Add setting the objective magnification when patching #287
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in fact, i am not sure why CLAM doesn't directly support patching at different magnification. For example, when i download wsi from TCGA, some wsi has no patch level corresponds to 20X magnification, but UNI/CONCH/Prov-Gigapath/TITAN all utilize 20X magnification |
For example, if the maximum objective magnification of WSI is 20x, slices can be directly performed at patch_level 0, but when the maximum magnification is 40x, slices need to be performed at 2 times the downsample rate. |
you are right. the other issue also point out this problem |
The current code only supports patching at a specified 'patch_level' of the WSI. However, in actual research, the objective magnification is usually specified for patching.
Therefore, I added functionality to the fast patching pipeline to allow specifying the objective magnification during patching. The objective magnification attribute is set to 'None' by default. When the objective magnification is specified, the 'patch_level' will be ignored, and the code will automatically select an appropriate 'patch_level' and corresponding 'custom_downsample' based on the WSI. Additionally, I made corresponding modifications to 'dataset_h5.py' to enable custom downsampling during feature extraction.