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SBU-BMI / wsinfer

🔥 🚀 Blazingly fast pipeline for patch-based classification in whole slide images
https://wsinfer.readthedocs.io
Apache License 2.0
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Incorrect command to convert model outputs to GeoJson in documentation #175

Closed swaradgat19 closed 11 months ago

swaradgat19 commented 11 months ago

The command to convert the model outputs to geojson format probably has a typo. On the documentation, it is given: wsirun togeojson results/ geojson-results/. This command gives the error: Command not found

On changing it to: wsinfer run togeojson Results/ geojson-Results/, it gives the following error: 

Try 'wsinfer run --help' for help.

Error: Missing option '-i' / '--wsi-dir'.

What is the correct command to convert the model-outputs to the geojson format?

Link to the command in documentation

kaczmarj commented 11 months ago

oops, the correct command is wsinfer togeojson. would you like to put in a pr with a fix?

swaradgat19 commented 11 months ago

Sure. I'll do it

swaradgat19 commented 11 months ago

For the Stony Brook format, is this the correct command?

  wsinfer tosbu \
      --wsi-dir slides/ \
      --execution-id UNIQUE_ID_HERE \
      --study-id STUDY_ID_HERE \
      --make-color-text \
      --num-processes 16 \
      results/ \
      results/model-outputs-sbubmi/
kaczmarj commented 11 months ago

For the Stony Brook format, is this the correct command?

it is, but the stony brook conversion isn't quite finished yet... i wouldn't use it at this point.