skan.Skeleton返回整数而非骨架对象，调用summarize触发类型错误

问题背景 #

已通过scikit-image的morphology.skeletonize完成图像骨架化，可通过skan的draw.overlay_skeleton_2d正常查看骨架，但调用Skeleton类和summarize方法统计分支长度时触发类型错误。

错误信息 #

TypeError                                 Traceback (most recent call last)
<ipython-input-3-5924e1b8ffc8> in <module>
      4 # fig, ax = plt.subplots()
      5 # draw.overlay_skeleton_2d(img, skeleton0, dilate=1, axes=ax)
----> 6 branch_data = summarize(Skeleton(skeleton0))
      7 branch_data.head()

~\AppData\Roaming\Python\Python38\site-packages\skan\csr.py in __init__(self, skeleton_image, spacing, source_image, _buffer_size_offset, keep_images, junction_mode, unique_junctions)
    383         self.nbgraph = csr_to_nbgraph(graph, pixel_values)
    384         self.coordinates = coords
--> 385         self.paths = _build_skeleton_path_graph(
    386                 self.nbgraph, _buffer_size_offset=_buffer_size_offset
    387                 )

~\AppData\Roaming\Python\Python38\site-packages\skan\csr.py in _build_skeleton_path_graph(graph, *, _buffer_size_offset=None)
    259 def _build_skeleton_path_graph(graph, *, _buffer_size_offset=None):
    260     if _buffer_size_offset is None:
--> 261         max_num_cycles = graph.indices.size // 4
    262         _buffer_size_offset = max_num_cycles
    263     degrees = np.diff(graph.indptr)

TypeError: expected dtype object, got 'numpy.dtype[int32]'

代码示例 #

import cv2
from skan import draw, skeleton_to_csgraph, Skeleton, summarize
from skimage import morphology
# import numpy as np

from matplotlib import pyplot as plt
%matplotlib notebook

# load image and convert to bool
img = cv2.imread(save_p + "\\" + img_name + ".png")
img = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
img = img.astype(bool)

# skeletonize
skeleton0 = morphology.skeletonize(img)

### check skeleton
# fig, ax = plt.subplots()
# draw.overlay_skeleton_2d(img, skeleton0, dilate=1, axes=ax)

### from Documentation
branch_data = summarize(Skeleton(skeleton0))      # ignoring scaling for now
branch_data.head()

# Skel_obj = Skeleton(skeleton0)        # testing this but same problem
# Skel_obj.path_lengths(0)

环境版本 #

• numpy 1.23.4
• scikit-image 0.19.3
• pandas 1.3.4
• skan 0.10.0
• numba 0.50.1
• Windows 10

解决方案建议 #

1. 版本兼容调整：skan 0.10.0属于旧版本，与numpy 1.23.x的类型处理逻辑存在冲突。可选择：
   • 降级numpy到1.21.x及以下版本，匹配skan 0.10.0的兼容范围
   • 升级skan到0.16.x及以上版本，新版本修复了与高版本numpy的兼容问题
2. 调整数组类型：将骨架图像转换为uint8类型后再传入Skeleton，需先导入numpy：

   import numpy as np
   # ... 原有代码 ...
   skeleton0 = morphology.skeletonize(img).astype(np.uint8)
   

3. 更新numba：当前numba 0.50.1版本过旧，无法很好适配numpy 1.23.x，可升级numba到0.56.x版本（与numpy 1.23兼容），再配合skan版本更新使用

内容的提问来源于stack exchange，提问作者mats_student_olie