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v3 tiff handling is not OME metadata friendly #953

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mlt opened this issue Mar 1, 2023 · 1 comment · May be fixed by #998
Open

v3 tiff handling is not OME metadata friendly #953

mlt opened this issue Mar 1, 2023 · 1 comment · May be fixed by #998
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plugin: tifffile type: bug

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@mlt
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mlt commented Mar 1, 2023

This is a follow up on #914. Here is the code that breaks

import imageio.v3 as iio
import imageio.v2 as iio2
import numpy, tifffile
data = numpy.random.randint(0, 255, (256, 256, 3), 'uint8')
tifffile.imwrite('bug.tif', data, ome=True)
image_rgb = iio2.imread('bug.tif') # <- ok
meta = iio.immeta('bug.tif') # <- explodes

The last line causes the following traceback

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[8], line 4
      2 import imageio.v2 as iio2
      3 image_rgb = iio2.imread('bug.tif') # <- ok
----> 4 meta = iio.immeta('bug.tif') # <- explodes

File ~\miniconda3\envs\scikit-env\lib\site-packages\imageio\v3.py:250, in immeta(uri, index, plugin, extension, exclude_applied, **kwargs)
    247     call_kwargs["index"] = index
    249 with imopen(uri, "r", **plugin_kwargs) as img_file:
--> 250     metadata = img_file.metadata(**call_kwargs)
    252 return metadata

File ~\miniconda3\envs\scikit-env\lib\site-packages\imageio\plugins\tifffile_v3.py:307, in TifffilePlugin.metadata(self, index, page, exclude_applied)
    305                 metadata.update(flavor_metadata[0])
    306             else:
--> 307                 metadata.update(flavor_metadata)
    308 else:
    309     # tifffile may return a TiffFrame instead of a page
    310     target = target.keyframe

ValueError: dictionary update sequence element #0 has length 1; 2 is required
@FirefoxMetzger
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Interesting find @mlt . Looking at the code, I can't say what could be the issue my guess is that we are probably not setting a flag correctly when reading OME.

Unfortunately, I have a bit of a backlog for ImageIO at the moment, so I can't say when I will have time to investigate this myself. However, if you want to have a go I can give you some guidance on where/how to look for the cause of the issue and then we can work on a fix together :)

mlt added a commit to mlt/imageio that referenced this issue May 30, 2023
@mlt
This fixes imageio#953
ffade45 
ome_metadata provided by Tifffile is a String
@FirefoxMetzger FirefoxMetzger linked a pull request May 31, 2023 that will close this issue
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@aseltmann aseltmann mentioned this issue Jul 4, 2023
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plugin: tifffile type: bug
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ome_metadata as provided by Tifffile is a string. Fixes #953 mlt/imageio
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@mlt @FirefoxMetzger