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--extra-readers option doesn't work if there were previous conversions? #34

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melissalinkert opened this issue Nov 23, 2022 · 0 comments · Fixed by #57
Closed

--extra-readers option doesn't work if there were previous conversions? #34

melissalinkert opened this issue Nov 23, 2022 · 0 comments · Fixed by #57

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@melissalinkert
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Initial report and test data is on a private thread, which this is mentioned on.

Test steps (on Windows, with 1.0.3):

  1. open NGFF-Converter
  2. set Convert to to OME-TIFF
  3. leave Extra Arguments empty
  4. add test input file, leave output file as default
  5. click Run Conversions
  6. conversion should finish almost instantly
  7. add --extra-readers to Extra Arguments box
  8. add test input file again, set output file to some other name so both OME-TIFF files are kept
  9. click Run Conversions
  10. conversion will again finish almost instantly
  11. close and reopen NGFF-Converter
  12. set Convert to to OME-TIFF
  13. add --extra-readers to Extra Arguments box
  14. add test input file, set output file to a third unique name (so all 3 OME-TIFF files are kept)
  15. click Run Conversions
  16. conversion should take much longer
  17. inspecting the in-progress .zarr or OME-TIFF after the fact should show lots of data, where the OME-TIFFs from the first 2 steps are very small

Logs suggest that the --extra-readers flag is passed to bioformats2raw in step 9 (as expected), but for some reason it's not being respected. I kind of suspect glencoesoftware/bioformats2raw#145 might be the root cause here, but don't have concrete proof. Bumping to bioformats2raw 0.5.0 would be the first thing to test.

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