volread on tifffile produces the wrong shape

This is a regression from 2.9.0 first shared by @mkcor in https://github.com/scikit-image/scikit-image/pull/5262.

Reproducing example:

img = iio.volread('http://cmci.embl.de/sampleimages/NPCsingleNucleus.tif')
img.shape  
# in v2.10.3 (30, 180, 183)
# in v2.9.0 (15, 2, 180, 183)

It traces back to something that, at least to me, is unexpected behavior in v2.9.0. Calling imageio.imread on the above tiff (in either version of ImageIO) returns a single page of the file, not a single image. I.e.,

import imageio as iio
img = iio.imread('http://cmci.embl.de/sampleimages/NPCsingleNucleus.tif')
img.shape  # (180, 183) not the expected (2, 180, 183)

Consequentially, iterating over single images and stacking them, doesn’t yield a stack of channel-first images, but a stack of pages:

reader = iio.get_reader('http://cmci.embl.de/sampleimages/NPCsingleNucleus.tif', mode="i") 
img = np.stack([reader.get_data(index=x) for x in range(reader.get_length())])
img.shape # (30, 180, 183)

Reading a volume, on the other hand, does the expected thing and produces a stack of channel-first images (in v2.9.0)

img = iio.volread('http://cmci.embl.de/sampleimages/NPCsingleNucleus.tif')
img.shape  # (15, 2, 180, 183)

however, does the page-stacking thing in v2.10.3:

img = iio.volread('http://cmci.embl.de/sampleimages/NPCsingleNucleus.tif')
img.shape  # (30, 180, 183)

@cgohlke @almarklein @mkcor (and others who use TIFF more than me) What is expected behavior here? Would you expect imread to return a single image (shape: (2, 180, 183)) or a single page (shape: (180, 183))? I am leaning towards a single image, but I am open for comments here.

Depending on this answer, I would either look into a bugfix fir get_data(index=...) (any version) or volread(...) (v2.10.3).

[FirefoxMetzger]

@GenevieveBuckley The fix should roll out to PyPI tonight.

[FirefoxMetzger]

Nope, sorry 😦 It looks like that really is it for ImageJ files

Indeed. I also just found the relevant section of code in our vendored tiffile: It literally just parses the metadata string and sets the shape according to the channel and frame entries . . .

https://github.com/imageio/imageio/blob/master/imageio/plugins/_tifffile.py#L2172-L2252

On the bright side though, it makes the fix efficient, because we don’t have to parse the full file to figure out the image’s shape. All that is needed is to read the first page and we can learn how many pages to read for a imread(index=N) call.

I especially liked “The ImageJ file format is undocumented.”

🤣 lol.

Makes you wonder how @cgohlke figured out how to correctly read ImageJ hyperstacks in the first place. Big props.