用 python 写一个 tiff 堆栈并保留文件名

Question

我有一个包含 5 张 tiff 图像的文件夹，我想将它们放在一个堆栈文件中。

img01.tiff、img20.tiff、img25.tif、img30.tif、img50.tif

处理后，我想将该堆栈转换为单个图像，并保留文件名。

我做的堆叠：

import tifffile as tiff
import os
from natsort import natsorted

path='img_folder'
output_filename='stack.tiff'
with tiff.TiffWriter(output_filename, bigtiff=True) as tif_writer:
    for idx, filename in enumerate(natsorted(os.listdir(path))):
        print(filename)
        img=tiff.imread(os.path.join(path,filename),name=filename)
        tif_writer.save(img)

我尝试在描述参数或元数据（信息和标签）上进行书写，但没有成功：

tif_writer.save(img, photometric='minisblack', metadata={'Info': filename}, description=filename)

无论如何文件名信息都丢失了，或者我现在不知道如何访问它。

如有任何帮助，我们将不胜感激！

Answer 1

来自source,

[description & metadata are] saved with the first page of a series only.

编辑：我更新了这个例子以包括@cgohlke

建议的两个选项

选项 1：编写单独的系列

默认情况下，像这样按顺序使用 TiffWriter.write 或 TiffWriter.save 将在结果图像中创建一个单独的系列并将描述保存到第一个 [=每个系列第 29=]页。

import numpy as np
import tifffile

with tifffile.TiffWriter('temp.tif') as tif:
  for i in range(4):
    filename = f"image_{i}"
    img = np.random.randint(0, 1023, (256, 256), 'uint16')
    tif.save(img, photometric='minisblack', description=filename)


with tifffile.TiffFile('temp.tif') as tif:
  for series in tif.series:
    first_page = series[0]
    print(first_page.description)
  
  # tif.asarray returns the first series by default, 
  # so `key` is needed to create the stack from multiple series.
  stack = tif.asarray(key=slice(None))
  print(stack.shape)

# image_0
# image_1
# image_2
# image_3
# (4, 256, 256)

选项 2：写一个系列

通过设置metadata=None，您可以将单独的页面写入同一系列并遍历页面以获取描述。

import numpy as np
import tifffile

with tifffile.TiffWriter('temp.tif') as tif:
  for i in range(4):
    filename = f"image_{i}"
    img = np.random.randint(0, 1023, (256, 256), 'uint16')
    tif.save(img, photometric='minisblack', description=filename, metadata=None)


with tifffile.TiffFile('temp.tif') as tif:
  for page in tif.pages:
    print(page.description)

  stack = tif.asarray() # no need for `key` because pages in same series
  print(stack.shape)

# image_0
# image_1
# image_2
# image_3
# (4, 256, 256)

用 python 写一个 tiff 堆栈并保留文件名

Write a tiff stack with python and keep file name

python

tiff

image

选项 1：编写单独的系列

选项 2：写一个系列