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mahmoodlab / CLAM

Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering
http://clam.mahmoodlab.org
GNU General Public License v3.0
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Coordinates mismatch #172

Closed nam1410 closed 1 year ago

nam1410 commented 1 year ago

@fedshyvana

When I try to print the shape of "data" from https://github.com/mahmoodlab/CLAM/blob/9482cbc72df522087cfbaa3e6b52da5207a7980a/utils/core_utils.py#L234 I get the size (M, 1024)

However, if I try to print the shape of "features" from https://github.com/mahmoodlab/CLAM/blob/9482cbc72df522087cfbaa3e6b52da5207a7980a/create_heatmaps.py#L34 I get a different size (N, 1024) for the same slide_id.

Note: Magnification levels are the same for both images, and I have not considered any explicit ROIs.

Kindly look into this.

Thank you.

fedshyvana commented 1 year ago

I don't think create_heatmaps use the same set of features/coordinates as what you previously generate/store by default. But you can specify the same process list with same patching/segmentation parameters as what you used before if you want to reproduce the original setting.

nam1410 commented 1 year ago

Thank you. I have figured out the mistake while passing the coordinates to the block map. (I was maintaining the same setting throughout the process)