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NKI-AI / slidescore-api

Python utilities to interface with SlideScore
Apache License 2.0
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No shapely annotations #16

Closed rharkes closed 2 years ago

rharkes commented 2 years ago

Describe the bug When getting annotations with shapely I get 0kb .json files.

To Reproduce My study with ID 1764 has 100 cases with 3 slides per case. If you try to get annotations using -o JSON I get 300 .json files in the output folder. If I try with -o SHAPELY I get a folder structure, but it contains .json files of 0kb

Expected behavior .json files with the annotations for each slide.

Environment SlideScore Python API version: 0.1.0 How installed: pip Python version: 3.9 Operating System: windows 10

Additional context I discussed this issue with Ajey on teams.

AjeyPaiK commented 2 years ago

Thanks Rolf for finding this bug in your use case. Currently, the shapely annotations are downloaded with the assumption that there is only one slide per case and hence, one annotation.

I will work on improving this to include multiple slides.

Great catch!

rharkes commented 2 years ago

Thanks. I just cloned the repository and tried to reproduce the error in a clean venv, but suddenly there was no error anymore. The .json files were there.

In my old environment I can still reproduce the error.

AjeyPaiK commented 2 years ago

Ah, it was probably an older version of the repository! Good to know!