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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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Question about extracting features on Camelyon16 #181

Closed Raymvp closed 1 year ago

Raymvp commented 1 year ago

When extracting features for camelyon16, when extracting tumou78, I encountered this error: These are the following parts of the error： File "/home/ubuntu/anaconda3/envs/clam/lib/python3.7/site-packages/torch/utils/data/_utils/worker.py", line 302, in _worker_loop data = fetcher.fetch(index) File "/home/ubuntu/anaconda3/envs/clam/lib/python3.7/site-packages/torch/utils/data/_utils/fetch.py", line 49, in fetch data = [self.dataset[idx] for idx in possibly_batched_index] File "/home/ubuntu/anaconda3/envs/clam/lib/python3.7/site-packages/torch/utils/data/_utils/fetch.py", line 49, in data = [self.dataset[idx] for idx in possibly_batched_index] File "/home/ubuntu/CLAM/datasets/dataset_h5.py", line 151, in getitem img = self.wsi.read_region(coord, self.patch_level, (self.patch_size, self.patch_size)).convert('RGB') File "/home/ubuntu/anaconda3/envs/clam/lib/python3.7/site-packages/openslide/init.py", line 237, in read_region self._osr, location[0], location[1], level, size[0], size[1] File "/home/ubuntu/anaconda3/envs/clam/lib/python3.7/site-packages/openslide/lowlevel.py", line 311, in read_region _read_region(slide, buf, x, y, level, w, h) File "/home/ubuntu/anaconda3/envs/clam/lib/python3.7/site-packages/openslide/lowlevel.py", line 225, in _check_error raise OpenSlideError(err) openslide.lowlevel.OpenSlideError: Corrupt JPEG data: premature end of data segment

Have you ever been in a similar situation before?

fedshyvana commented 1 year ago

I am not aware of this issue sorry : (