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Bug in colab notebook, TorchIO Getting Started tutorial

See original GitHub issue

Is there an existing issue for this?

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Bug summary

In the TorchIO Getting Started tutorial (https://colab.research.google.com/github/fepegar/torchio-notebooks/blob/main/notebooks/TorchIO_tutorial.ipynb), I noticed a bug which seems due to the version of TorchIO.

Switching from TorchIO version: 0.18.57

to TorchIO version: 0.18.76, it fixed the issue

Code for reproduction

In ## Training a network ### Whole images section

one_batch = next(iter(training_loader))

Actual outcome

A FileNotFoundError is produced

Error messages

FileNotFoundError: Caught FileNotFoundError in DataLoader worker process 0.
Original Traceback (most recent call last):
  File "/usr/local/lib/python3.7/dist-packages/torch/utils/data/_utils/worker.py", line 287, in _worker_loop
    data = fetcher.fetch(index)
  File "/usr/local/lib/python3.7/dist-packages/torch/utils/data/_utils/fetch.py", line 52, in fetch
    return self.collate_fn(data)
  File "/usr/local/lib/python3.7/dist-packages/torch/utils/data/_utils/collate.py", line 157, in default_collate
    return elem_type({key: default_collate([d[key] for d in batch]) for key in elem})
  File "/usr/local/lib/python3.7/dist-packages/torch/utils/data/_utils/collate.py", line 157, in <dictcomp>
    return elem_type({key: default_collate([d[key] for d in batch]) for key in elem})
  File "/usr/local/lib/python3.7/dist-packages/torch/utils/data/_utils/collate.py", line 157, in default_collate
    return elem_type({key: default_collate([d[key] for d in batch]) for key in elem})
  File "/usr/local/lib/python3.7/dist-packages/torchio/data/image.py", line 641, in __init__
    super().__init__(*args, **kwargs)
  File "/usr/local/lib/python3.7/dist-packages/torchio/data/image.py", line 156, in __init__
    self.path = self._parse_path(path)
  File "/usr/local/lib/python3.7/dist-packages/torchio/data/image.py", line 419, in _parse_path
    return [self._parse_single_path(p) for p in path]
  File "/usr/local/lib/python3.7/dist-packages/torchio/data/image.py", line 419, in <listcomp>
    return [self._parse_single_path(p) for p in path]
  File "/usr/local/lib/python3.7/dist-packages/torchio/data/image.py", line 409, in _parse_single_path
    raise FileNotFoundError(f'File not found: "{path}"')
FileNotFoundError: File not found: "data"

Expected outcome

one batch loaded

System info

No response

Issue Analytics

State:
Created a year ago
Comments:8 (6 by maintainers)

Top GitHub Comments

1reaction

AyedSamycommented, May 15, 2022

It works perfect thanks for the update! 😁

0reactions

allcontributors[bot]commented, May 15, 2022

@fepegar

I’ve put up a pull request to add @AyedSamy! 🎉

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