Problem with reading 2D dataset - Scale vector of length 3 to 2d data

[sebi06]

The bug is decribed here:

https://forum.image.sc/t/napari-napari-aicsimageio-faild-to-open-ome-tiff/68942?u=sebi06

[evamaxfield]

Will look at this maybe next week.

[toloudis]

I believe this is an issue for the napari plugin and not aicsimageio - is that correct?

[evamaxfield]

I believe it to be an issue with the plugin not aicsimageio-core

[psobolewskiPhD]

This issue relates to the fact that the original data looks like this:

In [4]: img = aicsimageio.AICSImage(path)
In [5]: img.shape
Out[5]: (1, 1, 1, 2755, 3675)

the plugin squeezes the singletons and returns a 2D array.
But the metadata used for the scale info is:

In [9]: img.physical_pixel_sizes
Out[9]: PhysicalPixelSizes(Z=1.0, Y=0.227, X=0.227)

Edit: in contrast, the test files report Z=None in these types of cases, so then it's handled here:

napari-aicsimageio/napari_aicsimageio/core.py

Lines 93 to 95 in a7aad09

	scale_val = getattr(img.physical_pixel_sizes, dim)
	if scale_val is not None:
	scale.append(scale_val)

I think I have an idea how to fix, will try a PR.

[psobolewskiPhD]

Should be fixed with #60 which has been released.
Feel free to re-open if this pops up again.