VOX = 3
+
+
+# =====================================================================
+# quick screen：不依賴鏡稱面（~0.3s/level）
+# =====================================================================
+def quick_screen(m):
+    """axial 投影 (y, x) 快速篩檢（不跑鏡稱面，對傾斜/旋轉穩健）：
+      - 「寬行」= 行內骨 voxel 數 >= 最大行的 50%（即椎體行；椎體左右
+        大致對稱 → 寬行 x 重心 ≈ 中線上的點）。
+      - 中線軌跡 x(y) = p0 + p1·y 只用寬行（椎體行）擬合：
+        * 用全部行擬合 → laminectomy 後側殘片行污染中線，deficit 被吃掉
+          （0005 L5 假正常）；
+        * 用固定垂直中線 → 傾斜棘突尖端被誤判為側方偏移
+          （0555/0609/0637 假切除）。椎體行兩者都不沾，故最穩。
+      - deficit = 最後側骨行 (y_min) 到「中線軌跡 ± 25% 椎體寬度 band
+        內有骨的最後側行」的行距（尖端在中線上 → 0；切除後 → ≈切除量）。
+      - rear3/rear6 = 最後側 3/6 行內、中線軌跡 ± 10% 寬度（窄中線帶）的
+        骨 voxel 數。
+      - top_off = 最後側一行 x 重心到中線軌跡的距離。
+    回傳 dict 或 None（資料不足）。"""
+    proj = m.max(axis=0)
+    ys_p, xs_p = np.where(proj > 0)
+    if ys_p.size < 50:
+        return None
+    ny = proj.shape[0]
+    cnt = np.bincount(ys_p, minlength=ny)
+    max_cnt = int(cnt.max())
+    if max_cnt < 4:
+        return None
+    xsum = np.bincount(ys_p, weights=xs_p.astype(np.float64), minlength=ny)
+    centroid = xsum / cnt.astype(float)
+    wide = cnt >= (0.5 * max_cnt)          # 椎體行
+    if int(wide.sum()) < 10:
+        return None
+    yv = np.where(wide)[0]
+    p1, p0 = np.polyfit(yv, centroid[wide], 1)   # 中線軌跡（椎體行擬合）
+    xmax = np.full(ny, -1.0)
+    xmin = np.full(ny, np.inf)
+    np.maximum.at(xmax, ys_p, xs_p)
+    np.minimum.at(xmin, ys_p, xs_p)
+    span_c = float(np.median(xmax[yv] - xmin[yv]))
+    if span_c < 10:
+        return None
+    line = p0 + p1 * ys_p
+    band = 0.25 * span_c                   # central band（椎體中央區）
+    narrow = 0.10 * span_c                  # 窄中線帶
+    y_min = int(ys_p.min())
+    # 「中線有骨」需 >= MIN_MID_VOX 個 voxel 才算數：棘突尖端在帶內有
+    # 多個 voxel，切除後的側方殘片在帶內通常只有 1-2 個游離 voxel
+    # （否則 0005 L5 的單 voxel 殘端會被當成尖端 → 假正常）。
+    bcnt = np.bincount(ys_p[np.abs(xs_p - line) <= band], minlength=ny)
+    idx = np.where(bcnt >= MIN_MID_VOX)[0]
+    y_mid = int(idx.min()) if idx.size else ny - 1
+    deficit = float(y_mid - y_min)
+    nn = np.abs(xs_p - line) <= narrow
+    rear3 = int(((ys_p <= y_min + 3.0) & nn).sum())
+    rear6 = int(((ys_p <= y_min + 6.0) & nn).sum())
+    top_off = float(abs(xs_p[ys_p == y_min].mean() - (p0 + p1 * y_min)))
+    return {'deficit': deficit, 'rear3': rear3, 'rear6': rear6,
+            'top_off': top_off, 'no_spinous': bool(deficit >= DEFICIT_MIN
+                                                   and rear3 <= REAR3_MAX)}
+
+
+# =====================================================================
+# full：鏡稱面 + 完整棘突/椎體分割（精確，較慢）
+# =====================================================================
+def full_check(m):
+    sym = best_symmetry_plane(m)
+    diag = diagnose_spinous_process(m, sym)
+    sp_mask, sp_th, sp_info = segment_spinous_process(m, sym)
+    ep = best_upper_endplate_plane(m)
+    vb, vb_th, vb_info = segment_vertebral_body(m, sym, ep, sp_th, sp_info['mode'])
+    row = {'deficit': float(diag['deficit']), 'rear3': diag['rear3'],
+           'rear6': diag['rear6'], 'top_off': diag['top_off'],
+           'no_spinous': bool(diag['no_spinous']),
+           'sp_mode': sp_info['mode'],
+           'sp_pct': 100.0 * sp_info['n_sp'] / max(int(m.sum()), 1),
+           'vb_mode': vb_info['mode'],
+           'vb_pct': (100.0 * vb_info['n_vb'] / max(int(m.sum()), 1))
+                     if vb is not None else None,
+           'vb_ap_th': vb_th}
+    return row
+
+
+# =====================================================================
+def load_binary(volume_dir, level):
+    # _binary.nii.gz 現為原解析度（未插值）；0.5mm 分析優 _binary_sdf（SDF 平滑遮罩）
+    p = os.path.join(volume_dir, f'{level}_binary_sdf.nii.gz')
+    if not os.path.exists(p):
+        p = os.path.join(volume_dir, f'{level}_binary.nii.gz')
+    if not os.path.exists(p):
+        return None
+    m = sitk.GetArrayFromImage(sitk.ReadImage(p, sitk.sitkUInt8)) > 0
+    if int(m.sum()) < 1000 or min(m.shape) < 8:
+        return None
+    return m
+
+
+def check_level(vid, level, use_full):
+    m = load_binary(os.path.join(standardized_dir, vid), level)
+    if m is None:
+        return {'vid': vid, 'level': level, 'note': 'missing/degenerate mask'}
+    t0 = time.time()
+    row = quick_screen(m) if not use_full else full_check(m)
+    row.update(vid=vid.rsplit('.', 1)[-1], level=level,
+               n_bone=int(m.sum()), sec=round(time.time() - t0, 2))
+    return row
+
+
+def parse_args(argv):
+    use_full = None
+    pos = []
+    for a in argv:
+        if a == '--full':
+            use_full = True
+        elif a == '--quick':
+            use_full = False
+        else:
+            pos.append(a)
+    if len(pos) > 2:
+        sys.exit('Usage: python xfr_check_spinous.py [--full|--quick] [volume_id] [level]')
+    vid_arg = pos[0] if len(pos) >= 1 else None
+    level_arg = pos[1] if len(pos) >= 2 else None
+    if level_arg and level_arg.upper() not in LEVELS:
+        sys.exit(f'Invalid level: {level_arg} (choose from {"/".join(LEVELS)})')
+    if level_arg and not vid_arg:
+        sys.exit('level requires volume_id')
+    if use_full is None:
+        use_full = bool(vid_arg and level_arg)     # 指定單 level → 精確模式
+    return vid_arg, (level_arg.upper() if level_arg else None), use_full
+
+
+def main():
+    os.makedirs(LOG_DIR, exist_ok=True)
+    vid_arg, level_arg, use_full = parse_args(sys.argv[1:])
+
+    volumes = [d for d in sorted(os.listdir(standardized_dir))
+               if os.path.isdir(os.path.join(standardized_dir, d))]
+    if vid_arg is not None:
+        key = vid_arg.lower()
+        vols = [v for v in volumes
+                if v.lower() == key or v.rsplit('.', 1)[-1] == key]
+        if not vols:
+            sys.exit(f'Volume not found: {vid_arg}')
+        volumes = vols
+    levels = (level_arg,) if level_arg else LEVELS
+    tasks = [(v, lvl) for v in volumes for lvl in levels]
+    mode = ('FULL (mirror plane)' if use_full
+        else 'QUICK screen -> FULL-verify candidates (2-stage)')
+    print(f'Mode: {mode} | {len(volumes)} volumes x {len(levels)} levels = {len(tasks)} tasks',
+          flush=True)
+
+    t0 = time.time()
+    rows = []
+    candidates = []      # (row 索引, volume 目錄名)
+    for i, (vid, lvl) in enumerate(tasks, 1):
+        try:
+            row = check_level(vid, lvl, use_full)
+        except Exception as e:
+            row = {'vid': vid.rsplit('.', 1)[-1], 'level': lvl, 'note': f'error: {e}'}
+        rows.append(row)
+        if 'note' in row:
+            print(f"[{i}/{len(tasks)}] {row['vid']} {row['level']}: {row['note']}", flush=True)
+        elif use_full:
+            top_str = 'n/a' if row['top_off'] is None else f"{row['top_off']:.1f}"
+            print(f"[{i}/{len(tasks)}] {row['vid']} {row['level']}: "
+                  f"deficit={row['deficit']:6.1f}  rear3={row['rear3']}  "
+                  f"top_off={top_str}  {'<<< NO-SPINUS' if row['no_spinous'] else 'ok'}  "
+                  f"sp={row['sp_mode']} {row['sp_pct']:.1f}%  "
+                  f"vb={row['vb_mode']} {row['vb_pct']:.1f}%", flush=True)
+        else:
+            mark = 'candidate' if row['no_spinous'] else 'ok'
+            print(f"[{i}/{len(tasks)}] {row['vid']} {row['level']}: "
+                  f"deficit={row['deficit']:6.1f}  rear3={row['rear3']:4d}  "
+                  f"rear6={row['rear6']:5d}  top_off={row['top_off']:5.1f}  {mark}",
+                  flush=True)
+        if not use_full and row.get('no_spinous'):
+            candidates.append((len(rows) - 1, vid))
+
+    # ---- Stage 2（quick 模式）：候選用 full（鏡稱面）驗證，以 full 為準 ----
+    flagged = []
+    cleared = []
+    if use_full:
+        for r in rows:
+            if r.get('no_spinous'):
+                flagged.append(f"{r['vid']} {r['level']}")
+    elif candidates:
+        print(f'\n=== stage 2: {len(candidates)} quick candidate(s) -> '
+              f'full (mirror plane) verification ===', flush=True)
+        for j, (k, vid_dir) in enumerate(candidates, 1):
+            row = rows[k]
+            try:
+                m = load_binary(os.path.join(standardized_dir, vid_dir), row['level'])
+                frow = full_check(m) if m is not None else {}
+            except Exception as e:
+                frow = {'note': f'verify error: {e}'}
+            for kk in ('deficit', 'rear3', 'rear6', 'top_off', 'no_spinous',
+                       'sp_mode', 'sp_pct', 'vb_mode', 'vb_pct', 'vb_ap_th'):
+                if kk in frow:
+                    row[kk] = frow[kk]
+            if not frow:
+                flag_str = '-> UNVERIFIED (mask missing/full failed)'
+                cleared.append(f"{row['vid']} {row['level']} (UNVERIFIED)")
+            elif row.get('no_spinous'):
+                flag_str = '<<< NO-SPINUS (confirmed)'
+                flagged.append(f"{row['vid']} {row['level']}")
+            else:
+                flag_str = '-> normal (quick false alarm)'
+                cleared.append(f"{row['vid']} {row['level']} "
+                               f"(full deficit={row.get('deficit', float('nan')):.1f})")
+            to = row.get('top_off')
+            print(f"[verify {j}/{len(candidates)}] {row['vid']} {row['level']}: "
+                  f"deficit={row.get('deficit', float('nan')):6.1f}  "
+                  f"rear3={row.get('rear3', '?')}  "
+                  f"top_off={'n/a' if to is None else format(to, '5.1f')}  "
+                  f"sp={row.get('sp_mode', '?')}  "
+                  f"vb={row.get('vb_mode', '?')} {row.get('vb_pct') or 0:.1f}%  {flag_str}",
+                  flush=True)
+
+    # ---- CSV ----
+    ts = time.strftime('%Y%m%d_%H%M%S')
+    fields = ['vid', 'level', 'n_bone', 'deficit', 'rear3', 'rear6', 'top_off',
+              'no_spinous', 'sp_mode', 'sp_pct', 'vb_mode', 'vb_pct', 'vb_ap_th',
+              'sec', 'note']
+    csv_path = os.path.join(LOG_DIR, f'spinous_check_{ts}.csv')
+    with open(csv_path, 'w', newline='') as f:
+        wtr = csv.DictWriter(f, fieldnames=fields, extrasaction='ignore')
+        wtr.writeheader()
+        for r in rows:
+            r['vid'] = r.get('vid', '')
+            wtr.writerow(r)
+
+    dt = (time.time() - t0) / 60.0
+    print('\n' + '=' * 64)
+    print(f'Done in {dt:.1f} min | {len(rows)} levels checked (mode: {mode})')
+    if flagged:
+        print(f'\n>>> {len(flagged)} level(s) with NO SPINOUS PROCESS (prior laminectomy/resection):')
+        for f_ in flagged:
+            print(f'    {f_}')
+        print('    (xfr_debug.py 執行這些 level 時會打 [NO-SP] 並自動改用放寬後側谷底的椎體切分)')
+    else:
+        print('\nNo missing spinous process detected.')
+    if cleared:
+        print(f'    (quick 候選、經 full 驗證為正常: {", ".join(cleared)})')
+    if use_full:
+        quant = [f"{r['vid']} {r['level']}" for r in rows
+                 if r.get('vb_mode') == 'quantile']
+        if quant:
+            print(f'\nWARNING: VBODY 退回 55 百分位切分（可能切進椎體）: {", ".join(quant)}')
+    print(f'CSV: {csv_path}')
+
+
+if __name__ == '__main__':
+    main()

xfr_debug.py

@@ -1,3 +1,6 @@
+#!/home/xfr/.conda/envs/cbt/bin/python
+
+import logging
 import os
 import re
 import sys
@@ -15,7 +18,7 @@ from core.objective import set_global_context
 from core.optimizer import run_pso_torch, run_de_torch, run_nm_torch, run_pso_torch_xfr
 from imaging.orientation import azimuth_rotation, analyze_vertebral_tilt_contour
 
-standardized_dir = '/mnt/1248/open2/cyrou/CBT/Seg/Resample/standardized-xfr/'
+standardized_dir = '/mnt/1248/open2/cyrou/CBT/Seg/Resample/standardized-xfr-3/'
 
 azimuth_rotation_dir = '/mnt/1248/open2/cyrou/azimuth_rotation'
 tilt_contour_dir = '/mnt/1248/open2/cyrou/tilt_contour'
@@ -25,6 +28,12 @@ LEVELS = ('L1', 'L2', 'L3', 'L4', 'L5')
 
 LOG_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'logs')
 
+# 單側任務的中繼結果（<run_id>/<volume_id>/<level>_<side>.json + plot lock）：
+# 同一 level 的 L/R 可跑在不同 GPU，較晚完成的一側讀到兩側結果後跑合併輸出
+SIDE_RESULT_DIR = os.path.join(LOG_DIR, 'side_results')
+
+logger = logging.getLogger('xfr_debug')
+
 
 # 目前任務標記（每個 worker 流程各自一份），讓交錯的 log 可以歸屬到 (volume, level, side)
 _TASK_TAG = {'vid': None, 'level': None, 'side': None}
@@ -32,10 +41,10 @@ _TASK_TAG = {'vid': None, 'level': None, 'side': None}
 _NP_WRAP_RE = re.compile(r'\bnp\.[A-Za-z_][A-Za-z0-9_]*\(([^()]*)\)')
 
 
-def set_task_tag(volume_id, level):
+def set_task_tag(volume_id, level, side=None):
     _TASK_TAG['vid'] = volume_id
     _TASK_TAG['level'] = level
-    _TASK_TAG['side'] = None
+    _TASK_TAG['side'] = side
 
 
 class _Tee:
@@ -123,6 +132,15 @@ def setup_tee(log_path):
     sys.stderr = _Tee(sys.stderr, log_fh)
 
 
+def _setup_logging():
+    """须在 setup_tee 之後呼叫，讓 handler 寫入 Tee（同時進 console 與 log 檔）"""
+    logging.basicConfig(
+        level=logging.INFO,
+        format="%(asctime)s [%(levelname)s] %(name)s: %(message)s",
+        datefmt="%Y-%m-%d %H:%M:%S",
+    )
+
+
 def get_device(gpu_id=None):
     if torch.cuda.is_available():
         if gpu_id is None:
@@ -135,10 +153,10 @@ def get_device(gpu_id=None):
                     max_free = free_mem
                     gpu_id = i
         device = torch.device(f"cuda:{gpu_id}")
-        print(f"Using GPU {gpu_id}: {torch.cuda.get_device_name(gpu_id)}")
+        logger.info(f"Using GPU {gpu_id}: {torch.cuda.get_device_name(gpu_id)}")
     else:
         device = torch.device("cpu")
-        print("CUDA not available, using CPU")
+        logger.info("CUDA not available, using CPU")
     return device
 
 def debug_orientation(volume_id, level):
@@ -146,9 +164,10 @@ def debug_orientation(volume_id, level):
 
     volume_dir = os.path.join(standardized_dir, volume_id)
 
-    cortical_path = os.path.join(volume_dir, f'{level}_cortical.nii.gz')
+    # _binary.nii.gz 現為原解析度；0.5mm 用 _binary_sdf（SDF 平滑遮罩）
-    binary_path = os.path.join(volume_dir, f'{level}_binary.nii.gz')
+    sdf = os.path.join(volume_dir, f'{level}_binary_sdf.nii.gz')
-    roi_path = os.path.join(volume_dir, f'{level}_roi2.nii.gz')
+    binary_path = sdf if os.path.exists(sdf) \
+        else os.path.join(volume_dir, f'{level}_binary.nii.gz')
 
     # azi = azimuth_rotation(binary_path)
     # res = analyze_vertebral_tilt_contour(binary_path, edge_type='superior', show_plot=False, debug=False)
@@ -156,11 +175,11 @@ def debug_orientation(volume_id, level):
     res = analyze_vertebral_tilt_contour(binary_path, edge_type='superior', show_plot=True, debug=False, save_plt=True, output_path=f'{tilt_contour_dir}/{level}_{volume_id}.png')
     alt = res['superior']['tilt_angle_deg']
 
-    print(binary_path)
+    logger.info(binary_path)
     # print(f'Azimuth: {azi}, Alt: {alt}')
-    print(f'Alt: {alt}')
+    logger.info(f'Alt: {alt}')
 
-def debug_pso(volume_id, level, device=None):
+def debug_pso(volume_id, level, device=None, side='both', run_id=None):
     # ====== PSO ======
     swarm_size = 100
     max_iter = 100
@@ -174,10 +193,16 @@ def debug_pso(volume_id, level, device=None):
     CBT = True
 
     volume_dir = os.path.join(standardized_dir, volume_id)
+    # _cortical 現只產出旋轉版（rotated/ 子資料夾）；_roi2 不再存檔，
+    # 改用旋轉後 _roi（CT）。
+    rotated_dir = os.path.join(volume_dir, 'rotated')
+    cortical_path = os.path.join(rotated_dir, f'{level}_cortical.nii.gz')
+    binary_path = os.path.join(rotated_dir, f'{level}_binary_sdf.nii.gz')
+    roi_path = os.path.join(rotated_dir, f'{level}_roi.nii.gz')
 
-    cortical_path = os.path.join(volume_dir, f'{level}_cortical.nii.gz')
+    missing = [p for p in (cortical_path, binary_path, roi_path) if not os.path.exists(p)]
-    binary_path = os.path.join(volume_dir, f'{level}_binary.nii.gz')
+    if missing:
-    roi_path = os.path.join(volume_dir, f'{level}_roi2.nii.gz')
+        raise ValueError(f'{volume_id} {level}: missing {missing}')
 
     cortical_image = sitk.ReadImage(cortical_path)
     binary_image = sitk.ReadImage(binary_path)
@@ -222,6 +247,11 @@ def debug_pso(volume_id, level, device=None):
         device=device,
         optimize_size=True,
         grid=grid,
+        side=side,
+        level=level,
+        patient_id=volume_id,
+        side_dir=SIDE_RESULT_DIR,
+        run_id=run_id,
         )
 
     # exit()
@@ -239,43 +269,62 @@ def list_gpu_ids():
         return []
 
 
-def gpu_worker(gpu_id, log_path, task_queue, result_queue):
+def gpu_worker(gpu_id, log_path, run_id, task_queue, result_queue):
     """每張 GPU 一個工作流程：先鎖死該 GPU，再從共享隊列領 (volume, level) 任務"""
     # worker 是獨立流程，要自己把輸出 tee 到 log 檔
     setup_tee(log_path)
+    _setup_logging()
     # 必須在任何 torch.cuda 呼叫前設定
     os.environ['CUDA_VISIBLE_DEVICES'] = str(gpu_id)
     torch.cuda.set_device(0)
     device = torch.device('cuda:0')
-    print(f'=== [GPU {gpu_id}] worker started ===', flush=True)
+    logger.info(f'=== [GPU {gpu_id}] worker started ===')
 
     while True:
         # 注意：multiprocessing.Queue 沒有 task_done()（只有 queue.Queue 有），別加回來
         item = task_queue.get()
         if item is None:
             break
-        volume_id, level = item
+        volume_id, level, side = item
-        set_task_tag(volume_id, level)
+        # tag 沿用 _Tee 的 LEFT/RIGHT 寫法（'L'/'R' 是 optimizer 的 side 值）
+        set_task_tag(volume_id, level, 'LEFT' if side == 'L' else 'RIGHT')
         try:
-            debug_pso(volume_id, level, device)
+            debug_pso(volume_id, level, device, side=side, run_id=run_id)
-            result_queue.put(('task', gpu_id, volume_id, level, True, ''))
+            result_queue.put(('task', gpu_id, volume_id, level, side, True, ''))
         except Exception as e:
-            print(f'[GPU {gpu_id}] Error in {volume_id} {level}: {e}', flush=True)
+            logger.error(f'[GPU {gpu_id}] Error in {volume_id} {level} {side}: {e}')
-            result_queue.put(('task', gpu_id, volume_id, level, False, str(e)))
+            result_queue.put(('task', gpu_id, volume_id, level, side, False, str(e)))
 
     result_queue.put(('done', gpu_id))
-    print(f'=== [GPU {gpu_id}] worker finished ===', flush=True)
+    logger.info(f'=== [GPU {gpu_id}] worker finished ===')
 
 
-def _run_sequential(tasks):
+def _run_sequential(tasks, run_id):
     """沒有（或只有一張）GPU 時的回退：單流程串行"""
     device = get_device()
-    for volume_id, level in tasks:
+    for volume_id, level, side in tasks:
-        set_task_tag(volume_id, level)
+        set_task_tag(volume_id, level, 'LEFT' if side == 'L' else 'RIGHT')
         try:
-            debug_pso(volume_id, level, device)
+            debug_pso(volume_id, level, device, side=side, run_id=run_id)
         except Exception as e:
-            print(f'Error in {volume_id} {level}: {e}')
+            logger.error(f'Error in {volume_id} {level} {side}: {e}')
+
+
+USAGE = 'Usage: python xfr_debug.py [volume_id] [level]'
+
+
+def parse_args(argv):
+    """volume_id 可用完整 ID 或末段（如 0005）；level 為 LEVELS 之一（L1~L5）。
+    兩者可省略（＝全部）；level 必須搭配 volume_id 使用。"""
+    vid_arg = argv[0] if len(argv) >= 1 else None
+    level_arg = argv[1] if len(argv) >= 2 else None
+    if len(argv) > 2:
+        sys.exit(f'{USAGE}\nToo many arguments')
+    if level_arg and level_arg.upper() not in LEVELS:
+        sys.exit(f'{USAGE}\nInvalid level: {level_arg} (choose from {"/".join(LEVELS)})')
+    if level_arg and not vid_arg:
+        sys.exit(f'{USAGE}\nlevel requires volume_id')
+    return vid_arg, (level_arg.upper() if level_arg else None)
 
 
 def main():
@@ -289,31 +338,48 @@ def main():
 
     # 要處理的 volume 數（並行模式下是「最多嘗試的 volume 數」）
     MAX_SUCCESSFUL_VOLUMES = 100
-    MAX_SUCCESSFUL_VOLUMES = 1
+    MAX_SUCCESSFUL_VOLUMES = 10
 
     # log 檔（console 與檔案同時輸出；各 GPU worker 也會 append 進同一個檔）
     os.makedirs(LOG_DIR, exist_ok=True)
-    log_path = os.path.join(LOG_DIR, f'xfr_debug_{time.strftime("%Y%m%d_%H%M%S")}.log')
+    run_id = time.strftime("%Y%m%d_%H%M%S")
+    log_path = os.path.join(LOG_DIR, f'xfr_debug_{run_id}.log')
     setup_tee(log_path)
-    print(f'Log file: {log_path}', flush=True)
+    _setup_logging()
-    print(f'Command: {sys.executable} {" ".join(sys.argv)}', flush=True)
+    logger.info(f'Log file: {log_path}')
-    print(f'Working directory: {os.getcwd()}', flush=True)
+    logger.info(f'Command: {sys.executable} {" ".join(sys.argv)}')
+    logger.info(f'Working directory: {os.getcwd()}')
 
     volumes = [d for d in sorted(os.listdir(standardized_dir))
                if os.path.isdir(os.path.join(standardized_dir, d))]
+
+    vid_arg, level_arg = parse_args(sys.argv[1:])
+    if vid_arg is not None:
+        key = vid_arg.lower()
+        vols = [v for v in volumes
+                if v.lower() == key or v.rsplit('.', 1)[-1] == key]
+        if not vols:
+            sys.exit(f'Volume not found: {vid_arg}')
+        volumes = vols
     volumes = volumes[:MAX_SUCCESSFUL_VOLUMES]
 
-    tasks = [(vid, level) for vid in volumes for level in LEVELS]
+    levels = (level_arg,) if level_arg else LEVELS
-    print(f'Total {len(volumes)} volumes / {len(tasks)} (volume, level) tasks', flush=True)
+    # 任務粒度 = (volume, level, side)：同一 level 的 L/R 是兩個獨立任務，
+    # 可被不同 GPU 的 worker 領走並行執行；順序 L1 L -> L1 R -> L2 L -> L2 R -> ...
+    tasks = [(vid, level, s) for vid in volumes for level in levels for s in ('L', 'R')]
+    logger.info(f'Total {len(volumes)} volumes / {len(tasks)} (volume, level, side) tasks '
+                f'(levels: {", ".join(levels)})')
+    if vid_arg or level_arg:
+        logger.info(f'Filter: volume_id={vid_arg!r} level={level_arg!r}')
 
     gpu_ids = list_gpu_ids()
 
     if len(gpu_ids) <= 1:
-        print(f'Only {len(gpu_ids)} GPU(s) available, running sequentially', flush=True)
+        logger.info(f'Only {len(gpu_ids)} GPU(s) available, running sequentially')
-        _run_sequential(tasks)
+        _run_sequential(tasks, run_id)
         return
 
-    print(f'Found {len(gpu_ids)} GPUs: {gpu_ids}, starting {len(gpu_ids)} workers (one per GPU)', flush=True)
+    logger.info(f'Found {len(gpu_ids)} GPUs: {gpu_ids}, starting {len(gpu_ids)} workers (one per GPU)')
 
     ctx = mp.get_context('spawn')
     task_queue = ctx.Queue()
@@ -323,8 +389,8 @@ def main():
     for _ in gpu_ids:
         task_queue.put(None)  # 每個 worker 一個結束哨兵
 
-    procs = [ctx.Process(target=gpu_worker, args=(g, log_path, task_queue, result_queue), name=f'cbt-gpu-{g}')
+    procs = [ctx.Process(target=gpu_worker, args=(g, log_path, run_id, task_queue, result_queue), name=f'cbt-gpu-{g}')
-             for g in gpu_ids]
+              for g in gpu_ids]
     for p in procs:
         p.start()
 
@@ -333,7 +399,7 @@ def main():
     finished = 0
     while finished < len(gpu_ids):
         if not any(p.is_alive() for p in procs):
-            print('Warning: a worker exited early; reaping remaining tasks...', flush=True)
+            logger.warning('A worker exited early; reaping remaining tasks...')
             break
         try:
             msg = result_queue.get(timeout=5)
@@ -357,27 +423,31 @@ def main():
         p.join(timeout=60)
 
     total_time = time.time() - start_time
-    ok = [r for r in results if r[4]]
+    ok = [r for r in results if r[5]]
-    fail = [r for r in results if not r[4]]
+    fail = [r for r in results if not r[5]]
     per_volume = {}
-    for _, _, vid, level, success, _ in results:
+    per_volume_n = {}
+    for _, _, vid, level, side, success, _ in results:
         per_volume.setdefault(vid, set()).add(success)
+        per_volume_n[vid] = per_volume_n.get(vid, 0) + 1
     missing = len(tasks) - len(results)
 
-    # 一個 volume 算「成功」必須它的(level)全部執行過且全部成功
+    # 一個 volume 算「成功」必須它的所有 (level, side) 任務都執行過且全部成功
-    n_success_volumes = sum(1 for vid in volumes
+    n_success_volumes = sum(
-                            if per_volume.get(vid, set()) == {True})
+        1 for vid in volumes
+        if per_volume.get(vid, set()) == {True}
+        and per_volume_n.get(vid, 0) == len(levels) * 2)
 
     print('=' * 60)
-    print(f'Finished in {total_time / 60:.1f} min | '
+    logger.info(f'Finished in {total_time / 60:.1f} min | '
-          f'tasks {len(results)}/{len(tasks)} (ok {len(ok)} / failed {len(fail)} / not-run {missing})')
+                f'tasks {len(results)}/{len(tasks)} (ok {len(ok)} / failed {len(fail)} / not-run {missing})')
     if missing:
-        print(f'Warning: {missing} task(s) were never executed (worker crash?)')
+        logger.warning(f'{missing} task(s) were never executed (worker crash?)')
-    print(f'Successful volumes (all levels OK): {n_success_volumes}/{len(volumes)}')
+    logger.info(f'Successful volumes (all levels OK): {n_success_volumes}/{len(volumes)}')
     if fail:
-        print('Failed tasks:')
+        logger.info('Failed tasks:')
-        for _, g, vid, level, _, err in fail:
+        for _, g, vid, level, side, _, err in fail:
-            print(f'  [GPU {g}] {vid} {level}: {err}')
+            logger.error(f'[GPU {g}] {vid} {level} {side}: {err}')
 
 
 if __name__ == '__main__':

xfr_plot_level.py

@@ -0,0 +1,97 @@
+#!/home/xfr/.conda/envs/cbt/bin/python
+"""
+為每個 (volume, level) 的骨頭遮罩（{level}_binary_sdf.nii.gz，缺則 _binary）繪製
+X-ray 四視角圖（不畫螺絲），存到 Output/{date}/{volume}/。
+
+輸出檔名：{volume} {level}_CBT.png
+（例：1.3.6.1.4.1.9328.50.4.0005 L1_CBT.png）
+
+Usage:
+  python xfr_plot_level.py                     # 全部 volume 的 L1~L5
+  python xfr_plot_level.py 0005                # 該 volume 的 L1~L5
+  python xfr_plot_level.py 0005 L1             # 單一 (volume, level)
+  python xfr_plot_level.py --dir <standardized_dir> --output <output_base>
+"""
+
+import argparse
+import os
+import sys
+
+from visualization.res_bone_figure import render_bone_figure
+
+standardized_dir = '/mnt/1248/open2/cyrou/CBT/Seg/Resample/standardized-xfr/'
+output_base = '/mnt/1248/open2/cyrou/Output'
+
+LEVELS = ('L1', 'L2', 'L3', 'L4', 'L5')
+
+USAGE = 'Usage: python xfr_plot_level.py [volume_id] [level] [--dir D] [--output O]'
+
+
+def parse_args(argv):
+    parser = argparse.ArgumentParser(description='繪製各 lumbar level 的骨頭 X-ray 圖（不畫螺絲）')
+    parser.add_argument('volume_id', nargs='?', default=None,
+                        help='volume ID（完整 UID 或末段，如 0005）；省略＝全部')
+    parser.add_argument('level', nargs='?', default=None,
+                        help=f'level（{" / ".join(LEVELS)}）；省略＝全部')
+    parser.add_argument('--dir', default=standardized_dir,
+                        help=f'standardized 資料夾（預設 {standardized_dir}）')
+    parser.add_argument('--output', default=output_base,
+                        help=f'輸出根目錄（預設 {output_base}）')
+    return parser.parse_args(argv)
+
+
+def main():
+    args = parse_args(sys.argv[1:])
+
+    if args.level is not None:
+        level_key = args.level.upper()
+        if level_key not in LEVELS:
+            print(f'Invalid level: {args.level} (choose from {"/".join(LEVELS)})')
+            sys.exit(1)
+    if args.level is not None and args.volume_id is None:
+        print(f'{USAGE}\nlevel requires volume_id')
+        sys.exit(1)
+
+    volumes = [d for d in sorted(os.listdir(args.dir))
+               if os.path.isdir(os.path.join(args.dir, d))]
+    if args.volume_id is not None:
+        key = args.volume_id.lower()
+        vols = [v for v in volumes
+                if v.lower() == key or v.rsplit('.', 1)[-1] == key]
+        if not vols:
+            print(f'Volume not found: {args.volume_id}')
+            sys.exit(1)
+        volumes = vols
+
+    levels = (args.level.upper(),) if args.level else LEVELS
+    tasks = [(vid, lvl) for vid in volumes for lvl in levels]
+    print(f'{len(volumes)} volume(s) x {len(levels)} level(s) = {len(tasks)} figure(s)',
+          flush=True)
+
+    ok, skip = [], []
+    for i, (vid, lvl) in enumerate(tasks, 1):
+        vol_dir = os.path.join(args.dir, vid)
+        # _binary.nii.gz 現為原解析度；0.5mm 用 _binary_sdf（SDF 平滑遮罩）
+        sdf_path = os.path.join(vol_dir, f'{lvl}_binary_sdf.nii.gz')
+        binary_path = sdf_path if os.path.exists(sdf_path) \
+            else os.path.join(vol_dir, f'{lvl}_binary.nii.gz')
+        cortical_path = os.path.join(vol_dir, f'{lvl}_cortical.nii.gz')
+        path = render_bone_figure(vid, lvl, binary_path, cortical_path,
+                                  base_folder=args.output)
+        if path is None:
+            skip.append((vid, lvl))
+            print(f'[{i}/{len(tasks)}] {vid} {lvl}: skipped', flush=True)
+        else:
+            ok.append((vid, lvl))
+            print(f'[{i}/{len(tasks)}] {vid} {lvl}: saved {path}', flush=True)
+
+    print('=' * 60)
+    print(f'Done. saved={len(ok)} skipped={len(skip)}')
+    if skip:
+        print('Skipped (missing/empty mask):')
+        for vid, lvl in skip:
+            print(f'  {vid} {lvl}')
+
+
+if __name__ == '__main__':
+    main()

xfr_preprocess.py

@@ -1,10 +1,32 @@
+#!/home/xfr/.conda/envs/cbt/bin/python
+
+import argparse
+import json
+import logging
 import os
+import sys
+import time
+
+import numpy as np
+import SimpleITK as sitk
+from tinydb import TinyDB, Query
 
 from imaging.preprocessing import process_dataset
+from config.constant import LABEL_MAP
+from imaging.orientation import (best_symmetry_plane, best_upper_endplate_plane,
+                                  segment_spinous_process, segment_vertebral_body,
+                                  smooth_mask_sdf)
+from visualization.res_bone_figure import (render_bone_figure,
+                                           compute_normalizing_rotation,
+                                           rotate_volume_to, rotated_grid,
+                                           rotated_sitk_image_at,
+                                           _rotate_plane_params,
+                                           _shift_plane_params)
 
 data_root   = '/mnt/1220/Public/dataset/Spine/CTSpine1K/data/'
 label_root  = '/mnt/1220/Public/dataset/Spine/CTSpine1K/label/'
 output_dir = '/mnt/1248/open2/cyrou/CBT/Seg/Resample/standardized-xfr-2/'
+output_dir = '/mnt/1248/open2/cyrou/CBT/Seg/Resample/standardized-xfr-3/'
 
 label_map = {
     'colon': 'conlon',
@@ -13,12 +35,407 @@ label_map = {
     'liver': 'Liver',
 }
 
-def main(): 
+LUMBAR_LEVELS = ('L1', 'L2', 'L3', 'L4', 'L5', 'L6')
+MAX_Z_SPACING_MM = 4.0  # z spacing (mm) 大於此值者跳過整支 pipeline
+MIN_LUMBAR_LEVELS = 2   # 符合 lumbar 的 label 少於此值者跳過整支 pipeline
+
+LOG_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'logs')
+METADATA_DB = os.path.join(os.path.dirname(os.path.abspath(__file__)),
+                           'xfr_image_metadata.json')
+
+logger = logging.getLogger('xfr_preprocess')
+
+
+def _upsert_by_name(table, name, meta):
+    """以 'name' 欄位為鍵 upsert（TinyDB 4.9 insert 不支援自訂 doc_id）。"""
+    q = Query().name == name
+    entry = dict(table.get(q) or {})
+    entry.update(meta)
+    entry['name'] = name
+    if table.get(q) is None:
+        table.insert(entry)
+    else:
+        table.update(entry, q)
+
+
+def _migrate_legacy_metadata(path):
+    """舊版純 JSON 檔（{name: {...}}、無 TinyDB 的 _default 結構）：
+    改名成 .legacy-<timestamp> 備份，內容匯入新 TinyDB。"""
+    if not os.path.exists(path):
+        return
+    try:
+        with open(path) as f:
+            data = json.load(f)
+    except (json.JSONDecodeError, OSError):
+        return
+    legacy = {k: v for k, v in data.items()
+              if isinstance(v, dict)} if isinstance(data, dict) else {}
+    if not (isinstance(data, dict) and '_default' not in data and legacy):
+        return
+    bak = f'{path}.legacy-{time.strftime("%Y%m%d_%H%M%S")}'
+    os.replace(path, bak)
+    print(f'Metadata db {path} is old pure-JSON format; renamed to {bak} '
+          f'and migrating {len(legacy)} entrie(s)')
+    t = TinyDB(path).table('images')
+    for k, v in legacy.items():
+        _upsert_by_name(t, k, dict(v))
+
+
+class ImageMetadataDB:
+    """影像 metadata 快取（TinyDB，table 'images'）：
+    以影像檔名前綴（= 輸出資料夾名，如 1.3.6.1.4.1.9328.50.4.0001、
+    liver_100、volume-covid19-A-0011_ct）為 key（存於文件 'name' 欄位），
+    記錄 {'spacing': [x, y, z], 'labels': [label id]}。
+
+    供 process_single_image 做跳過判定（z spacing / lumbar 層數），
+    命中時不必讀影像 / label 檔。TinyDB 每次操作自動落檔，
+    中途重跑可繼承。
+    """
+
+    def __init__(self, path=METADATA_DB):
+        self.path = path
+        _migrate_legacy_metadata(path)
+        self._table = TinyDB(path).table('images')
+
+    def get(self, name):
+        return self._table.get(Query().name == name)
+
+    def put(self, name, meta):
+        _upsert_by_name(self._table, name, meta)
+
+    def __len__(self):
+        return len(self._table)
+
+
+class _Tee:
+    """同時輸出到 console 與 log 檔，逐行寫入。"""
+
+    def __init__(self, console, log_fh):
+        self.console = console
+        self.log_fh = log_fh
+        self.buf = ''
+
+    def _emit(self, line):
+        self.console.write(line + '\n')
+        self.log_fh.write(line + '\n')
+
+    def write(self, data):
+        if not data:
+            return
+        self.buf += data
+        while True:
+            idx_n = self.buf.find('\n')
+            idx_r = self.buf.find('\r')
+            candidates = [i for i in (idx_n, idx_r) if i != -1]
+            if not candidates:
+                break
+            idx = min(candidates)
+            self._emit(self.buf[:idx])
+            self.buf = self.buf[idx + 1:]
+
+    def flush(self):
+        if self.buf:
+            self._emit(self.buf)
+            self.buf = ''
+        self.console.flush()
+        self.log_fh.flush()
+
+    def isatty(self):
+        return False
+
+
+def setup_tee(log_path):
+    """把這個流程的 stdout/stderr 同時寫到 log_path（append、line-buffered）"""
+    log_fh = open(log_path, 'a', buffering=1)
+    sys.stdout = _Tee(sys.stdout, log_fh)
+    sys.stderr = _Tee(sys.stderr, log_fh)
+
+
+def _cortical_from_roi(roi_arr, bin_arr):
+    """皮質遮罩（與舊未旋轉 _cortical.nii.gz 同定義）：
+    門檻 = 骨頭 mask（bin_arr）內 CT 的 median HU；
+    cortical = mask 內且 門檻 <= HU <= 10000。
+    roi_arr / bin_arr 須同 grid（(z, y, x)）；回傳 uint8 0/1，
+    輸入缺失或 mask 為空時回傳 None。"""
+    if roi_arr is None or bin_arr is None:
+        return None
+    inside = bin_arr > 0
+    if int(inside.sum()) == 0:
+        return None
+    threshold = float(np.median(roi_arr[inside]))
+    return (inside & (roi_arr >= threshold) & (roi_arr <= 10000)).astype(np.uint8)
+
+
+def _write_rotated_level(vol_dir, level, smd_path, mask_path, roi_path):
+    """對單一 level：計算對齊旋轉（鏡稱面 -> +X、上終板 normal y=0），
+    存到 <vol_dir>/rotated/（先旋轉 _binary_nn，再以它的非零 bbox（±4
+    體素）作為所有旋轉輸出的裁切 grid，尺寸不求同未旋轉版、整顆骨頭
+    保留，origin 隨裁切平移）：
+      - _smd_resampled.nii.gz  三线性旋轉後 SMD（內負/外正）
+      - _binary_sdf.nii.gz     旋轉 SMD 於 0.5 閾值（與未旋轉版一致）
+      - _binary_nn.nii.gz      NN 旋轉後 0/1 遮罩（對比用，裁切基準）
+      - _roi.nii.gz
+      - _cortical.nii.gz       旋轉 CT 以骨頭 mask 內 median HU 為門檻
+                               （取代舊的未旋轉 _cortical，定義相同）
+    再畫「rotated」平面圖，並在旋轉體上做 VBODY / 棘突分割存 label map
+    （1=VBODY、2=棘突、3=other bone、0=background）。
+    平面參數經 R 剛性旋轉並換元到輸出 grid 的局部座標。
+
+    旋轉來源 + 幾何模板：patient 未旋轉的 0.5mm _smd_resampled.nii.gz
+    （float、裁物件 bbox，SMD < 0.5 = 內部，與 _binary_sdf 同幾何）；
+    缺失或格式不符時回退 _binary_nn.nii.gz（0.5mm 最近邻 0/1），
+    此情形只產出 _binary_nn（+ roi / cortical / 圖 / label）。
+    mask_path（未旋轉 0.5mm 0/1 遮罩，如 _binary_sdf）只供畫圖
+    （render_bone_figure 以 uint8 讀取；float 檔會被讀成全 0），
+    缺失時自動回退 _binary_nn。
+    """
+    volume_id = os.path.basename(vol_dir)
+
+    template = None
+    smd_arr = None
+    if smd_path is not None and os.path.exists(smd_path):
+        sa = sitk.GetArrayFromImage(sitk.ReadImage(smd_path)).astype(np.float32)
+        if sa.size > 0 and np.isfinite(sa).all() and sa.min() < 0.0 and sa.max() > 0.0:
+            template = sitk.ReadImage(smd_path)   # 0.5mm 幾何模板
+            smd_arr = sa
+        else:
+            logger.warning(f'[rotated] {volume_id} {level}: _smd_resampled 不可用 '
+                           f'(value)，改用 _binary_nn')
+    if template is None:
+        nn_in_path = os.path.join(vol_dir, f'{level}_binary_nn.nii.gz')
+        if not os.path.exists(nn_in_path):
+            logger.warning(f'[rotated] {volume_id} {level}: _smd_resampled / _binary_nn 皆不可用, skip')
+            return
+        template = sitk.ReadImage(nn_in_path)
+
+    # 平面估計輸入：SMD 時取 0.5 閾值內部，與 _binary_sdf 同定義
+    if smd_arr is not None:
+        bin_arr = (smd_arr < 0.5).astype(np.uint8)
+    else:
+        bin_arr = (sitk.GetArrayFromImage(template) > 0).astype(np.uint8)
+    if int(bin_arr.sum()) == 0:
+        logger.warning(f'[rotated] {volume_id} {level}: empty binary, skip')
+        return
+
+    # 圖用遮罩須與模板同幾何（SDF 與 SMD 皆裁 bbox2；NN fallback 只有
+    # NN 遮罩一致）；0.5mm 0/1，float 檔會被 uint8 讀取成全 0
+    nn_in_path = os.path.join(vol_dir, f'{level}_binary_nn.nii.gz')
+    if smd_arr is None:
+        mask_path = nn_in_path if os.path.exists(nn_in_path) else mask_path
+    if mask_path is None or not os.path.exists(mask_path):
+        mask_path = nn_in_path if os.path.exists(nn_in_path) else None
+
+    sym = best_symmetry_plane(bin_arr)
+    symp = best_upper_endplate_plane(bin_arr)
+    R, c_xyz = compute_normalizing_rotation(bin_arr, sym, symp)
+
+    # 輸出 grid：未旋轉緊密 bbox 的 8 角點旋轉後的最小包圍盒 + margin——
+    # 尺寸不受未旋轉版約束，保證旋轉後整顆骨頭保留（同尺寸旋轉切角落）
+    start, size = rotated_grid(bin_arr.shape, R, c_xyz, margin=4)
+
+    rotated_dir = os.path.join(vol_dir, 'rotated')
+    os.makedirs(rotated_dir, exist_ok=True)
+
+    # 先旋轉 _binary_nn（order=0，未旋轉 _binary_nn 先重採樣到模板 grid
+    # 再旋轉），以其非零 bbox（外扩 4 體素）定所有旋轉輸出的裁切 grid
+    # （fstart/fsize，模板 index 系）；NN 缺失 / 為空時回退緊密包圍盒
+    rot_nn = None
+    fstart = (int(start[0]), int(start[1]), int(start[2]))
+    fsize = (int(size[0]), int(size[1]), int(size[2]))
+    if os.path.exists(nn_in_path):
+        nn_img = sitk.ReadImage(nn_in_path)
+        nn_arr = (sitk.GetArrayFromImage(
+            sitk.Resample(nn_img, template, interpolator=sitk.sitkNearestNeighbor,
+                          defaultPixelValue=0)) > 0).astype(np.uint8)
+        rot_nn_full = (rotate_volume_to(nn_arr, R, c_xyz, start, size,
+                                        order=0, cval=0.0) > 0.5).astype(np.uint8)
+        p_nn = os.path.join(rotated_dir, f'{level}_binary_nn.nii.gz')
+        if int(rot_nn_full.sum()) > 0:
+            zz, yy, xx = np.where(rot_nn_full > 0)
+            m = 4
+            z0 = max(0, int(zz.min()) - m)
+            z1 = min(rot_nn_full.shape[0] - 1, int(zz.max()) + m)
+            y0 = max(0, int(yy.min()) - m)
+            y1 = min(rot_nn_full.shape[1] - 1, int(yy.max()) + m)
+            x0 = max(0, int(xx.min()) - m)
+            x1 = min(rot_nn_full.shape[2] - 1, int(xx.max()) + m)
+            fstart = (fstart[0] + x0, fstart[1] + y0, fstart[2] + z0)
+            fsize = (x1 - x0 + 1, y1 - y0 + 1, z1 - z0 + 1)
+            rot_nn = rot_nn_full[z0:z1 + 1, y0:y1 + 1, x0:x1 + 1]
+        else:
+            rot_nn = rot_nn_full
+        sitk.WriteImage(rotated_sitk_image_at(template, rot_nn, fstart), p_nn)
+        logger.info(f'[rotated] saved {p_nn} (grid={list(fsize)}, start={fstart})')
+
+    # 旋轉後 SMD：未旋轉 _smd_resampled 的 SMD 場經三线性旋轉得以保留
+    # （float32 來源，map_coordinates 輸出維持浮點，<0.5 即為真閾值）；
+    # 體外填充值取正 SMD（背景側），避免裁切邊界出現假的閾值穿越
+    rot_sdf_bin = None
+    if smd_arr is not None:
+        rot_smd = rotate_volume_to(smd_arr, R, c_xyz, fstart, fsize,
+                                   order=1, cval=float(smd_arr.max()))
+        p_smd = os.path.join(rotated_dir, f'{level}_smd_resampled.nii.gz')
+        sitk.WriteImage(rotated_sitk_image_at(template, rot_smd.astype(np.float32),
+                                              fstart), p_smd)
+        logger.info(f'[rotated] saved {p_smd}')
+
+        # _binary_sdf.nii.gz：旋轉 SMD 於 0.5 閾值（與未旋轉版一致）
+        rot_sdf_bin = (rot_smd < 0.5).astype(np.uint8)
+        p_sdf = os.path.join(rotated_dir, f'{level}_binary_sdf.nii.gz')
+        sitk.WriteImage(rotated_sitk_image_at(template, rot_sdf_bin, fstart), p_sdf)
+        logger.info(f'[rotated] saved {p_sdf}')
+
+    # 旋轉後的 roi（三线性）：先重採樣到模板 grid，再旋轉到裁切 grid
+    roi_arr = None
+    rot_roi_arr = None
+    if roi_path is not None and os.path.exists(roi_path):
+        roi_img = sitk.ReadImage(roi_path)
+        roi_arr = sitk.GetArrayFromImage(
+            sitk.Resample(roi_img, template, defaultPixelValue=0.0))
+        rot_roi = rotate_volume_to(roi_arr, R, c_xyz, fstart, fsize,
+                                   order=1, cval=0.0)
+        p_roi = os.path.join(rotated_dir, f'{level}_roi.nii.gz')
+        sitk.WriteImage(rotated_sitk_image_at(template, rot_roi, fstart), p_roi)
+        logger.info(f'[rotated] saved {p_roi}')
+        rot_roi_arr = rot_roi
+
+    # 分割 / cortical 輸入：SMD 時直接用旋轉 _binary_sdf（0.5 閾值、
+    # 次體素平滑）；NN fallback 時以 smooth_mask_sdf 記憶體內平滑（不存檔）
+    if rot_sdf_bin is not None:
+        rot_bin_seg = rot_sdf_bin
+    else:
+        rot_bin_seg = smooth_mask_sdf(rot_nn, sigma=1.5).astype(np.uint8)
+
+    # 旋轉後的 cortical：旋轉 CT 以骨頭 mask 內 median HU 為門檻
+    #（取代舊的未旋轉 _cortical.nii.gz，定義相同）
+    rot_cort = _cortical_from_roi(rot_roi_arr, rot_bin_seg)
+    if rot_cort is not None:
+        p_cort = os.path.join(rotated_dir, f'{level}_cortical.nii.gz')
+        sitk.WriteImage(rotated_sitk_image_at(template, rot_cort, fstart), p_cort)
+        logger.info(f'[rotated] saved {p_cort}')
+    else:
+        logger.warning(f'[rotated] {volume_id} {level}: 無旋轉 CT / mask，跳過 _cortical')
+
+    # 用旋轉後的平面畫圖（rotated 版 planes）；皮質著色由未旋轉 CT + mask
+    # 現算（未旋轉 _cortical 不再存檔）
+    p_fig = os.path.join(rotated_dir, f'{level}_planes.png')
+    if mask_path is not None:
+        fig_cortical = _cortical_from_roi(roi_arr, bin_arr)
+        fig = render_bone_figure(volume_id, level, mask_path, fig_cortical,
+                                 planes_only=True, rotation=(R, c_xyz), output_path=p_fig)
+        if fig is not None:
+            logger.info(f'[rotated] saved {fig}')
+    else:
+        logger.warning(f'[rotated] {volume_id} {level}: 無可用 0/1 遮罩，跳過平面圖')
+
+    # 旋轉體上的 VBODY / 棘突分割：平面參數隨 R 剛性旋轉（rotated 體與
+    # 原始體只差一個剛性變換，平面隨動即可，不需重新偵測），
+    # label map 存同資料夾：1 = VBODY（椎體），2 = 棘突（spinous process），
+    # 3 = other bone（其餘骨頭），0 = background。
+    # 換元到輸出 grid 的局部座標（origin 在模板 index fstart 處）
+    sym_rot = _shift_plane_params(_rotate_plane_params(sym, R, c_xyz), fstart)
+    symp_rot = (_shift_plane_params(_rotate_plane_params(symp, R, c_xyz), fstart)
+                if symp is not None else None)
+    sp_mask, sp_th, sp_info = segment_spinous_process(rot_bin_seg, sym_rot)
+    vb_mask, vb_th, vb_info = segment_vertebral_body(rot_bin_seg, sym_rot, symp_rot,
+                                                     sp_th, sp_info['mode'])
+    label_arr = np.zeros(rot_bin_seg.shape, dtype=np.uint8)
+    label_arr[rot_bin_seg > 0] = 3                       # other bone
+    if vb_mask is not None:
+        label_arr[vb_mask] = 1                        # VBODY
+    if sp_mask is not None:
+        label_arr[sp_mask] = 2                        # spinous process
+    p_lbl = os.path.join(rotated_dir, f'{level}_label.nii.gz')
+    sitk.WriteImage(rotated_sitk_image_at(template, label_arr, fstart), p_lbl)
+    logger.info(f'[rotated] saved {p_lbl} '
+                f'(vbody={int((label_arr == 1).sum())}, spinous={int((label_arr == 2).sum())}, '
+                f'other={int((label_arr == 3).sum())}, '
+                f'sp_mode={sp_info["mode"]}, vb_mode={vb_info["mode"]})')
+
+
+def make_lumbar_post_process():
+    """每個 volume 處理完後，對其 lumbar level：
+    1) 畫「骨頭 + 方向平面」圖（不畫螺絲、不做棘突 / 椎體分割）-> <volume_dir>/lumbar/
+    2) 計算對齊旋轉，存旋轉後的 smd_resampled / binary_sdf / binary_nn / roi
+       + cortical + 旋轉平面圖 + label map -> <volume_dir>/rotated/
+
+    post_process 由 process_dataset 呼叫：(volume_dir, processed_labels)。
+    processed_labels 為該 volume 實際存在的 label id（int），對照 LABEL_MAP。
+    """
+
+    def _post_process(vol_dir, processed_labels):
+        volume_id = os.path.basename(vol_dir)
+        lumbar_dir = os.path.join(vol_dir, 'lumbar')
+        for n in processed_labels:
+            level = LABEL_MAP.get(int(n))
+            if level not in LUMBAR_LEVELS:
+                continue
+            smd_res_path = os.path.join(vol_dir, f'{level}_smd_resampled.nii.gz')
+            nn_path = os.path.join(vol_dir, f'{level}_binary_nn.nii.gz')
+            if not os.path.exists(smd_res_path) and not os.path.exists(nn_path):
+                continue
+            # 畫圖用 0/1 遮罩：優 _binary_sdf（0.5mm 平滑），缺則 _binary_nn
+            sdf_path = os.path.join(vol_dir, f'{level}_binary_sdf.nii.gz')
+            mask_path = sdf_path if os.path.exists(sdf_path) else nn_path
+            roi_path = os.path.join(vol_dir, f'{level}_roi.nii.gz')
+
+            # 1) 原始（未旋轉）planes 圖；皮質著色由未旋轉 CT + mask 現算
+            #（未旋轉 _cortical 不再存檔）
+            output_path = os.path.join(lumbar_dir, f'{level}_planes.png')
+            if os.path.exists(mask_path):
+                fig_cortical = None
+                if os.path.exists(roi_path):
+                    mask_img = sitk.ReadImage(mask_path)
+                    roi_img = sitk.ReadImage(roi_path)
+                    roi_arr = sitk.GetArrayFromImage(
+                        sitk.Resample(roi_img, mask_img, defaultPixelValue=0.0))
+                    fig_cortical = _cortical_from_roi(
+                        roi_arr, sitk.GetArrayFromImage(mask_img))
+                path = render_bone_figure(volume_id, level, mask_path, fig_cortical,
+                                          planes_only=True, output_path=output_path)
+                if path is not None:
+                    logger.info(f'[lumbar] saved {path}')
+
+            # 2) 旋轉對齊：rotated/ 的 smd_resampled + binary_sdf + binary_nn
+            #    + roi + cortical + planes 圖 + label
+            _write_rotated_level(vol_dir, level, smd_res_path, mask_path, roi_path)
+
+    return _post_process
+
+
+def main():
+    parser = argparse.ArgumentParser(description='Preprocess CT spine dataset.')
+    parser.add_argument('--max-images', type=int, default=None, dest='max_images',
+                        help='Process at most this number of images per dataset (default: all).')
+    args = parser.parse_args()
+
+    # log 檔（console 與檔案同時輸出）
+    os.makedirs(LOG_DIR, exist_ok=True)
+    log_path = os.path.join(LOG_DIR, f'xfr_preprocess_{time.strftime("%Y%m%d_%H%M%S")}.log')
+    setup_tee(log_path)
+    # basicConfig 在 setup_tee 之後，讓 handler 寫入 Tee（同時進 console 與 log 檔）
+    logging.basicConfig(
+        level=logging.INFO,
+        format="%(asctime)s [%(levelname)s] %(name)s: %(message)s",
+        datefmt="%Y-%m-%d %H:%M:%S",
+    )
+    logger.info(f'Log file: {log_path}')
+    logger.info(f'Command: {sys.executable} {" ".join(sys.argv)}')
+    logger.info(f'Working directory: {os.getcwd()}')
+
+    # metadata db：跳過判定（z spacing / lumbar 層數）命中時免讀影像 / label 檔
+    metadata_db = ImageMetadataDB()
+    logger.info(f'Metadata db: {metadata_db.path} ({len(metadata_db)} entries)')
+
+    post_process = make_lumbar_post_process()
 
     for key, value in label_map.items():
         data_dir = os.path.join(data_root, key)
         label_dir = os.path.join(label_root, value)
-        process_dataset(data_dir, label_dir, output_dir)
+        process_dataset(data_dir, label_dir, output_dir, max_images=args.max_images,
+                        post_process=post_process, max_z_spacing=MAX_Z_SPACING_MM,
+                        allowed_levels=LUMBAR_LEVELS, min_levels=MIN_LUMBAR_LEVELS,
+                        metadata_cache=metadata_db)
 
 if __name__ == '__main__':
     main()