search

jamesdolezal / slideflow

Deep learning library for digital pathology, with both Tensorflow and PyTorch support.
https://slideflow.dev
GNU General Public License v3.0
230 stars 38 forks source link

[BUG] ValueError: DataLoader does not contain any batches when using attention/transmil MIL method #358

Open NaokiThread opened 2 months ago

NaokiThread commented 2 months ago

Description

I encountered a ValueError when using the transmil MIL method and histossl Extractor method in my code. The error occurs when calling the train_mil function.

The relevant code snippet is:

train_mil(
    # ...
)
The error traceback is as follows:
Traceback (most recent call last):
  File "myhome/itona/sf-test/mil.py", line 59, in <module>
    train_mil(
  File "myhome/micromamba/envs/slideflow/lib/python3.9/site-packages/slideflow/mil/train/__init__.py", line 80, in train_mil
    return _train_mil(config, **mil_kwargs)
  File "myhome/micromamba/envs/slideflow/lib/python3.9/site-packages/slideflow/mil/train/__init__.py", line 157, in _train_mil
    return train_fn(
  File "myhome/micromamba/envs/slideflow/lib/python3.9/site-packages/slideflow/mil/train/__init__.py", line 728, in train_fastai
    learner, (n_in, n_out) = build_fastai_learner(
  File "myhome/micromamba/envs/slideflow/lib/python3.9/site-packages/slideflow/mil/train/__init__.py", line 550, in build_fastai_learner
    learner, (n_in, n_out) = _fastai.build_learner(
  File "myhome/micromamba/envs/slideflow/lib/python3.9/site-packages/slideflow/mil/train/_fastai.py", line 80, in build_learner
    return _build_fastai_learner(config, _args,_ *kwargs)
  File "myhome/micromamba/envs/slideflow/lib/python3.9/site-packages/slideflow/mil/train/_fastai.py", line 261, in _build_fastai_learner
    batch = train_dl.one_batch()
  File "myhome/micromamba/envs/slideflow/lib/python3.9/site-packages/fastai/data/load.py", line 171, in one_batch
    if self.n is not None and len(self)==0: raise ValueError(f'This DataLoader does not contain any batches')
ValueError: This DataLoader does not contain any batches

The code worked correctly when using the clam-sb or clam-sm MIL methods. The issue occurs specifically when using the trans/attention MIL method.