search

Project-MONAI / MONAI

AI Toolkit for Healthcare Imaging
https://monai.io/
Apache License 2.0
5.73k stars 1.05k forks source link

Update pathology tools to handle deparate `WSIReader` #6276

Closed yiheng-wang-nv closed 1 year ago

yiheng-wang-nv commented 1 year ago

Since monai.data.image_reader.WSIReader is deparate, I think we should avoid calling it. For example, class LesionFROC still uses it (see here BY the way, this class is also used in bundle: https://github.com/Project-MONAI/model-zoo/blob/dev/models/pathology_tumor_detection/scripts/lesion_froc.py

In addition, there may have some typos in the deparate class, may need to double confirm related places. For example: https://github.com/Project-MONAI/MONAI/blob/05533abc2974631cf65d08d8719c09a27f16bed9/monai/data/image_reader.py#L1241 The msg_suffix is wrong since we do not have monai.wsi_reader.WSIReader.

yiheng-wang-nv commented 1 year ago

Hi @drbeh , may need your help to address this ticket, thanks in advance!

drbeh commented 1 year ago

Hi @yiheng-wang-nv, that is addressed in #6262, so after the PR is merged, this issue should be resolved.

drbeh commented 1 year ago

close it in favor of #6262.