Project-MONAI / Project-MONAI/MONAI
WSIReader mirror flip inference map
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Pathology/Microscopy
- Dominant language
- Python
- Stars
- 8.7k
- Forks
- 1.6k
- Avg merge
- 5d 1h
- Merged PRs (30d)
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Description
Describe the bug
I am using WSIReader as either transform or SlidingPatchWSIDataset, the resultant maps are mirror flipped always.
To Reproduce
Steps to reproduce the behavior:
- Go to https://github.com/Project-MONAI/tutorials/blob/main/pathology/hovernet/inference.py
- Either convert this line to WSIReader https://github.com/Project-MONAI/tutorials/blob/02911a9bf11934516d4f93f29a46b3acd3dcc58e/pathology/hovernet/inference.py#L69
or remove it and use SlidingPatchWSIDataset. - Run the script and check the resultant maps.
Expected behavior
It should have the same orientation as the inputed images. The current implementation of the script works well.
CC. @drbeh
Thank you
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with pathology/hovernet/inference.py at the referenced line and reproduce the orientation issue using WSIReader, then compare it with the current implementation and SlidingPatchWSIDataset. Done means the resultant maps have the same orientation as the input images in both paths.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- computer-vision, data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100