openfl-fets error

[ZhifangDeng]

I install the dependencies according to the Fets_Challenge official guide, but get something wrong:

`No 'TrainOrVal' column found in split_subdirs csv, so performing automated split using percent_train of 0.8
[08:53:18] INFO Updating aggregator.settings.rounds_to_train to 70... native.py:83
INFO Updating aggregator.settings.db_store_rounds to 2... native.py:83
/home/zss/anaconda3/envs/FL/lib/python3.7/site-packages/pandas/core/frame.py:4913: SettingWithCopyWarning:
A value is trying to be set on a copy of a slice from a DataFrame

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
errors=errors,
Traceback (most recent call last):
File "fets_challenge_task1.py", line 654, in
device=device)
File "/data1/zsscode/Fong/code/FL/HFL/Task_1/fets_challenge/experiment.py", line 289, in run_challenge_experiment
task_runner = copy(plan).get_task_runner(list(collaborator_data_loaders.values())[0])
File "/home/zss/anaconda3/envs/FL/lib/python3.7/site-packages/openfl/federated/plan/plan.py", line 340, in get_task_runner
self.runner_ = Plan.Build(**defaults)
File "/home/zss/anaconda3/envs/FL/lib/python3.7/site-packages/openfl/federated/plan/plan.py", line 179, in Build
module = import_module(module_path)
File "/home/zss/anaconda3/envs/FL/lib/python3.7/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1006, in _gcd_import
File "", line 983, in _find_and_load
File "", line 967, in _find_and_load_unlocked
File "", line 677, in _load_unlocked
File "", line 728, in exec_module
File "", line 219, in _call_with_frames_removed
File "/root/.local/workspace/impl/fets_challenge_model.py", line 53, in
from fets.models.pytorch.brainmage.losses import MCD_loss, MCD_MSE_loss, dice_loss
File "/home/zss/anaconda3/envs/FL/lib/python3.7/site-packages/fets/models/pytorch/brainmage/init.py", line 1, in
from .brainmage import BrainMaGeModel
File "/home/zss/anaconda3/envs/FL/lib/python3.7/site-packages/fets/models/pytorch/brainmage/brainmage.py", line 38, in
from openfl import load_yaml
ImportError: cannot import name 'load_yaml' from 'openfl' (/home/zss/anaconda3/envs/FL/lib/python3.7/site-packages/openfl/init.py)
(FL) root@omnisky:/data1/zsscode/Fong/code/FL/HFL/Task_1# python
Python 3.7.11 (default, Jul 27 2021, 14:32:16)
[GCC 7.5.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.

from openfl.models.pytorch import PyTorchFLModel
Traceback (most recent call last):
File "", line 1, in
ModuleNotFoundError: No module named 'openfl.models'

`
and I also try to install from source according to the specified branch, but i get same wrong. Is there anything wrong with my installation process？

[sarthakpati]

I have transferred this to a discussion under the FeTS-AI/Challenge repo.

Can you confirm that you are following the instructions in https://github.com/FETS-AI/Challenge/tree/main/Task_1#getting-started? If no, can you please do a fresh checkout and try again? If yes, could you please re-initialize a new virtual environment and try again?

If you are still facing issues, can you provide details about the OS, python version, and other information that we could use to try and reproduce the problem?

[ZhifangDeng]

Oh, I'm sorry about it.
I reinstalled the environment according to the the instructions in https://github.com/FETS-AI/Challenge/tree/main/Task_1#getting-started, the above errors disappeared, and there is another error:

No 'TrainOrVal' column found in split_subdirs csv, so performing automated split using percent_train of 0.8
[20:13:00] INFO Updating aggregator.settings.rounds_to_train to 70... native.py:83
INFO Updating aggregator.settings.db_store_rounds to 2... native.py:83
/home/zss/anaconda3/envs/test_FL/lib/python3.7/site-packages/pandas/core/frame.py:4913: SettingWithCopyWarning:
A value is trying to be set on a copy of a slice from a DataFrame

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
errors=errors,
Traceback (most recent call last):
File "fets_challenge_task1.py", line 654, in
device=device)
File "/data1/zsscode/Fong/FLcode/Challenge-reproducibility/Task_1/fets_challenge/experiment.py", line 289, in run_challenge_experiment
task_runner = copy(plan).get_task_runner(list(collaborator_data_loaders.values())[0])
File "/home/zss/anaconda3/envs/test_FL/lib/python3.7/site-packages/openfl/federated/plan/plan.py", line 340, in get_task_runner
self.runner_ = Plan.Build(**defaults)
File "/home/zss/anaconda3/envs/test_FL/lib/python3.7/site-packages/openfl/federated/plan/plan.py", line 180, in Build
instance = getattr(module, class_name)(**settings)
File "/root/.local/workspace/impl/fets_challenge_model.py", line 108, in init
self.__init_2(val_input_shape=val_input_shape, val_output_shape=val_output_shape, data=data, **kwargs)
File "/root/.local/workspace/impl/fets_challenge_model.py", line 319, in __init_2
self.channel_keys= self.get_channel_keys()
File "/root/.local/workspace/impl/fets_challenge_model.py", line 343, in get_channel_keys
for subject in self.data.get_train_loader():
File "/home/zss/anaconda3/envs/test_FL/lib/python3.7/site-packages/torch/utils/data/dataloader.py", line 530, in next
data = self._next_data()
File "/home/zss/anaconda3/envs/test_FL/lib/python3.7/site-packages/torch/utils/data/dataloader.py", line 570, in _next_data
data = self._dataset_fetcher.fetch(index) # may raise StopIteration
File "/home/zss/anaconda3/envs/test_FL/lib/python3.7/site-packages/torch/utils/data/_utils/fetch.py", line 52, in fetch
return self.collate_fn(data)
File "/home/zss/anaconda3/envs/test_FL/lib/python3.7/site-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 "/home/zss/anaconda3/envs/test_FL/lib/python3.7/site-packages/torch/utils/data/_utils/collate.py", line 157, in
return elem_type({key: default_collate([d[key] for d in batch]) for key in elem})
File "/home/zss/anaconda3/envs/test_FL/lib/python3.7/site-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 "/home/zss/anaconda3/envs/test_FL/lib/python3.7/site-packages/torchio/data/image.py", line 140, in init
self.path = self._parse_path(path)
File "/home/zss/anaconda3/envs/test_FL/lib/python3.7/site-packages/torchio/data/image.py", line 377, in _parse_path
return [self._parse_single_path(p) for p in path]
File "/home/zss/anaconda3/envs/test_FL/lib/python3.7/site-packages/torchio/data/image.py", line 377, in
return [self._parse_single_path(p) for p in path]
File "/home/zss/anaconda3/envs/test_FL/lib/python3.7/site-packages/torchio/data/image.py", line 365, in _parse_single_path
raise FileNotFoundError(f'File not found: "{path}"')
FileNotFoundError: File not found: "affine"

I debug it, and it maybe read an image in the end of dataloader? like that:

/data1/zsscode/Fong/dataset/MICCAI_FeTS2021_TrainingData/FeTS21_Training_103/FeTS21_Training_103_seg.nii.gz /data1/zsscode/Fong/dataset/MICCAI_FeTS2021_TrainingData/FeTS21_Training_103/FeTS21_Training_103_seg.nii.gz
------------ {'data': tensor([[[[[0., 0., 0.,  ..., 0., 0., 0.],
           [0., 0., 0.,  ..., 0., 0., 0.],
           [0., 0., 0.,  ..., 0., 0., 0.],
           ...,
           [0., 0., 0.,  ..., 0., 0., 0.],
           [0., 0., 0.,  ..., 0., 0., 0.],
           [0., 0., 0.,  ..., 0., 0., 0.]],

          [[0., 0., 0.,  ..., 0., 0., 0.],
           [0., 0., 0.,  ..., 0., 0., 0.],
           [0., 0., 0.,  ..., 0., 0., 0.],
           ...,
           [0., 0., 0.,  ..., 0., 0., 0.],
           [0., 0., 0.,  ..., 0., 0., 0.],
           [0., 0., 0.,  ..., 0., 0., 0.]],

          [[0., 0., 0.,  ..., 0., 0., 0.],
           [0., 0., 0.,  ..., 0., 0., 0.],
           [0., 0., 0.,  ..., 0., 0., 0.],
           ...,
           [0., 0., 0.,  ..., 0., 0., 0.],
           [0., 0., 0.,  ..., 0., 0., 0.],
           [0., 0., 0.,  ..., 0., 0., 0.]],

          ...,

          [[0., 0., 0.,  ..., 0., 0., 0.],
           [0., 0., 0.,  ..., 0., 0., 0.],
           [0., 0., 0.,  ..., 0., 0., 0.],
           ...,
           [0., 0., 0.,  ..., 0., 0., 0.],
           [0., 0., 0.,  ..., 0., 0., 0.],
           [0., 0., 0.,  ..., 0., 0., 0.]],

          [[0., 0., 0.,  ..., 0., 0., 0.],
           [0., 0., 0.,  ..., 0., 0., 0.],
           [0., 0., 0.,  ..., 0., 0., 0.],
           ...,
           [0., 0., 0.,  ..., 0., 0., 0.],
           [0., 0., 0.,  ..., 0., 0., 0.],
           [0., 0., 0.,  ..., 0., 0., 0.]],

          [[0., 0., 0.,  ..., 0., 0., 0.],
           [0., 0., 0.,  ..., 0., 0., 0.],
           [0., 0., 0.,  ..., 0., 0., 0.],
           ...,
           [0., 0., 0.,  ..., 0., 0., 0.],
           [0., 0., 0.,  ..., 0., 0., 0.],
           [0., 0., 0.,  ..., 0., 0., 0.]]]]]), 'affine': tensor([[[ -1.,   0.,   0., -58.],
         [  0.,  -1.,   0., 193.],
         [  0.,   0.,   1.,   6.],
         [  0.,   0.,   0.,   1.]]], dtype=torch.float64), 'path': ['/data1/zsscode/Fong/dataset/MICCAI_FeTS2021_TrainingData/FeTS21_Training_103/FeTS21_Training_103_t1.nii.gz'], 'stem': ['FeTS21_Training_103_t1'], 'type': ['intensity']}

It makes me confused. My OS: Ubuntu 20.04.4 LTS.

[sarthakpati]

Hi @ZhifangDeng, could you please format your answer [ref] so that I can parse it better? I am unable to figure out which portion is the traceback and which is text you are writing.

[ZhifangDeng]

I am sorry for this and thank you for your timely reply. I have edited my question again.

[sarthakpati]

Can you check what your train and val csvs are like? There seems to be something with "affine" in them...

[ZhifangDeng]

Thank u very much. I solved this problem by changing the python version to 3.6. My python version was 3.7 before.