Python Tifffile：在 SageMaker 中加载图像的问题答案

【问题标题】：Python Tifffile: Problems with loading images in SageMakerPython Tifffile：在 SageMaker 中加载图像的问题
【发布时间】：2021-03-14 14:37:20
【问题描述】：

我正在使用 Tifffile 加载 .tiff-image 文件，然后将它们转换为 PIL 图像以进行处理。我使用此解决方法是因为其他方法在某些特定 TIFF 图像上存在问题。在我的本地机器上，以下代码运行良好。但是当我在 SageMaker 环境中运行代码时，它不起作用

from keras.preprocessing.image import ImageDataGenerator
import numpy as np
import scipy.ndimage
import os
import random
import tifffile
from PIL import Image
from PIL.ExifTags import TAGS
import matplotlib
#import imagecodecs
# Causes errors with some pictures
#image = np.expand_dims(scipy.ndimage.imread(image_path), 0)
    
# Causes errors with some pictures
#image = np.expand_dims(matplotlib.pyplot.imread(image_path), 0)
    
# This works on my local machine, but not in Amazon SageMaker
# Use tifffile to load the image
img = tifffile.imread(image_path)
# Make into "PIL Image" and carry on as usual
image = Image.fromarray(img)

我收到以下错误：

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-137-fe721f47a3dc> in <module>
----> 1 batch_image_augmentation(test_images, 20)

<ipython-input-134-b0ca28d40a9c> in batch_image_augmentation(path_list, n)
      3         target_dir = "./Test/" + path[:-5] + "_AUG"
      4         print(path)
----> 5         augment_image(path, target_dir, n)

<ipython-input-131-cdef2a00cd5f> in augment_image(image_path, target_dir, n)
     24     #Some images cause problems, so I try the same workaround as in the PNG-conversion script
     25     # Use tifffile to load the image
---> 26     img = tifffile.imread(image_path)
     27     # Make into "PIL Image" and carry on as usual
     28     image = Image.fromarray(img)

/usr/local/lib/python3.6/dist-packages/tifffile/tifffile.py in imread(files, **kwargs)
    719         if isinstance(files, (str, os.PathLike)) or hasattr(files, 'seek'):
    720             with TiffFile(files, **kwargs_file) as tif:
--> 721                 return tif.asarray(**kwargs)
    722 
    723     with TiffSequence(files, **kwargs_seq) as imseq:

/usr/local/lib/python3.6/dist-packages/tifffile/tifffile.py in asarray(self, key, series, level, out, maxworkers)
   2805                     typecode, product(series.shape), out=out)
   2806         elif len(pages) == 1:
-> 2807             result = pages[0].asarray(out=out, maxworkers=maxworkers)
   2808         else:
   2809             result = stack_pages(pages, out=out, maxworkers=maxworkers)

/usr/local/lib/python3.6/dist-packages/tifffile/tifffile.py in asarray(self, out, squeeze, lock, reopen, maxworkers)
   5646 
   5647             for _ in self.segments(
-> 5648                 func=func, lock=lock, maxworkers=maxworkers, sort=True
   5649             ):
   5650                 pass

/usr/local/lib/python3.6/dist-packages/tifffile/tifffile.py in segments(self, lock, maxworkers, func, sort)
   5510                 *self._offsetscounts, lock=lock, sort=sort, flat=True
   5511             ):
-> 5512                 yield decode(segment)
   5513         else:
   5514             # reduce memory overhead by processing chunks of up to

/usr/local/lib/python3.6/dist-packages/tifffile/tifffile.py in decode(args, decodeargs, keyframe, func)
   5499 
   5500         def decode(args, decodeargs=decodeargs, keyframe=keyframe, func=func):
-> 5501             result = keyframe.decode(*args, **decodeargs)
   5502             if func is not None:
   5503                 return func(result)

/usr/local/lib/python3.6/dist-packages/tifffile/tifffile.py in decode(exc, *args, **kwargs)
   5228         except KeyError as exc:
   5229             def decode(*args, exc=str(exc)[1:-1], **kwargs):
-> 5230                 raise ValueError(f'TiffPage {self.index}: {exc}')
   5231             return cache(decode)
   5232 
ValueError: TiffPage 0: <COMPRESSION.LZW: 5> requires the 'imagecodecs' package

当我尝试安装 imagecodecs 时，pip 告诉我它已经安装：

bash-4.2$ pip install imagecodecs
Requirement already satisfied: imagecodecs in /opt/conda/lib/python3.7/site-packages (2020.5.30)
Requirement already satisfied: numpy>=1.15.1 in /opt/conda/lib/python3.7/site-packages (from imagecodecs) (1.19.4)
bash-4.2$

但无论如何，如果我将 import imagecodecs 添加到导入中，我会收到以下错误：

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
<ipython-input-138-920d3e93091b> in <module>
      8 from PIL.ExifTags import TAGS
      9 import matplotlib
---> 10 import imagecodecs
     11 
     12 # https://gis.stackexchange.com/questions/365950/how-can-i-solve-this-error-from-tiff-file

ModuleNotFoundError: No module named 'imagecodecs'

有人知道这个问题的解决方案吗？

【问题讨论】：

您正在混用并且无法匹配您的 pip 和 python 版本。查看来自pip install imagecodecs 的错误消息，您会看到它是为 Python 3.7 安装的，但其余错误消息表明您正在运行 Python 3.6
谢谢，我将整个环境更改为 Pyhon 3.7，并在导入前添加了!pip install imagecodecs。现在我不再收到导入错误，但我仍然收到与 ValueError: TiffPage 0: <COMPRESSION.LZW: 5> requires the 'imagecodecs' package 相同的错误消息堆栈

标签： python image-processing python-imaging-library tiff

【解决方案1】：

我在 google colab 中遇到了类似的错误。我在“for”循环之前尝试了以下方法来读取图像： pip 安装图像编解码器

起初它不起作用，我得到了同样的错误。然后我重新启动代码，图片加载成功。

【讨论】：