MAINT: TIFFReader OME-TIFF Multiplex

[vqdang]

Prototype for OME TIFF written for multiple images, and a bit of bug fix. This is mainly for reference and discussion, feel free to delete/close .

[vqdang]

@John-P Aside from the adhoc implementation for multiplex OME TIFF no z-axis, no time axis. This is the fix location of what I think is a bug.

https://github.com/TissueImageAnalytics/tiatoolbox/blob/794662db6043c9fa230b8e4a01d7b7dd01a06661/tiatoolbox/wsicore/wsireader.py#L3552-L3585

[rogertrullo]

@vqdang @John-P this seems related to https://github.com/TissueImageAnalytics/tiatoolbox/issues/452, if so, maybe we can include the fix on resolution reading in this PR

[shaneahmed]

@vqdang you created this branch from quite an old commit. Please can you check this merge? https://github.com/TissueImageAnalytics/tiatoolbox/pull/471/commits/cd1dc048ec0e76b6a2e9a37ad1a0423359cf8313

[shaneahmed]

@vqdang @John-P this seems related to #452, if so, maybe we can include the fix on resolution reading in this PR

Thanks @rogertrullo We are looking into #452 but would keep it separate from this PR as this is only related to adding multiplex imaging support.

[codecov[bot]]

Codecov Report

Merging #471 (0d293b0) into develop (ec654f5) will decrease coverage by 0.36%. The diff coverage is 31.57%.

@@             Coverage Diff             @@
##           develop     #471      +/-   ##
===========================================
- Coverage    99.62%   99.26%   -0.37%     
===========================================
  Files           61       61              
  Lines         6214     6229      +15     
  Branches      1033     1039       +6     
===========================================
- Hits          6191     6183       -8     
- Misses          10       29      +19     
- Partials        13       17       +4     

Impacted Files	Coverage Δ
tiatoolbox/wsicore/wsireader.py	95.18% <23.52%> (-2.88%)	:arrow_down:
tiatoolbox/models/engine/semantic_segmentor.py	100.00% <100.00%> (ø)

:mega: We’re building smart automated test selection to slash your CI/CD build times. Learn more

[John-P]

This probably needs more thorough testing etc but as a quick fix to get things working this looks good.

[John-P]

Closing for now while we create a new PR to improve TIFF support in general.