导入HistomicsTK遇ModuleNotFoundError，疑与Cython相关求解决

问题重现 #

在Windows系统按照官方说明安装HistomicsTK（一款数字病理图像分析Python包）后，执行导入代码时触发ModuleNotFoundError，提示找不到histomicstk.segmentation.label._trace_object_boundaries_cython模块。

导入代码：

import histomicstk as htk

import numpy as np
import scipy as sp

import skimage.io
import skimage.measure
import skimage.color

import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
%matplotlib inline

#Some nice default configuration for plots
plt.rcParams['figure.figsize'] = 10, 10
plt.rcParams['image.cmap'] = 'gray'
titlesize = 24

错误回溯：

ModuleNotFoundError                       Traceback (most recent call last)
Cell In[1], line 1
----> 1 import histomicstk as htk
      3 import numpy as np
      4 import scipy as sp

File \HistomicsTK\histomicstk\__init__.py:2
      1 # import sub-packages to support nested calls
----> 2 from . import segmentation  # must be imported before features
      3 from . import utils  # must be imported before other packages
      4 from . import (annotations_and_masks, features, filters, preprocessing,
      5                saliency, workflows)

File \HistomicsTK\histomicstk\segmentation\__init__.py:11
      8 from histomicstk.utils.simple_mask import simple_mask
     10 # import sub-packages to support nested calls
---> 11 from . import label, level_set, nuclear, positive_pixel_count
     12 from .embed_boundaries import embed_boundaries
     13 from .rag import rag

File \HistomicsTK\histomicstk\segmentation\label\__init__.py:18
     16 from .shuffle import shuffle
     17 from .split import split
---> 18 from .trace_object_boundaries import trace_object_boundaries
     19 from .width_open import width_open
     21 # list out things that are available for public use

File \HistomicsTK\histomicstk\segmentation\label\trace_object_boundaries.py:3
      1 import numpy as np
----> 3 from ._trace_object_boundaries_cython import _trace_object_boundaries_cython
      6 def trace_object_boundaries(im_label,
      7                             conn=4, trace_all=False,
      8                             x_start=None, y_start=None,
      9                             max_length=None,
     10                             simplify_colinear_spurs=True,
     11                             eps_colinear_area=0.01):
     12     """Performs exterior boundary tracing of one or more objects in a label
     13     mask. If a starting point is not provided then a raster scan will be performed
     14     to identify the starting pixel.
   (...)
     63 
     64     """

ModuleNotFoundError: No module named 'histomicstk.segmentation.label._trace_object_boundaries_cython'

解决方案 #

这个错误的核心是Cython扩展模块未被正确编译或安装，以下是具体修复步骤：

• 安装Cython依赖
  先确保系统中已安装Cython，执行命令：

  pip install cython
  

• 从源码重新编译安装HistomicsTK
  预编译的HistomicsTK包在Windows环境可能存在兼容性问题，建议直接从源码编译：

  1. 克隆项目源码（若已下载可跳过此步）：

     git clone https://github.com/DigitalSlideArchive/HistomicsTK.git
     

  2. 进入项目目录：

     cd HistomicsTK
     

  3. 以开发模式安装并编译Cython扩展：

     pip install -e .
     

     此命令会自动编译所有Cython模块，并将包以可编辑模式安装到当前Python环境。

• 确认Python环境一致性
  确保安装和运行代码使用的是同一个Python环境，避免conda与pip混用导致路径冲突。可通过以下命令查看当前Python路径：

  where python  # Windows系统
  

  安装时使用对应路径的pip，例如：

  python -m pip install -e .
  

• 验证编译结果
  进入histomicstk/segmentation/label/目录，检查是否生成了类似_trace_object_boundaries_cython.cp310-win_amd64.pyd的文件（cp310对应Python3.10版本，版本号会随你的Python版本变化），若存在则说明Cython模块编译成功。

内容的提问来源于stack exchange，提问作者hailey