FEAT: tifffile v3

[FirefoxMetzger]

Closes: #818, #437 (must be closed manually)

This PR updates the tifffile plugin to use the v3 plugin API. It still needs some documentation, but I want to park it here so that interested parties can give feedback :)

[FirefoxMetzger]

Note to self: This PR needs updating to use index=... instead of index=None when bulk reading.

[lschr]

Thanks for this!

When looking through the code, I found a possible inconsistency: in metadata, it seems like index refers to the page, while in all other methods, index refers to the series and page refers to the page.

[FirefoxMetzger]

@ishr Yes, that's true. I have to dig a bit further into tifffile to see if and how series-level metadata is handled and then update TifffilePlugin.metadata.

[FirefoxMetzger]

Okay, now everything should be implemented and documented. What is still missing is to get full code coverage and then a final review.

[lschr]

Awesome!

It seems like the documentation of properties() is not quite right though. What is described as behavior for index=None is actually true for index=Ellipsis.

[FirefoxMetzger]

Oh yes, good catch. The documentation also needs to update to index=... instead of index=None

[FirefoxMetzger]

@mkcor I know you have been using tifffile a lot, so this might be interesting for you. I've written a v3 plugin for tifffile to expose all its "new" features in ImageIO. Feel free to give it a try and tell me what you think :)

The PR is ready and I will merge towards the end of the week unless anything major pops up.

[mlt]

I'm getting a regression with metadata description field containing XML (Open Microscopy Environment). I can navigate metadata dict alright with v2 but not with v3 & immeta :(

ValueError                                Traceback (most recent call last)
Cell In[13], line 12
     10 image_rgb = iio.imread(filename)
     11 # meta = image_rgb.meta
---> 12 meta = iio.immeta(filename)
     13 fig = plt.figure()
     14 ax = fig.gca()

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]

@mlt Interesting find. Could you create a dedicated issue for that?