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impromptuRong / hd_wsi

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Error on WSI inferences #3

Open NaokiThread opened 7 months ago

NaokiThread commented 7 months ago

When I tried hd_wsi on WSI inference with --save_images, this error occurred. 

TypeError: write() got an unexpected keyword argument 'compress'

Additionally, In order to resolve this, I tried removing "compress" from config.py, but then the error below occurred.

ValueError: data too large for standard TIFF file ⇒ ask author

If you know the way to solve this problem, please let me know.

NaokiThread commented 7 months ago

If you do not know the way to solve this problem, could you please tell me the way to make annotated WSI thumbnails from tensor or csv data that are output by run_wsi_inference.py?

impromptuRong commented 5 months ago

Hi Naoki,

Sorry about the delay. The issue is caused by a changes in package tifffile and file size . I updated the code to support bigtiff and latest tifffile. To generate thumbnails for WSI and annotated WSI, you can try run summarize_tme_features.py, the script will export reduced sizes of slide thumbnail and annotation thumbnail.

Let me know if you still meet similar problem.