Tifffile error when accessing dims attribute

[jplumail]

System and Software

• aicsimageio Version: 4.11.0
• Python Version: 3.10.11
• Operating System: Ubuntu on WSL2

Description

When I open an TIFF image with AICSImage and ask for the dims attribute, I get an error: TypeError: unexpected keyword argument: is_mmstack.

Full Traceback:

Traceback (most recent call last):
  File "/home/plumail/aics-bug/bug.py", line 4, in <module>
    print(AICSImage(p).dims)
  File "/home/plumail/miniconda3/envs/aicsimageio2/lib/python3.10/site-packages/aicsimageio/aics_image.py", line 574, in dims
    dims=self.xarray_dask_data.dims, shape=self.shape
  File "/home/plumail/miniconda3/envs/aicsimageio2/lib/python3.10/site-packages/aicsimageio/aics_image.py", line 438, in xarray_dask_data
    and dimensions.DimensionNames.MosaicTile in self.reader.dims.order
  File "/home/plumail/miniconda3/envs/aicsimageio2/lib/python3.10/site-packages/aicsimageio/readers/reader.py", line 532, in dims
    self._dims = Dimensions(dims=self.xarray_dask_data.dims, shape=self.shape)
  File "/home/plumail/miniconda3/envs/aicsimageio2/lib/python3.10/site-packages/aicsimageio/readers/reader.py", line 359, in xarray_dask_data
    self._xarray_dask_data = self._read_delayed()
  File "/home/plumail/miniconda3/envs/aicsimageio2/lib/python3.10/site-packages/aicsimageio/readers/tiff_reader.py", line 459, in _read_delayed
    with TiffFile(open_resource, is_mmstack=False) as tiff:
  File "/home/plumail/miniconda3/envs/aicsimageio2/lib/python3.10/site-packages/tifffile/tifffile.py", line 3142, in __init__
    raise TypeError(f'unexpected keyword argument: {key}')
TypeError: unexpected keyword argument: is_mmstack

Expected Behavior

It should return the Dims object.

Reproduction

conda create -n aicsimageio-all-env python=3.10
conda activate aicsimageio-all-env
pip install aicsimageio[all]

Run

from aicsimageio import AICSImage
print(AICSImage("https://people.math.sc.edu/Burkardt/data/tif/at3_1m4_01.tif").dims)"

Environment

The version of tifffile installed is 2022.4.8.

When I install aicsimageio without [all], I get tifffile version 2023.4.12 and the bug disappears.

[jplumail]

This line

aicsimageio/aicsimageio/readers/tiff_reader.py

Line 459 in e0f9b0d

with TiffFile(open_resource, is_mmstack=False) as tiff:

is causing trouble.

Tifffile requirements should be over 2023.3.15: is_mmstack was added in this commit cgohlke/tifffile@fc5f5a4

Currently the requirements are

aicsimageio/setup.py

Line 111 in e0f9b0d

"tifffile>=2021.8.30",

and when you install aicsimageio[all], it installs bfio which requires tifffile to be under a certain version

aicsimageio/setup.py

Line 39 in e0f9b0d

"bfio": ["bfio>=2.3.0", "tifffile<2022.4.22"],

which causes the bug !

[toloudis]

Thanks for the detailed report! We are looking into this and will try to resolve it soon.

[BrianWhitneyAI]

Hey, @jplumail! thanks for submitting this. As of tifffile 2023.3.15 the default reading of mmstack images has changed to require the flag is_mmstack and as a result of this, we had to adjust our tiff readers to have a minimum dependency of 2023.3.15.

Unfortunately, our installation of bfio with this version of tifffile breaks tests when dealing with tiled reading because of an issue with bfio backend. I've created an issue for that here: PolusAI/bfio#42 (comment).

Once that is resolved we can unpin tifffile for bfio and aicsimageio[all] will work smoothly again, In the meantime you may need to manually decide which version to use depending on what reader you are looking to use. let me know if you have any questions!

[jplumail]

I've been using aicsimageio without [all] since then. Thanks!

[Nicholas-Schaub]

Hey all.

We originally used tifffile as a starting point for our accelerated tiff reader. Since then, we have played this continual cat and mouse game with tifffile, where we make updates to bfio, and shortly thereafter the devs on tifffile create a new change that breaks it.

We will investigate a solution.

[jplumail]

It seems that bfio is now fixed: PolusAI/bfio#42

[toloudis]

Thanks for the heads-up on this!