bugfix/squeeze-extra-dims

[evamaxfield]

Pull request recommendations:

• Name your pull request your-development-type/short-description. Ex: feature/read-tiff-files
• Link to any relevant issue in the PR description. Ex: Resolves [admin/build-py39 #12], adds tiff file format support

Resolves #24

• Provide context of changes.

Simple fix. xarray provides a squeeze function that also squeezes the dims out too

Tagging @psobolewskiPhD if you are happy with the shape changes reported in the tests please let me know. Will merge and release a new version on Monday.

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[codecov-commenter]

Codecov Report

Merging #32 (1b7785c) into main (0e888bc) will not change coverage.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##             main      #32   +/-   ##
=======================================
  Coverage   83.05%   83.05%           
=======================================
  Files           5        5           
  Lines         177      177           
=======================================
  Hits          147      147           
  Misses         30       30           

Impacted Files	Coverage Δ
napari_aicsimageio/tests/test_core.py	100.00% <ø> (ø)
napari_aicsimageio/core.py	85.45% <100.00%> (ø)

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[psobolewskiPhD]

Awesome!
For the regular TIFF: s_1_t_1_c_1_z_1.tiff I get:

AICSImageIO: Reader will load image in-memory: False
10:19:20 ERROR Failed to parse XML for the provided file.
10:19:20 ERROR not well-formed (invalid token): line 1, column 6
10:19:20 ERROR Failed to parse XML for the provided file.
10:19:20 ERROR not well-formed (invalid token): line 1, column 6
AICSImageIO: Reader will load image in-memory: False

But I think it opened properly.
But the CZI and LIF (s_1_t_1_c_2_z_1.lif) files work great!

[evamaxfield]

Awesome!
For the regular TIFF: s_1_t_1_c_1_z_1.tiff I get:

AICSImageIO: Reader will load image in-memory: False
10:19:20 ERROR Failed to parse XML for the provided file.
10:19:20 ERROR not well-formed (invalid token): line 1, column 6
10:19:20 ERROR Failed to parse XML for the provided file.
10:19:20 ERROR not well-formed (invalid token): line 1, column 6
AICSImageIO: Reader will load image in-memory: False

But I think it opened properly.
But the CZI and LIF (s_1_t_1_c_2_z_1.lif) files work great!

Yep. It is simply running through the readers. It tries the OME-TIFF reader and fails but then rolls back to the TIFF reader. No worries.

[psobolewskiPhD]

Not to nag, but...any idea when this fix may end up in a release?
❤️

[evamaxfield]

If blocking I can release a new patch right now but likely next week.

The plan of work is as follows:

1. Remove CZI install pattern from base aicsimageio: admin/remove-czi-install-pattern aicsimageio#376
2. Release 4.6.0 version of aicsimageio
3. Update this very old PR to use aicsimageio>=4.6.0 and incorporate the above install pattern changes / dep changes

So really just waiting on eyes on 1, the CZI install pattern changes. But now that I look at this, nothing is directly holding it up. I could make and release the dep changes now.

I will do so now.