feat(core): improve scoring logic and add X-ray projection rendering

Implement a more robust scoring mechanism for screw optimization and
add functionality to generate synthetic X-ray projections (AP and
lateral views) from CT data.

Key changes:
- core: add `generate_cylinder_butt_torch` to create a mask for the
  screw entrance (0.25mm) to exempt it from bone-breaching penalties.
- core: update `cl_score_torch_xfr` to include a diameter preference
  bonus and utilize the entrance mask.
- core: adjust optimizer bounds and scoring weights to favor larger
  diameter screws and improve convergence.
- xfr_cbt_native: implement `render_xray_projections` to generate
  synthetic AP and lateral X-ray images for visualization.
- visualization: enhance `render_bone_figure` with semi-transparent
  spinous process rendering and improved depth sorting for screws.
- xfr_debug: improve level detection to support arbitrary lumbar
  levels (L1-L9) and add safe volume-level cleanup for CBT writing.
- config: update allowed diameters and lengths constants.
This commit is contained in:
xfr 2026-09-13 09:14:55 +08:00
parent 0a928d8f8e
commit 4204d2cd4c
9 changed files with 631 additions and 51 deletions

View file

@ -19,17 +19,17 @@ ALLOWED_DIAMETERS = [
5.0, 5.0,
5.5, 5.5,
6.0, 6.0,
6.5, # 6.5,
# 7.0, # 7.0,
# 7.5, # 7.5,
] ]
ALLOWED_LENGTHS = [ ALLOWED_LENGTHS = [
# 25, # 25,
30, # 30,
35, 35,
40, 40,
45, 45,
# 50, 50,
# 60, # 60,
# 70, # 70,
# 80, # 80,

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@ -275,6 +275,61 @@ def generate_cylinder_numpy(diameter, length, position_z, position_y, position_x
return cylinder_mask return cylinder_mask
def generate_cylinder_butt_torch(
diameter,
position_z, position_y, position_x,
azimuth, altitude,
shape, spacing, device, grid=None,
butt_mm=0.25 # 入口端最後 butt_mmmm
) -> torch.Tensor:
"""生成圓柱「最後端」mask入口端z_rot=0遠離 VBODY 的一端)
最靠近的 butt_mm 圓柱短柱 generate_cylinder_n_torch 同慣例同直徑
尖端在 z_rot=length VBODY 不在此 mask
mask 是完整圓柱的子集可直接用於 not_in_bone 豁免"""
if grid is None:
z_t, y_t, x_t = create_coordinate_grid(shape, device)
else:
z_t, y_t, x_t = grid
azimuth_rad_t = torch.deg2rad(torch.tensor(azimuth, device=device, dtype=torch.float32))
altitude_rad_t = torch.deg2rad(torch.tensor(altitude, device=device, dtype=torch.float32))
z_t = z_t - position_z
y_t = y_t - position_y
x_t = x_t - position_x
x_rot = (
x_t * torch.cos(azimuth_rad_t) * torch.cos(altitude_rad_t)
+ y_t * torch.sin(azimuth_rad_t) * torch.cos(altitude_rad_t)
- z_t * torch.sin(altitude_rad_t)
)
y_rot = -x_t * torch.sin(azimuth_rad_t) + y_t * torch.cos(azimuth_rad_t)
z_rot = (
x_t * torch.cos(azimuth_rad_t) * torch.sin(altitude_rad_t)
+ y_t * torch.sin(azimuth_rad_t) * torch.sin(altitude_rad_t)
+ z_t * torch.cos(altitude_rad_t)
)
# 與 generate_cylinder_n_torch 相同的 spacing/單位處理;
# 長度固定為 butt_mmmm→ voxel
if spacing == [1, 1, 1]:
radius = diameter / 2.0
butt_len = butt_mm
elif spacing == [0.5, 0.5, 0.5]:
radius = (diameter / 2.0) * 2
butt_len = butt_mm * 2
else:
raise ValueError(f"Unsupported spacing: {spacing}")
mask = (
(x_rot**2 + y_rot**2 <= radius**2)
& (z_rot >= 0)
& (z_rot < butt_len)
)
return mask.to(torch.uint8)
def generate_cylinder_tip_torch( def generate_cylinder_tip_torch(
diameter, length, diameter, length,
position_z, position_y, position_x, position_z, position_y, position_x,

View file

@ -8,7 +8,7 @@ from scipy.ndimage import map_coordinates
import numpy as np import numpy as np
import torch import torch
from core.cylinder import generate_cylinder_n_torch, generate_cylinder_o_torch, snap_to_discrete_values, generate_cylinder_tip_torch, snap_to_discrete_values_xfr from core.cylinder import generate_cylinder_n_torch, generate_cylinder_o_torch, snap_to_discrete_values, generate_cylinder_tip_torch, generate_cylinder_butt_torch, snap_to_discrete_values_xfr
from core.intersection import center_line_intersections_torch from core.intersection import center_line_intersections_torch
from core.scoring import cl_score_torch, cl_score_torch_xfr from core.scoring import cl_score_torch, cl_score_torch_xfr
@ -120,12 +120,22 @@ def cylinder_circle_line_intersection_loss_deductions_torch(
ctx.image2_shape, ctx.spacing, ctx.device, ctx.grid ctx.image2_shape, ctx.spacing, ctx.device, ctx.grid
) )
# 最後端(入口端,遠離 VBODY 的一端0.25mm 豁免 mask
cyl_butt = generate_cylinder_butt_torch(
diameter,
position_z, position_y, position_x,
float(azimuth), float(altitude),
ctx.image2_shape, ctx.spacing, ctx.device, ctx.grid
)
# loss_value = cl_score_torch( # loss_value = cl_score_torch(
loss_value = cl_score_torch_xfr( loss_value = cl_score_torch_xfr(
ctx.cortical_tensor, ctx.spine_tensor, ctx.cortical_tensor, ctx.spine_tensor,
cyl_fwd, cyl_opp, intersections, cyl_fwd, cyl_opp, intersections,
diameter=diameter, length=length,
cylinder_tip_torch=cyl_tip, cylinder_tip_torch=cyl_tip,
vbody_tensor=ctx.vbody_tensor vbody_tensor=ctx.vbody_tensor,
cylinder_butt_torch=cyl_butt
) )
return loss_value return loss_value

View file

@ -10,7 +10,7 @@ from imaging.orientation import (azimuth_rotation, analyze_vertebral_tilt_contou
from config.constant import ALLOWED_DIAMETERS, ALLOWED_LENGTHS from config.constant import ALLOWED_DIAMETERS, ALLOWED_LENGTHS
from core.objective import OptimizationContext, make_objective_function, make_objective_function_xfr from core.objective import OptimizationContext, make_objective_function, make_objective_function_xfr
from pyswarm import pso from pyswarm import pso
from core.cylinder import generate_cylinder_n_torch, generate_cylinder_o_torch, snap_to_discrete_values, create_coordinate_grid, snap_to_discrete_values_xfr from core.cylinder import generate_cylinder_n_torch, generate_cylinder_o_torch, snap_to_discrete_values, create_coordinate_grid, snap_to_discrete_values_xfr, generate_cylinder_butt_torch
from core.intersection import center_line_intersections_torch from core.intersection import center_line_intersections_torch
from core.scoring import compute_overlap_ratio_from_cylinder_mask, is_solution_ok, cl_score_torch_xfr from core.scoring import compute_overlap_ratio_from_cylinder_mask, is_solution_ok, cl_score_torch_xfr
from config.constant import OVERLAP_THRESH from config.constant import OVERLAP_THRESH
@ -64,8 +64,12 @@ def refine_lateral_longer(
return None return None
inter, _ = center_line_intersections_torch(z_c, y_c, x_c, az_c, alt_c, 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)
cyl_butt = generate_cylinder_butt_torch(d_c, z_c, y_c, x_c, az_c, alt_c,
image_shape, spacing, device, grid)
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) diameter=d_c,
vbody_tensor=vbody_tensor,
cylinder_butt_torch=cyl_butt)
in_bone = ((spine_tensor == 1) & (cyl == 1)).sum().item() / cyl.sum().item() in_bone = ((spine_tensor == 1) & (cyl == 1)).sum().item() / cyl.sum().item()
return {'pos': cand, 'loss': loss, 'in_bone': in_bone} return {'pos': cand, 'loss': loss, 'in_bone': in_bone}
@ -364,7 +368,7 @@ def run_pso_torch_xfr(
# z_bounds = (0, image_shape[0]-1) # z_bounds = (0, image_shape[0]-1)
# z_bounds = (z1, (z1+z2)/2) # z_bounds = (z1, (z1+z2)/2)
# z_bounds = (.1*image_shape[0], .8*image_shape[0]) # z_bounds = (.1*image_shape[0], .8*image_shape[0])
z_bounds = (0, z1+z_height*.8) z_bounds = (0, z1+z_height*.7)
# x_bounds_right = (image_shape[2]/2 + image_shape[2]/10, image_shape[2] - 1) # x_bounds_right = (image_shape[2]/2 + image_shape[2]/10, image_shape[2] - 1)
# x_bounds_left = (0, image_shape[2]/2 - image_shape[2]/10 - 1) # x_bounds_left = (0, image_shape[2]/2 - image_shape[2]/10 - 1)

View file

@ -2,6 +2,11 @@ import torch
from core.cylinder import generate_cylinder_n_torch, generate_cylinder_tip_torch from core.cylinder import generate_cylinder_n_torch, generate_cylinder_tip_torch
from config.constant import OVERLAP_THRESH from config.constant import OVERLAP_THRESH
# 直徑偏好 bonus每 mmALLOWED_DIAMETERS 相鄰等級間隔 0.5 mm
# 20000/mm ⇒ 每級差 10000 分,約等於容許 1 個額外 out-of-bone voxel
# 10000 分/voxel 懲罰)換 0.5 mm 直徑,讓結果在安全前提下偏好較粗螺絲。
DIAMETER_BONUS_PER_MM = 20000.0
def cl_score_torch_xfr( def cl_score_torch_xfr(
cortical_tensor: torch.Tensor, cortical_tensor: torch.Tensor,
spine_tensor: torch.Tensor, spine_tensor: torch.Tensor,
@ -11,10 +16,13 @@ def cl_score_torch_xfr(
diameter: float = None, diameter: float = None,
length: 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) 0/1None = 不計 VBODY 獎勵 vbody_tensor: torch.Tensor = None, # VBODY椎體mask (z,y,x) 0/1None = 不計 VBODY 獎勵
cylinder_butt_torch: torch.Tensor = None # 最後端(入口端,遠離 VBODY 的一端0.25mm mask
) -> float: ) -> float:
""" """
漸進式評分優先確保找到骨頭再改善細節 漸進式評分優先確保找到骨頭再改善細節
diameter 提供時附加直徑偏好 bonus偏好較粗螺絲
cylinder_butt_torch 提供時 mask not_in_bone voxel 免除 10000/voxel 扣分
""" """
cyl_total = cylinder_torch.sum().item() cyl_total = cylinder_torch.sum().item()
overlap = ((cortical_tensor == 1) & (cylinder_torch == 1)).sum().item() # in cortical overlap = ((cortical_tensor == 1) & (cylinder_torch == 1)).sum().item() # in cortical
@ -32,6 +40,11 @@ def cl_score_torch_xfr(
in_bone= ((spine_tensor == 1) & (cylinder_torch == 1)).sum().item() in_bone= ((spine_tensor == 1) & (cylinder_torch == 1)).sum().item()
not_in_bone= ((spine_tensor == 0) & (cylinder_torch == 1)).sum().item() not_in_bone= ((spine_tensor == 0) & (cylinder_torch == 1)).sum().item()
# 最後端(入口端,遠離 VBODY 的一端0.25mm 豁免:
# 這些 voxel 即使 not_in_bone 也不計 10000/voxel 扣分
if cylinder_butt_torch is not None:
not_in_bone -= ((cylinder_butt_torch == 1) & (cylinder_torch == 1)
& (spine_tensor == 0)).sum().item()
if cyl_total == 0: if cyl_total == 0:
return float(1e9) # 極差的情況 return float(1e9) # 極差的情況
@ -43,17 +56,24 @@ def cl_score_torch_xfr(
score = cyl_total score = cyl_total
# 直徑偏好 bonus相同幾何下偏好較大直徑diameter 單位 mm
# bonus 遠小於 breaching 懲罰10000 分/voxel不會把螺絲推出骨頭。
if diameter is not None and diameter > 0:
score += DIAMETER_BONUS_PER_MM * diameter
allowed_error = cyl_total/100
# if in_bone == 0: # if in_bone == 0:
# return float(not_in_bone*200) # return float(not_in_bone*200)
score += 10 * in_bone # 10 實在太低 score += 10 * in_bone # 10 實在太低
score += 100 * overlap # in cortical score += 100 * overlap # in cortical
score += 100 * in_corti_vb # (cortical + VBODY) 每 voxel 再加分 score += 200 * in_corti_vb # (cortical + VBODY) 每 voxel 再加分
score += 50 * in_vbody # VBODY 每 voxel 再加分 score += 50 * in_vbody # VBODY 每 voxel 再加分
# score -= 1000 * not_in_bone score -= 10000 * not_in_bone
score -= 1000 * max(0, not_in_bone-10) # score -= 10000 * max(0, not_in_bone-allowed_error)
# score -= 2000 * null_vox2 score -= 20000 * null_vox2
score -= 2000 * max(0, null_vox2-10) # score -= 2000 * max(0, null_vox2-10)
return float(-score) return float(-score)

View file

@ -24,6 +24,8 @@ BONE_MU_CORTICAL = 0.02 # 1/mm
BONE_MU_TRABECULAR = 0.005 # 1/mm BONE_MU_TRABECULAR = 0.005 # 1/mm
BONE_MARKER_SIZE = 3.0 # 骨散點點面積 (pt^2) BONE_MARKER_SIZE = 3.0 # 骨散點點面積 (pt^2)
BONE_SUBSAMPLE = 1 # 抽稀1 = 全畫) BONE_SUBSAMPLE = 1 # 抽稀1 = 全畫)
SPINOUS_MU = 0.075 # 1/mm棘突吸收係數半透明紫色層密度約皮質骨 3 倍:
# 看得見紫色、後方螺絲路徑仍透見)
def set_axes_equal_3d(ax): def set_axes_equal_3d(ax):
@ -265,10 +267,13 @@ def render_bone_figure(volume_id, level, binary_path, cortical_path,
"""統一骨頭 X-ray 四視角圖(合併原 render_bone_figure + res_plt_2_torch """統一骨頭 X-ray 四視角圖(合併原 render_bone_figure + res_plt_2_torch
四視角預設 / axial俯視 XY/ 冠狀後視/ 矢狀 四視角預設 / axial俯視 XY/ 冠狀後視/ 矢狀
內容皮質 vs 鬆質吸收骨椎體(gold)棘突(purple獨立層覆蓋椎體) 內容皮質 vs 鬆質吸收骨椎體(gold)棘突(purple 半透明獨立層覆蓋椎體)
中矢狀鏡稱面(orange)上終板面(green)螺絲模式另畫中心線() 中矢狀鏡稱面(orange)上終板面(green)螺絲模式另畫中心線()
+ 圓柱L darkcyan / R blueo 層粉 + 圓柱L darkcyan / R blueo 層粉
繪製採固定分層不依深度排序基底骨 < VBODY < 棘突 < 終板 < 鏡稱面 < 螺絲 繪製採固定分層不依深度排序
基底骨 < VBODY < 螺絲(棘突後方) < 棘突(半透明) < 終板 < 鏡稱面 < 螺絲(棘突前方)
螺絲與棘突另依各視角相機深度拆分比棘突中位深度深的螺絲畫在棘突之下
被半透明紫色正確遮擋仍可透見螺絲路徑較淺的螺絲照舊畫在最上層
骨骼輸入 骨骼輸入
binary_path 骨頭遮罩path (nifti) (z,y,x) ndarray / torch tensor binary_path 骨頭遮罩path (nifti) (z,y,x) ndarray / torch tensor
@ -339,6 +344,7 @@ def render_bone_figure(volume_id, level, binary_path, cortical_path,
voxel_mm = float(spacing[0]) voxel_mm = float(spacing[0])
alpha_cortical = 1.0 - np.exp(-BONE_MU_CORTICAL * voxel_mm) alpha_cortical = 1.0 - np.exp(-BONE_MU_CORTICAL * voxel_mm)
alpha_trabecular = 1.0 - np.exp(-BONE_MU_TRABECULAR * voxel_mm) alpha_trabecular = 1.0 - np.exp(-BONE_MU_TRABECULAR * voxel_mm)
alpha_spinous = 1.0 - np.exp(-SPINOUS_MU * voxel_mm)
# 骨頭 voxel 拆成皮質 / 鬆質兩組(同 res_plt_2_torch # 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_corti, y_corti, x_corti = np.where((spine) & (cortical))
@ -451,7 +457,8 @@ def render_bone_figure(volume_id, level, binary_path, cortical_path,
# x_bone 保留完整點雲(含 VBODY / SP供下方平面 patch 算範圍 # x_bone 保留完整點雲(含 VBODY / SP供下方平面 patch 算範圍
#VBODY 前側是整顆骨最前緣,剔除後綠色終板 patch 會縮小); #VBODY 前側是整顆骨最前緣,剔除後綠色終板 patch 會縮小);
# mpl 3D scatter 在同一 collection 內依深度排序 markers # mpl 3D scatter 在同一 collection 內依深度排序 markers
# 「棘突覆蓋椎體、螺絲覆蓋骨頭」改以固定 zorder 分層達成(見 _fill_ax # 「棘突覆蓋椎體」以固定 zorder 分層達成;螺絲與棘突的遮擋則依各視角
# 相機深度拆分(半透明棘突正確遮擋其後方的螺絲,見 _fill_ax
base_idx = ~(vb_flag | sp_flag) base_idx = ~(vb_flag | sp_flag)
x_base, y_base, z_base = x_bone[base_idx], y_bone[base_idx], z_bone[base_idx] x_base, y_base, z_base = x_bone[base_idx], y_bone[base_idx], z_bone[base_idx]
rgba_base, size_base = bone_rgba[base_idx], bone_size[base_idx] rgba_base, size_base = bone_rgba[base_idx], bone_size[base_idx]
@ -473,7 +480,8 @@ def render_bone_figure(volume_id, level, binary_path, cortical_path,
spacing = list(spacing) # core.cylinder 以 list 比對 spacing spacing = list(spacing) # core.cylinder 以 list 比對 spacing
import torch import torch
from core.cylinder import (generate_cylinder_n_torch, from core.cylinder import (generate_cylinder_n_torch,
generate_cylinder_o_torch) generate_cylinder_o_torch,
generate_cylinder_butt_torch)
from core.intersection import center_line_intersections_torch from core.intersection import center_line_intersections_torch
from core.scoring import cl_score_torch, cl_score_torch_xfr from core.scoring import cl_score_torch, cl_score_torch_xfr
@ -538,9 +546,14 @@ def render_bone_figure(volume_id, level, binary_path, cortical_path,
loss = cl_score_torch(cortical_tensor, spine_tensor, loss = cl_score_torch(cortical_tensor, spine_tensor,
cyl_n, cyl_o, inter) cyl_n, cyl_o, inter)
else: else:
cyl_butt = generate_cylinder_butt_torch(
d, pos[0], pos[1], pos[2], pos[3], pos[4],
image_shape, spacing, device, grid)
loss = cl_score_torch_xfr(cortical_tensor, spine_tensor, loss = cl_score_torch_xfr(cortical_tensor, spine_tensor,
cyl_n, cyl_o, inter, cyl_n, cyl_o, inter,
vbody_tensor=vbody_tensor) diameter=d,
vbody_tensor=vbody_tensor,
cylinder_butt_torch=cyl_butt)
cyl_points = int(torch.sum(cyl_n).item()) cyl_points = int(torch.sum(cyl_n).item())
ovc = (100.0 * int(((cortical_tensor == 1) & (cyl_n == 1)).sum().item()) ovc = (100.0 * int(((cortical_tensor == 1) & (cyl_n == 1)).sum().item())
/ cyl_points) if cyl_points else 0.0 / cyl_points) if cyl_points else 0.0
@ -633,9 +646,21 @@ def render_bone_figure(volume_id, level, binary_path, cortical_path,
if sp_corti is not None: if sp_corti is not None:
legend_handles.append(Line2D([], [], marker="o", ls="", ms=6, color="purple", label="SpinousProcess")) legend_handles.append(Line2D([], [], marker="o", ls="", ms=6, color="purple", label="SpinousProcess"))
def _fill_ax(ax): def _view_dir(elev_d, azim_d):
"""本視角相機位置方向(從場景中心指向相機),(x, y, z) 資料座標系。
view_init(elev, azim) 的球座標慣例azim +z +x 起算"""
e, a = np.radians(elev_d), np.radians(azim_d)
return np.array([np.cos(e) * np.cos(a),
np.cos(e) * np.sin(a),
np.sin(e)])
def _fill_ax(ax, elev, azim):
# 固定分層(關 depth zorder否則半透明骨頭會被重繪到螺絲上方 # 固定分層(關 depth zorder否則半透明骨頭會被重繪到螺絲上方
# 基底骨(5) < VBODY gold(6) < 棘突 purple(6.5) < 終板(7) < 鏡稱面(8) < 螺絲(10) # 基底骨(5) < VBODY gold(6) < 螺絲「棘突後方」(6.2)
# < 棘突 purple(6.5, 半透明) < 終板(7) < 鏡稱面(8) < 螺絲「棘突前方」(10)
# 螺絲與棘突按本視角相機深度拆分depth = P·cam大 = 靠近相機)。
# 比棘突中位深度深farther的螺絲先畫、被半透明紫色擋住但仍透見
# (正確遮蔽螺絲路徑);較淺的螺絲照舊畫在最上層。無棘突時不拆分。
ax.computed_zorder = False ax.computed_zorder = False
sc_bone = ax.scatter(x_base, y_base, z_base, c=rgba_base, s=size_base, marker="o") sc_bone = ax.scatter(x_base, y_base, z_base, c=rgba_base, s=size_base, marker="o")
sc_bone.set_zorder(5) sc_bone.set_zorder(5)
@ -644,8 +669,28 @@ def render_bone_figure(volume_id, level, binary_path, cortical_path,
sc_vb = ax.scatter(x_vb, y_vb, z_vb, c=np.array([to_rgba("gold", 0.95)]), sc_vb = ax.scatter(x_vb, y_vb, z_vb, c=np.array([to_rgba("gold", 0.95)]),
s=BONE_MARKER_SIZE, marker="o") s=BONE_MARKER_SIZE, marker="o")
sc_vb.set_zorder(6) sc_vb.set_zorder(6)
# 螺絲拆「棘突前方 / 後方」front = 本視角較淺或等深):無螺絲時
# None無棘突時全 True維持舊行為有棘突時依相機深度 vs 棘突
# 中位深度拆分
if x_screw is None:
front = None
elif x_sp.size:
cam = _view_dir(elev, azim)
d_screw = x_screw * cam[0] + y_screw * cam[1] + z_screw * cam[2]
d_sp = x_sp * cam[0] + y_sp * cam[1] + z_sp * cam[2]
front = d_screw >= np.median(d_sp)
else:
front = np.ones(len(x_screw), dtype=bool)
if front is not None and (~front).any():
m = ~front
sc_bh = ax.scatter(x_screw[m], y_screw[m], z_screw[m],
c=screw_rgba[m], s=screw_size[m], marker="o")
sc_bh.set_zorder(6.2)
if x_sp.size: if x_sp.size:
sc_sp = ax.scatter(x_sp, y_sp, z_sp, c=np.array([to_rgba("purple", 0.95)]), sc_sp = ax.scatter(x_sp, y_sp, z_sp,
c=np.array([to_rgba("purple", float(alpha_spinous))]),
s=BONE_MARKER_SIZE, marker="o") s=BONE_MARKER_SIZE, marker="o")
sc_sp.set_zorder(6.5) sc_sp.set_zorder(6.5)
if _EX is not None: if _EX is not None:
@ -655,19 +700,19 @@ def render_bone_figure(volume_id, level, binary_path, cortical_path,
plane = ax.plot_surface(_Xp, _Yp, _Zp, color="orange", alpha=0.30, plane = ax.plot_surface(_Xp, _Yp, _Zp, color="orange", alpha=0.30,
linewidth=1.0, edgecolor="orange", rstride=1, cstride=1) linewidth=1.0, edgecolor="orange", rstride=1, cstride=1)
plane.set_zorder(8) plane.set_zorder(8)
if x_screw is not None: if front is not None and front.any():
sc_screw = ax.scatter(x_screw, y_screw, z_screw, sc_screw = ax.scatter(x_screw[front], y_screw[front], z_screw[front],
c=screw_rgba, s=screw_size, marker="o") c=screw_rgba[front], s=screw_size[front], marker="o")
sc_screw.set_zorder(10) sc_screw.set_zorder(10)
ax1 = fig.add_subplot(221, projection="3d") ax1 = fig.add_subplot(221, projection="3d")
_fill_ax(ax1) _fill_ax(ax1, 30, -60) # matplotlib 3D 預設視角
ax1.set_xlabel("X-axis"); ax1.set_ylabel("Y-axis"); ax1.set_zlabel("Z-axis") ax1.set_xlabel("X-axis"); ax1.set_ylabel("Y-axis"); ax1.set_zlabel("Z-axis")
set_axes_equal_3d(ax1) set_axes_equal_3d(ax1)
ax2 = fig.add_subplot(222, projection="3d") ax2 = fig.add_subplot(222, projection="3d")
ax2.view_init(elev=90, azim=-90, roll=0) ax2.view_init(elev=90, azim=-90, roll=0)
_fill_ax(ax2) _fill_ax(ax2, 90, -90)
ax2.set_xlabel("X-axis"); ax2.set_ylabel("Y-axis"); ax2.set_zlabel("Z-axis") ax2.set_xlabel("X-axis"); ax2.set_ylabel("Y-axis"); ax2.set_zlabel("Z-axis")
set_axes_equal_3d(ax2) set_axes_equal_3d(ax2)
if legend_handles: if legend_handles:
@ -676,13 +721,13 @@ def render_bone_figure(volume_id, level, binary_path, cortical_path,
ax3 = fig.add_subplot(223, projection="3d") ax3 = fig.add_subplot(223, projection="3d")
# 後視圖:相機在 y 後側x 軸畫面左小右大 # 後視圖:相機在 y 後側x 軸畫面左小右大
ax3.view_init(elev=0, azim=-90, roll=0) ax3.view_init(elev=0, azim=-90, roll=0)
_fill_ax(ax3) _fill_ax(ax3, 0, -90)
ax3.set_xlabel("X-axis"); ax3.set_ylabel("Y-axis"); ax3.set_zlabel("Z-axis") ax3.set_xlabel("X-axis"); ax3.set_ylabel("Y-axis"); ax3.set_zlabel("Z-axis")
set_axes_equal_3d(ax3) set_axes_equal_3d(ax3)
ax4 = fig.add_subplot(224, projection="3d") ax4 = fig.add_subplot(224, projection="3d")
ax4.view_init(elev=0, azim=0, roll=0) ax4.view_init(elev=0, azim=0, roll=0)
_fill_ax(ax4) _fill_ax(ax4, 0, 0)
ax4.set_xlabel("X-axis"); ax4.set_ylabel("Y-axis"); ax4.set_zlabel("Z-axis") ax4.set_xlabel("X-axis"); ax4.set_ylabel("Y-axis"); ax4.set_zlabel("Z-axis")
set_axes_equal_3d(ax4) set_axes_equal_3d(ax4)

View file

@ -4,6 +4,10 @@
L1-L5 x L/R最多 10 存成單一 label 體積 L1-L5 x L/R最多 10 存成單一 label 體積
Output_dir/<run_date>/<volume_id>/cbt.nii.gz Output_dir/<run_date>/<volume_id>/cbt.nii.gz
Output_dir/<run_date>/<volume_id>/x-ap.jpg 合成前後(AP) X 光投影视圖
Output_dir/<run_date>/<volume_id>/x-lat.jpg 合成側位 X 光投影视圖
只投影脊椎骨 + 螺絲不含軟組織
render_xray_projections
label L1L=1 L1R=2 L2L=3 L2R=4 L3L=5 L3R=6 L4L=7 L4R=8 L5L=9 L5R=10 label L1L=1 L1R=2 L2L=3 L2R=4 L3L=5 L3R=6 L4L=7 L4R=8 L5L=9 L5R=10
0 = 背景 0 = 背景
@ -74,6 +78,7 @@ META_DB = os.path.join(_PROJ_DIR, 'xfr_image_metadata.json')
LEVELS = ('L1', 'L2', 'L3', 'L4', 'L5') LEVELS = ('L1', 'L2', 'L3', 'L4', 'L5')
LEVEL_LABEL_VAL = {v: int(k) for k, v in LABEL_MAP.items() if v in LEVELS} # {'L1': 20, ...} LEVEL_LABEL_VAL = {v: int(k) for k, v in LABEL_MAP.items() if v in LEVELS} # {'L1': 20, ...}
PROJ_FILENAME = {'ap': 'x-ap.jpg', 'lateral': 'x-lat.jpg'}
logger = logging.getLogger('xfr_cbt_native') logger = logging.getLogger('xfr_cbt_native')
@ -258,9 +263,129 @@ def write_volume_cbt(volume_id, run_id, output_root=Output_dir, date=None):
logger.warning(f'{volume_id}: failed sides: {", ".join(skipped)}') logger.warning(f'{volume_id}: failed sides: {", ".join(skipped)}')
logger.info(f'{volume_id}: {n_screws}/10 screws -> {out_path} ' logger.info(f'{volume_id}: {n_screws}/10 screws -> {out_path} '
f'(transform.json={n_tf}, re-est={n_fb}, ap_flip={ap_flip})') f'(transform.json={n_tf}, re-est={n_fb}, ap_flip={ap_flip})')
# 收尾:原 CT + 螺絲 -> 合成 AP / Lateral X 光投影视圖 (x-ap.jpg / x-lat.jpg)
try:
render_xray_projections(out_path, ct_path, out_dir)
except Exception as e:
logger.warning(f'{volume_id}: X-ray projection render failed: {e}')
return out_path, n_screws return out_path, n_screws
def render_xray_projections(cbt_path, ct_path, out_dir,
views=('ap', 'lateral'), margin_mm=50.0):
"""原 CT + cbt.nii.gznative 同一 grid 的螺絲 label-> 合成「只有骨頭」X 光投影视圖。
只投影脊椎骨 + 螺絲不含軟組織
- spine masknative 分割 label1-24 = C1..L5 config.constant.LABEL_MAP
label / grid 不符時退回 HU 300-3000 閾值
- μ = clip(HU, 0, 2000)/400松質骨~0.2-1皮質/終板~2-5
- 螺絲 voxel μ = 60金屬等效最亮白
投影视圖 = 沿中心射線 μ 的線積分AP 沿 yLateral 沿 x裁到螺絲 bbox
margin_mm spine 區域骨用 percentile(1,99) 獨立視窗螺絲再疊加裁白
方向SimpleITK LPSxyzAP =病人右在畫面左R 標記
Lateral =前位在左後位在右A/P 標記
spacing 各軸不等時先重取樣到 min(spacing) 各向同性格維持投影 aspect ratio
輸出 x-ap.jpg / x-lat.jpg回傳 {view: jpg_path}"""
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
vid = os.path.basename(os.path.normpath(out_dir))
ct = sitk.ReadImage(ct_path)
cbt = sitk.ReadImage(cbt_path)
if ct.GetSize() != cbt.GetSize():
raise ValueError(f'cbt/CT grid 尺寸不符 {cbt.GetSize()} vs {ct.GetSize()}')
sp = np.array(ct.GetSpacing(), float) # (x,y,z)
native_size = ct.GetSize()
# spacing 各軸不等:先重取樣 CT/螺絲(與後面的分割 label
# min(spacing) 的各向同性格,維持投影视圖正確的 aspect ratio
min_sp = float(sp.min())
isosp = isosize = None
if not np.allclose(sp, min_sp):
isosp = [min_sp, min_sp, min_sp]
isosize = [max(1, int(round(s * v / min_sp))) for s, v in zip(sp, ct.GetSize())]
o, d = ct.GetOrigin(), ct.GetDirection()
ct = sitk.Resample(sitk.Cast(ct, sitk.sitkFloat32), isosize, sitk.Transform(),
sitk.sitkLinear, o, isosp, d, 0.0)
cbt = sitk.Resample(cbt, isosize, sitk.Transform(),
sitk.sitkNearestNeighbor, o, isosp, d, 0)
ct_arr = sitk.GetArrayFromImage(ct).astype(np.float32) # (z,y,x)
cbt_arr = sitk.GetArrayFromImage(cbt)
sp = np.array(ct.GetSpacing(), float)
metal = cbt_arr > 0
try:
_, lb_path, _ = find_native_paths(vid)
lb_img = sitk.ReadImage(lb_path)
# 比對「重取樣前」的 native gridlabel 與原 CT 同格)
if lb_img.GetSize() != native_size:
raise ValueError(f'label/CT grid 尺寸不符 {lb_img.GetSize()} vs {native_size}')
if isosp is not None:
lb_img = sitk.Resample(lb_img, isosize, sitk.Transform(),
sitk.sitkNearestNeighbor,
ct.GetOrigin(), isosp, ct.GetDirection(), 0)
lb = sitk.GetArrayFromImage(lb_img)
spine = (lb >= 1) & (lb <= 24) # LABEL_MAP: C1..L5 全為脊椎
except Exception as e:
logger.warning(f'{vid}: native 分割 label 不可用({e}'
f'退回 HU 300-3000 閾值當脊椎骨')
spine = (ct_arr >= 300) & (ct_arr <= 3000)
bone_mu = np.where(spine & ~metal, np.clip(ct_arr, 0, 2000) / 400.0, 0.0)
metal_mu = 60.0 * metal
z, y, x = np.where(metal)
if z.size == 0:
raise ValueError(f'{vid}: cbt 無螺絲 voxel')
mz, my, mx = (int(margin_mm / s) for s in (sp[2], sp[1], sp[0]))
zs = slice(max(0, z.min() - mz), min(ct_arr.shape[0], z.max() + mz + 1))
ys = slice(max(0, y.min() - my), min(ct_arr.shape[1], y.max() + my + 1))
xs = slice(max(0, x.min() - mx), min(ct_arr.shape[2], x.max() + mx + 1))
proj = {
'ap': (bone_mu[zs, :, xs].sum(axis=1), metal_mu[zs, :, xs].sum(axis=1)), # 沿 y 積分
'lateral': (bone_mu[zs, ys, :].sum(axis=2), metal_mu[zs, ys, :].sum(axis=2)) # 沿 x 積分
}
flip_x = {'ap': True, 'lateral': False}
markers = {'ap': ('R', 'L'), 'lateral': ('A', 'P')} # 畫面左=前位(A)、右=後位(P)
os.makedirs(out_dir, exist_ok=True)
paths = {}
for view in views:
if view not in proj:
continue
b, m = proj[view]
b = b[::-1, ::-1] if flip_x[view] else b[::-1, :] # 頂=頭端
m = m[::-1, ::-1] if flip_x[view] else m[::-1, :]
bnz = b[b > 0]
if bnz.size:
lo, hi = np.percentile(bnz, 1), np.percentile(bnz, 99)
bone = np.clip((b - lo) / (hi - lo + 1e-9), 0, 1) ** 0.7
else:
bone = np.zeros_like(b)
mmax = float(m.max())
metal_img = (m / (mmax + 1e-9)) ** 0.5 if mmax > 0 else m * 0
img = np.clip(bone + metal_img, 0, 1)
ll, rl = markers[view]
h, w = img.shape
fig, ax = plt.subplots(figsize=(8.0 * w / h, 8.0), dpi=110)
ax.imshow(img, cmap='gray', interpolation='nearest')
ax.set_title(f'{view.upper()} projection (spine + screws) - {vid}',
color='white', fontsize=13)
ax.text(0.01, 0.98, ll, transform=ax.transAxes, color='cyan', fontsize=13,
va='top', ha='left', fontweight='bold')
ax.text(0.99, 0.98, rl, transform=ax.transAxes, color='cyan', fontsize=13,
va='top', ha='right', fontweight='bold')
ax.axis('off')
fig.tight_layout(pad=0.5)
p = os.path.join(out_dir, PROJ_FILENAME[view])
fig.savefig(p, format='jpg', facecolor='black')
plt.close(fig)
paths[view] = p
logger.info(f'{vid}: {view} projection -> {p}')
return paths
def main(): def main():
parser = argparse.ArgumentParser( parser = argparse.ArgumentParser(
description='Write <Output_dir>/<date>/<volume_id>/cbt.nii.gz (screws mapped to native space) ' description='Write <Output_dir>/<date>/<volume_id>/cbt.nii.gz (screws mapped to native space) '

View file

@ -8,6 +8,7 @@ import time
import queue as queue_module import queue as queue_module
import subprocess import subprocess
import multiprocessing as mp import multiprocessing as mp
from concurrent.futures import ThreadPoolExecutor
import SimpleITK as sitk import SimpleITK as sitk
import torch import torch
@ -27,7 +28,24 @@ azimuth_rotation_dir = '/mnt/1248/open2/cyrou/azimuth_rotation'
tilt_contour_dir = '/mnt/1248/open2/cyrou/tilt_contour' tilt_contour_dir = '/mnt/1248/open2/cyrou/tilt_contour'
Output_dir = '/mnt/1248/open/cyrou/Output' Output_dir = '/mnt/1248/open/cyrou/Output'
LEVELS = ('L1', 'L2', 'L3', 'L4', 'L5') def available_levels(volume_id):
"""該 volume 可跑 debug_pso 的全部 lumbar levelrotated/ 中輸入三件
_cortical / _binary_sdf / _roi齊全的 L\\d volume 層數不同
有的只有 L1~L3有的含 L6故不用固定 LEVELS 清單"""
rotated_dir = os.path.join(standardized_dir, volume_id, 'rotated')
if not os.path.isdir(rotated_dir):
return ()
levels = []
for fn in os.listdir(rotated_dir):
m = re.fullmatch(r'(L[1-9]\d*)_cortical\.nii\.gz', fn)
if not m:
continue
level = m.group(1)
if (os.path.exists(os.path.join(rotated_dir, f'{level}_binary_sdf.nii.gz'))
and os.path.exists(os.path.join(rotated_dir, f'{level}_roi.nii.gz'))):
levels.append(level)
return tuple(sorted(levels, key=lambda lv: int(lv[1:])))
LOG_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'logs') LOG_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'logs')
@ -303,29 +321,49 @@ def gpu_worker(gpu_id, log_path, run_id, task_queue, result_queue):
logger.info(f'=== [GPU {gpu_id}] worker finished ===') logger.info(f'=== [GPU {gpu_id}] worker finished ===')
def _write_cbt_safe(volume_id, run_id):
"""per-volume 收尾cbt.nii.gz + x-ap/x-lat 投影(錯誤已 log回傳 ok"""
try:
xfr_cbt_native.write_volume_cbt(volume_id, run_id)
return True
except Exception as e:
logger.error(f'[CBT-NATIVE] {volume_id}: {e}')
return False
def _run_sequential(tasks, run_id): def _run_sequential(tasks, run_id):
"""沒有或只有一張GPU 時的回退:單流程串行""" """沒有或只有一張GPU 時的回退:單流程串行。
tasks (volume, level, side) 分組排列一個 volume (level, side)
全部跑完後立刻寫它的 cbt.nii.gz + 投影不等其他 volume"""
device = get_device() device = get_device()
current_vid = None
for volume_id, level, side in tasks: for volume_id, level, side in tasks:
if volume_id != current_vid:
if current_vid is not None:
_write_cbt_safe(current_vid, run_id)
current_vid = volume_id
set_task_tag(volume_id, level, 'LEFT' if side == 'L' else 'RIGHT') set_task_tag(volume_id, level, 'LEFT' if side == 'L' else 'RIGHT')
try: try:
debug_pso(volume_id, level, device, side=side, run_id=run_id) debug_pso(volume_id, level, device, side=side, run_id=run_id)
except Exception as e: except Exception as e:
logger.error(f'Error in {volume_id} {level} {side}: {e}') logger.error(f'Error in {volume_id} {level} {side}: {e}')
if current_vid is not None:
_write_cbt_safe(current_vid, run_id)
USAGE = 'Usage: python xfr_debug.py [volume_id] [level]' USAGE = 'Usage: python xfr_debug.py [volume_id] [level]'
def parse_args(argv): def parse_args(argv):
"""volume_id 可用完整 ID 或末段(如 0005level 為 LEVELS 之一L1~L5 """volume_id 可用完整 ID 或末段(如 0005level 為 L\\d 形式L1、L2、…
不限定 L1~L5實際執行以各 volume 資料中有的 level 為準 available_levels
兩者可省略全部level 必須搭配 volume_id 使用""" 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 vid_arg = argv[0] if len(argv) >= 1 else None
level_arg = argv[1] if len(argv) >= 2 else None level_arg = argv[1] if len(argv) >= 2 else None
if len(argv) > 2: if len(argv) > 2:
sys.exit(f'{USAGE}\nToo many arguments') sys.exit(f'{USAGE}\nToo many arguments')
if level_arg and level_arg.upper() not in LEVELS: if level_arg and not re.fullmatch(r'L[1-9]\d*', level_arg.upper()):
sys.exit(f'{USAGE}\nInvalid level: {level_arg} (choose from {"/".join(LEVELS)})') sys.exit(f'{USAGE}\nInvalid level: {level_arg} (expected L1, L2, ...)')
if level_arg and not vid_arg: if level_arg and not vid_arg:
sys.exit(f'{USAGE}\nlevel requires volume_id') sys.exit(f'{USAGE}\nlevel requires volume_id')
return vid_arg, (level_arg.upper() if level_arg else None) return vid_arg, (level_arg.upper() if level_arg else None)
@ -342,7 +380,7 @@ def main():
# 要處理的 volume 數(並行模式下是「最多嘗試的 volume 數」) # 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 = 100
MAX_SUCCESSFUL_VOLUMES = 10 # 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) # 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) os.makedirs(LOG_DIR, exist_ok=True)
@ -367,12 +405,23 @@ def main():
volumes = vols volumes = vols
volumes = volumes[:MAX_SUCCESSFUL_VOLUMES] volumes = volumes[:MAX_SUCCESSFUL_VOLUMES]
levels = (level_arg,) if level_arg else LEVELS # 各 volume 的 lumbar level未指定 level 時,取該 volume 實際有的全部 lumbar level
# (見 available_levels指定 level 時只跑該 level該 volume 缺檔會直接報錯)
vol_levels = {}
for vid in volumes:
vol_levels[vid] = (level_arg,) if level_arg else available_levels(vid)
no_levels = [vid for vid in volumes if not level_arg and not vol_levels[vid]]
if no_levels:
logger.warning(f'{len(no_levels)} volume(s) have no available lumbar level, '
f'skipped: {", ".join(no_levels)}')
# 任務粒度 = (volume, level, side):同一 level 的 L/R 是兩個獨立任務, # 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 -> ... # 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')] tasks = [(vid, level, s) for vid in volumes for level in vol_levels[vid] for s in ('L', 'R')]
expected = {vid: len(vol_levels[vid]) * 2 for vid in volumes}
all_levels = sorted({level for lv in vol_levels.values() for level in lv},
key=lambda lv: int(lv[1:]))
logger.info(f'Total {len(volumes)} volumes / {len(tasks)} (volume, level, side) tasks ' logger.info(f'Total {len(volumes)} volumes / {len(tasks)} (volume, level, side) tasks '
f'(levels: {", ".join(levels)})') f'(levels: {", ".join(all_levels) if all_levels else "(none)"})')
if vid_arg or level_arg: if vid_arg or level_arg:
logger.info(f'Filter: volume_id={vid_arg!r} level={level_arg!r}') logger.info(f'Filter: volume_id={vid_arg!r} level={level_arg!r}')
@ -393,6 +442,26 @@ def main():
for _ in gpu_ids: for _ in gpu_ids:
task_queue.put(None) # 每個 worker 一個結束哨兵 task_queue.put(None) # 每個 worker 一個結束哨兵
# per-volume 收尾:一個 volume 排入的 (level, side) 任務全部回報後
# (成功或失敗),立刻在背景執行緒寫它的 cbt.nii.gz + 投影,不等全部 case
write_pool = ThreadPoolExecutor(max_workers=4, thread_name_prefix='cbt-write')
write_futures = set()
pending_writes = set(volumes)
remaining = {vid: expected[vid] for vid in volumes}
def _fire_write(vid):
pending_writes.discard(vid)
write_futures.add(write_pool.submit(_write_cbt_safe, vid, run_id))
def _on_task_result(msg):
results.append(msg)
vid = msg[2]
if vid in remaining:
remaining[vid] -= 1
if remaining[vid] <= 0 and vid in pending_writes:
logger.info(f'{vid}: screw tasks complete, writing cbt + projections now')
_fire_write(vid)
procs = [ctx.Process(target=gpu_worker, args=(g, log_path, run_id, 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: for p in procs:
@ -412,7 +481,7 @@ def main():
if msg[0] == 'done': if msg[0] == 'done':
finished += 1 finished += 1
else: else:
results.append(msg) _on_task_result(msg)
# 抽乾剩下排進來的結果 # 抽乾剩下排進來的結果
while True: while True:
@ -421,11 +490,22 @@ def main():
except queue_module.Empty: except queue_module.Empty:
break break
if msg[0] == 'task': if msg[0] == 'task':
results.append(msg) _on_task_result(msg)
for p in procs: for p in procs:
p.join(timeout=60) p.join(timeout=60)
# 補漏worker 提早退出、有任務未回報的 volume 仍照舊嘗試寫
# (無 side 結果時 write_volume_cbt 會自行 skip
for vid in volumes:
if vid in pending_writes:
_fire_write(vid)
# 等待所有 per-volume cbt.nii.gz / 投影寫出完成
write_ok = sum(1 for f in write_futures if f.result())
write_fail = len(write_futures) - write_ok
write_pool.shutdown(wait=True)
total_time = time.time() - start_time total_time = time.time() - start_time
ok = [r for r in results if r[5]] ok = [r for r in results if r[5]]
fail = [r for r in results if not r[5]] fail = [r for r in results if not r[5]]
@ -437,10 +517,11 @@ def main():
missing = len(tasks) - len(results) missing = len(tasks) - len(results)
# 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 # 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
# expected 為該 volume 實際排入的任務數,各 volume 的 level 數可不同)
n_success_volumes = sum( n_success_volumes = sum(
1 for vid in volumes 1 for vid in volumes
if per_volume.get(vid, set()) == {True} if per_volume.get(vid, set()) == {True}
and per_volume_n.get(vid, 0) == len(levels) * 2) and per_volume_n.get(vid, 0) == expected.get(vid, 0))
print('=' * 60) print('=' * 60)
logger.info(f'Finished in {total_time / 60:.1f} min | ' logger.info(f'Finished in {total_time / 60:.1f} min | '
@ -453,13 +534,11 @@ def main():
for _, g, vid, level, side, _, err in fail: for _, g, vid, level, side, _, err in fail:
logger.error(f'[GPU {g}] {vid} {level} {side}: {err}') logger.error(f'[GPU {g}] {vid} {level} {side}: {err}')
# 收尾:螺絲位置映回原 CT 空間 -> Output_dir/<run_date>/<volume_id>/cbt.nii.gz # cbt.nii.gz + x-ap.jpg / x-lat.jpg 已於各 volume 的螺絲任務完成後立刻
# label 1-10 = L1L L1R L2L L2R ... L5L L5R無 side 結果的 volume 跳過) # 寫出_fire_write Output_dir/<run_date>/<volume_id>/label 1-10 =
for vid in volumes: # L1L L1R L2L L2R ... L5L L5R不再等全部 case 跑完才統一收尾
try: logger.info(f'CBT writes: {write_ok}/{len(volumes)} volume(s) ok'
xfr_cbt_native.write_volume_cbt(vid, run_id) + (f', {write_fail} failed (見 [CBT-NATIVE] log)' if write_fail else ''))
except Exception as e:
logger.error(f'[CBT-NATIVE] {vid}: {e}')
if __name__ == '__main__': if __name__ == '__main__':

242
xfr_rerender_spinous.py Normal file
View file

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