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markowetzlab / pathml-tutorial

A tutorial demonstration of pathml on an example dataset for the manuscript "PathML: A unified framework for WSI analysis with deep learning" by Berman et al.
GNU General Public License v3.0
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error running the tutorial datasets : #5

Open archanabhardwaj opened 2 years ago

archanabhardwaj commented 2 years ago

Thanks for this interesting method. I have started following the pathml-tutorial datasets. While running the sample code, I am getting following error :

FileNotFoundError: [Errno 2] No such file or directory: '../pathml/pathml/models/deep-tissue-detector_densenet_state-dict.pt'

But looking back at the "code", I realized that pathml library path is properly defined as expected. sys.path.append('/user/processing/pathml') sys.path.append('/user/processing/pathml-tutorial/Pytorch-UNet')

I would appreciate if you can help me to fix this issue.

Thanks in Advance A

agberman commented 2 years ago

Hi A,

I've seen this issue crop up before on some machines. If I recall, the way to fix it is to go into the code and modify the path '../pathml/pathml/models/deep-tissue-detector_densenet_state-dict.pt' where it appears in line 1648 of the slide.py file and change it to be an absolute path to that state dict file within the pathml folder.

archanabhardwaj commented 2 years ago

Hi I modify the path and its working. Thanks.