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try to use optimized codepath through ome-types #478

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merged 4 commits into from
Apr 5, 2023

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toloudis
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@toloudis toloudis commented Apr 3, 2023

Description

Using OmeTiffReader often shows this warning

....../site-packages/ome_types/_convenience.py:106: FutureWarning: The default XML parser will be changing from 'xmlschema'
 to 'lxml' in version 0.4.0.  To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the 
new behavior), or'xmlschema' (to retain the old behavior).

Passing "lxml" explicitly will not only remove the warning but actually causes a very noticeable speedup in initial parsing of ome-tiff metadata.

Addresses #479 (coincidentally reported after this PR) and a report from an internal user.

There is also a "bonus" test fix due to calling a deprecated iteritems in a pandas Series object.

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codecov-commenter commented Apr 3, 2023

Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (65226e2) 94.16% compared to head (4498eaf) 94.16%.

Additional details and impacted files
@@           Coverage Diff           @@
##             main     #478   +/-   ##
=======================================
  Coverage   94.16%   94.16%           
=======================================
  Files          48       48           
  Lines        4197     4197           
=======================================
  Hits         3952     3952           
  Misses        245      245           
Impacted Files Coverage Δ
aicsimageio/readers/tiff_glob_reader.py 86.77% <ø> (ø)
aicsimageio/readers/ome_tiff_reader.py 92.98% <100.00%> (ø)
aicsimageio/tests/writers/test_ome_tiff_writer.py 100.00% <100.00%> (ø)
aicsimageio/writers/ome_tiff_writer.py 92.30% <100.00%> (ø)

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@toloudis toloudis marked this pull request as ready for review April 4, 2023 15:42
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@evamaxfield evamaxfield left a comment

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Yay. Less warnings!

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@SeanLeRoy SeanLeRoy left a comment

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🙌

@toloudis toloudis merged commit e2dd9c7 into main Apr 5, 2023
@toloudis toloudis deleted the feature/optimized-ome-types branch April 5, 2023 21:54
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5 participants