Missing parameters in sample configs about gandlf HOT 8 CLOSED

Thanks, the error is gone now. :)

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Hey Karol,

I believe this is fixed in the refactor branch. 😄

https://github.com/CBICA/GaNDLF/blob/refactor/GANDLF/data/ImagesFromDataFrame.py#L71

We were using psize earlier and have since moved to using the more verbose (and in our opinion, clearer) variable name of patch_size in the refactor branch. Hope this clears up the confusion!

Cheers!

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This is actually the refactor branch^^
https://github.com/CBICA/GaNDLF/blob/a5a7d9c945edb003d02f50dc3a69eb830d564247/GANDLF/preprocessing.py#L179
psize is still in the init() here.
There are about 20 more places in the code where psize is assigned or checked, but I don't know if that is relevant to the problem.

Best
Karol

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Got it. I have made fixes in the training side, while @Geeks-Sid is working on the inference part.

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Awesome! Glad we are able to keep this working with a short turnaround! 😄

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There are actually still some psize errors when I try to run inference. But training is working :)

Traceback (most recent call last):
  File "/home/me/Documents/GitKraken/GaNDLF/gandlf_run", line 75, in <module>
    main()
  File "/home/me/Documents/GitKraken/GaNDLF/gandlf_run", line 72, in main
    InferenceManager(dataframe=data_full, headers = headers, outputDir=model_path, parameters=parameters, device=device)
  File "/home/me/Documents/GitKraken/GaNDLF/GANDLF/inference_manager.py", line 36, in InferenceManager
    inferenceLoopRad(inferenceDataFromPickle=inferenceData_full, headers=headers, outputDir=outputDir,
  File "/home/me/Documents/GitKraken/GaNDLF/GANDLF/inference_loop.py", line 41, in inferenceLoopRad
    psize = parameters['psize']
KeyError: 'psize'

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Yup, inference is not yet complete (this is on @Geeks-Sid's plate at this moment).

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I believe this should now be fixed. @Karol-G please comment/re-open if you see issues.

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