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John-P / wsic

Whole Slide image (WSI) conversion for brightfield histology images
MIT License
33 stars 4 forks source link

✨ Add Support For Writing To Other Zarr Stores #117

Closed John-P closed 1 year ago

John-P commented 1 year ago

Adds support for using other zarr stores when reading and writing. A zarr.StoreLike object (e.g. a MutableMapping) may be passed e.g:

writer = ZarrWriter(store=zarr.SQliteStore("mydb.sqlite"))

For the CLI, this can be specified with --store= e.g.:

wsic convert -i=... -o="mydb.sqlite" --store="sqlite"
wsic convert -i=... -o="output.zarr" --store="zip"
codecov[bot] commented 1 year ago

Codecov Report

Merging #117 (a88616c) into dev (d7095d6) will decrease coverage by 0.69%. The diff coverage is 56.09%.

@@            Coverage Diff             @@
##              dev     #117      +/-   ##
==========================================
- Coverage   88.11%   87.43%   -0.69%     
==========================================
  Files          15       15              
  Lines        2036     2069      +33     
==========================================
+ Hits         1794     1809      +15     
- Misses        242      260      +18
Impacted Files Coverage Δ
wsic/cli.py 80.80% <36.00%> (-11.28%) :arrow_down:
wsic/writers.py 86.42% <83.33%> (-0.18%) :arrow_down:
wsic/magic.py 94.02% <100.00%> (ø)
wsic/readers.py 83.15% <100.00%> (ø)

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