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szc19990412 / TransMIL

TransMIL: Transformer based Correlated Multiple Instance Learning for Whole Slide Image Classification
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assert self.key_type is Any or isinstance(self.key_type, type)报错 #33

Open ljhOfGithub opened 11 months ago

ljhOfGithub commented 11 months ago 
/home/jupyter-ljh/.local/lib/python3.9/site-packages/pytorch_lightning/utilities/distributed.py:50: UserWarning: Experiment logs directory logs/Camelyon/TransMIL/fold0 exists and is not empty. Previous log files in this directory will be deleted when the new ones are saved!
  warnings.warn(*args, **kwargs)
/home/jupyter-ljh/.local/lib/python3.9/site-packages/pytorch_lightning/utilities/distributed.py:50: UserWarning: Could not log computational graph since the `model.example_input_array` attribute is not set or `input_array` was not given
  warnings.warn(*args, **kwargs)
Traceback (most recent call last):
  File "/mnt/data0/LI_jihao/mydata/TransMIL-main/train.py", line 96, in <module>
    main(cfg)
  File "/mnt/data0/LI_jihao/mydata/TransMIL-main/train.py", line 74, in main
    if cfg.General.server == 'train':
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/pytorch_lightning/trainer/trainer.py", line 475, in fit
    self.setup_trainer(model)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/pytorch_lightning/trainer/trainer.py", line 423, in setup_trainer
    self.logger.save()
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/pytorch_lightning/loggers/base.py", line 388, in save
    logger.save()
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/pytorch_lightning/utilities/distributed.py", line 40, in wrapped_fn
    return fn(*args, **kwargs)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/pytorch_lightning/loggers/csv_logs.py", line 197, in save
    self.experiment.save()
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/pytorch_lightning/loggers/csv_logs.py", line 85, in save
    save_hparams_to_yaml(hparams_file, self.hparams)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/pytorch_lightning/core/saving.py", line 387, in save_hparams_to_yaml
    OmegaConf.save(hparams, fp)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/omegaconf.py", line 218, in save
    data = OmegaConf.to_yaml(config, resolve=resolve)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/omegaconf.py", line 746, in to_yaml
    cfg = _ensure_container(cfg)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/_utils.py", line 953, in _ensure_container
    target = OmegaConf.create(target, flags=flags)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/omegaconf.py", line 176, in create
    return OmegaConf._create_impl(
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/omegaconf.py", line 846, in _create_impl
    return DictConfig(
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/dictconfig.py", line 111, in __init__
    format_and_raise(node=None, key=key, value=None, cause=ex, msg=str(ex))
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/dictconfig.py", line 109, in __init__
    self._set_value(content, flags=flags)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/dictconfig.py", line 647, in _set_value
    raise e
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/dictconfig.py", line 644, in _set_value
    self._set_value_impl(value, flags)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/dictconfig.py", line 690, in _set_value_impl
    self.__setitem__(k, v)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/dictconfig.py", line 314, in __setitem__
    self._format_and_raise(key=key, value=value, cause=e)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/base.py", line 231, in _format_and_raise
    format_and_raise(
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/dictconfig.py", line 308, in __setitem__
    self.__set_impl(key=key, value=value)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/dictconfig.py", line 318, in __set_impl
    self._set_item_impl(key, value)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/basecontainer.py", line 618, in _set_item_impl
    self._wrap_value_and_set(key, value, target_type_hint)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/basecontainer.py", line 626, in _wrap_value_and_set
    wrapped = _maybe_wrap(
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/omegaconf.py", line 1090, in _maybe_wrap
    return _node_wrap(
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/omegaconf.py", line 1012, in _node_wrap
    node = DictConfig(
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/dictconfig.py", line 111, in __init__
    format_and_raise(node=None, key=key, value=None, cause=ex, msg=str(ex))
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/dictconfig.py", line 79, in __init__
    metadata=ContainerMetadata(
  File "<string>", line 12, in __init__
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/base.py", line 91, in __post_init__
    assert self.key_type is Any or isinstance(self.key_type, type)
AssertionError

您好，非常棒的工作！我分割patch之后提取了特征，将数据放在了~/data/mntdata/data0/LI_jihao/camelyon_clam/camelyon16/training_fea/pt_files_copy文件夹下面，使用了您的fold0.csv，并且修改了TransMIL.yaml文件，如下：

General:
    comment: 
    seed: 2021
    fp16: True
    amp_level: O2
    precision: 16 
    multi_gpu_mode: dp
    gpus: [0]
    # gpus: [1]
    epochs: &epoch 200 
    grad_acc: 2
    frozen_bn: False
    patience: 10
    server: train
    log_path: logs/

Data:
    dataset_name: camel_data
    data_shuffle: False
    # data_dir: Camelyon16/pt_files/
    data_dir: ~/data/mntdata/data0/LI_jihao/camelyon_clam/camelyon16/training_fea/pt_files_copy
    label_dir: dataset_csv/camelyon16/
    # label_dir: ~/data/mntdata/data0/LI_jihao/camelyon_clam/camelyon16/
    label_dir: ~/data/mydata/TransMIL-main/dataset_csv/camelyon16/
    fold: 0
    nfold: 4

    train_dataloader:
        batch_size: 1 
        num_workers: 8

    test_dataloader:
        batch_size: 1
        num_workers: 8

Model:
    name: TransMIL
    n_classes: 2

Optimizer:
    opt: lookahead_radam
    lr: 0.0002
    opt_eps: null 
    opt_betas: null
    momentum: null 
    weight_decay: 0.00001

Loss:
    base_loss: CrossEntropyLoss

但是我得到了一开始的错误，请问我的问题出在哪里，我该怎么样修改

lihua8848 commented 11 months ago

我也遇到了同样的问题，请问您解决了吗 Package Version

absl-py 1.4.0 addict 2.2.1 aiohttp 3.8.5 aiosignal 1.3.1 albumentations 0.4.3 antlr4-python3-runtime 4.9.3 async-timeout 4.0.2 asynctest 0.13.0 attrs 23.1.0 cachetools 5.3.1 certifi 2023.7.22 charset-normalizer 3.2.0 cycler 0.11.0 einops 0.3.0 fonttools 4.38.0 frozenlist 1.3.3 fsspec 2023.1.0 future 0.18.3 google-auth 2.22.0 google-auth-oauthlib 0.4.6 grpcio 1.56.2 h5py 3.8.0 idna 3.4 imageio 2.31.1 imgaug 0.2.6 importlib-metadata 6.7.0 kiwisolver 1.4.4 Markdown 3.4.4 MarkupSafe 2.1.3 matplotlib 3.5.1 mkl-fft 1.3.1 mkl-random 1.2.2 mkl-service 2.4.0 multidict 6.0.4 networkx 2.6.3 numpy 1.20.3 nvidia-cublas-cu11 11.10.3.66 nvidia-cuda-nvrtc-cu11 11.7.99 nvidia-cuda-runtime-cu11 11.7.99 nvidia-cudnn-cu11 8.5.0.96 nystrom-attention 0.0.9 oauthlib 3.2.2 olefile 0.46 omegaconf 2.2.3 opencv-python 4.2.0.34 opencv-python-headless 4.2.0.34 packaging 23.1 pandas 1.2.3 Pillow 8.4.0 pip 23.2.1 protobuf 3.20.3 pyasn1 0.5.0 pyasn1-modules 0.3.0 pyparsing 3.1.0 python-dateutil 2.8.2 pytorch-lightning 1.2.3 pytorch-toolbelt 0.6.3 pytorchtools 0.0.2 pytz 2023.3 PyWavelets 1.3.0 PyYAML 6.0.1 requests 2.31.0 requests-oauthlib 1.3.1 rsa 4.9 scikit-image 0.19.3 scipy 1.7.3 setuptools 68.0.0 six 1.16.0 tensorboard 2.11.2 tensorboard-data-server 0.6.1 tensorboard-plugin-wit 1.8.1 tifffile 2021.11.2 torch 1.11.0+cu113 torchaudio 0.11.0+cu113 torchmetrics 0.6.2 torchvision 0.12.0+cu113 tqdm 4.65.0 typing_extensions 4.7.1 urllib3 1.26.16 Werkzeug 2.2.3 wheel 0.41.0 yarl 1.9.2 zipp 3.15.0

ekansh09 commented 11 months ago

I solved this by "pip uninstall omegaconf".

lihua8848 commented 11 months ago

uninstall omegaconf后出现如下问题，请问如何解决谢谢

image
ekansh09 commented 11 months ago

Please ensure that you have correctly installed the specified version (0.0.9) of the 'nystrom_attention' library using the command "pip install nystrom_attention==0.0.9".

Afterwards, modify the line "q = self.scale" to "q = q self.scale" within the 'nystrom_attention.py' file that is located in your Conda environment. You can find this file in a directory resembling "/miniconda3/envs/transmil/lib/python'version'/site-packages/nystrom_attention/nystrom_attention.py".

To illustrate, if your Python version is 3.7 (as recommended by the authors), the path might be: "/miniconda3/envs/transmil/lib/python3.7/site-packages/nystrom_attention/nystrom_attention.py".

ljhOfGithub commented 11 months ago

Please ensure that you have correctly installed the specified version (0.0.9) of the 'nystrom_attention' library using the command "pip install nystrom_attention==0.0.9".

Afterwards, modify the line "q = self.scale" to "q = q self.scale" within the 'nystrom_attention.py' file that is located in your Conda environment. You can find this file in a directory resembling "/miniconda3/envs/transmil/lib/python'version'/site-packages/nystrom_attention/nystrom_attention.py".

To illustrate, if your Python version is 3.7 (as recommended by the authors), the path might be: "/miniconda3/envs/transmil/lib/python3.7/site-packages/nystrom_attention/nystrom_attention.py".

Thanks! It works well.However,I have a new problem:

Traceback (most recent call last):
  File "/home/jupyter-ljh/.local/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 651, in run_train
    self.train_loop.run_training_epoch()
  File "/home/jupyter-ljh/.local/lib/python3.7/site-packages/pytorch_lightning/trainer/training_loop.py", line 578, in run_training_epoch
    self.trainer.run_evaluation(on_epoch=True)
  File "/home/jupyter-ljh/.local/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 755, in run_evaluation
    deprecated_eval_results = self.evaluation_loop.evaluation_epoch_end()
  File "/home/jupyter-ljh/.local/lib/python3.7/site-packages/pytorch_lightning/trainer/evaluation_loop.py", line 187, in evaluation_epoch_end
    deprecated_results = self.__run_eval_epoch_end(self.num_dataloaders)
  File "/home/jupyter-ljh/.local/lib/python3.7/site-packages/pytorch_lightning/trainer/evaluation_loop.py", line 225, in __run_eval_epoch_end
    eval_results = model.validation_epoch_end(eval_results)
  File "/mnt/data0/LI_jihao/mydata/TransMIL-main/models/model_interface.py", line 155, in validation_epoch_end
    self.log('auc', self.AUROC(probs, target.squeeze()), prog_bar=True, on_epoch=True, logger=True)
  File "/home/jupyter-ljh/.conda/envs/transmil/lib/python3.7/site-packages/torch/nn/modules/module.py", line 1194, in _call_impl
    return forward_call(*input, **kwargs)
  File "/home/jupyter-ljh/.local/lib/python3.7/site-packages/torchmetrics/metric.py", line 234, in forward
    self._forward_cache = self._forward_reduce_state_update(*args, **kwargs)
  File "/home/jupyter-ljh/.local/lib/python3.7/site-packages/torchmetrics/metric.py", line 301, in _forward_reduce_state_update
    batch_val = self.compute()
  File "/home/jupyter-ljh/.local/lib/python3.7/site-packages/torchmetrics/metric.py", line 530, in wrapped_func
    value = compute(*args, **kwargs)
  File "/home/jupyter-ljh/.local/lib/python3.7/site-packages/torchmetrics/classification/auroc.py", line 112, in compute
    return _binary_auroc_compute(state, self.thresholds, self.max_fpr)
  File "/home/jupyter-ljh/.local/lib/python3.7/site-packages/torchmetrics/functional/classification/auroc.py", line 89, in _binary_auroc_compute
    fpr, tpr, _ = _binary_roc_compute(state, thresholds, pos_label)
  File "/home/jupyter-ljh/.local/lib/python3.7/site-packages/torchmetrics/functional/classification/roc.py", line 53, in _binary_roc_compute
    fps, tps, thresholds = _binary_clf_curve(preds=state[0], target=state[1], pos_label=pos_label)
  File "/home/jupyter-ljh/.local/lib/python3.7/site-packages/torchmetrics/functional/classification/precision_recall_curve.py", line 67, in _binary_clf_curve
    distinct_value_indices = torch.where(preds[1:] - preds[:-1])[0]
RuntimeError: numel: integer multiplication overflow

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "train.py", line 100, in <module>
    main(cfg)
  File "train.py", line 78, in main
    trainer.fit(model = model, datamodule = dm)
  File "/home/jupyter-ljh/.local/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 520, in fit
    self.dispatch()
  File "/home/jupyter-ljh/.local/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 560, in dispatch
    self.accelerator.start_training(self)
  File "/home/jupyter-ljh/.local/lib/python3.7/site-packages/pytorch_lightning/accelerators/accelerator.py", line 74, in start_training
    self.training_type_plugin.start_training(trainer)
  File "/home/jupyter-ljh/.local/lib/python3.7/site-packages/pytorch_lightning/plugins/training_type/training_type_plugin.py", line 111, in start_training
    self._results = trainer.run_train()
  File "/home/jupyter-ljh/.local/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 683, in run_train
    self.train_loop.on_train_end()
  File "/home/jupyter-ljh/.local/lib/python3.7/site-packages/pytorch_lightning/trainer/training_loop.py", line 138, in on_train_end
    self.trainer.call_hook("on_train_end")
  File "/home/jupyter-ljh/.local/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 1121, in call_hook
    output = accelerator_hook(*args, **kwargs)
  File "/home/jupyter-ljh/.local/lib/python3.7/site-packages/pytorch_lightning/accelerators/gpu.py", line 32, in on_train_end
    torch.cuda.empty_cache()
  File "/home/jupyter-ljh/.conda/envs/transmil/lib/python3.7/site-packages/torch/cuda/memory.py", line 125, in empty_cache
    torch._C._cuda_emptyCache()
RuntimeError: CUDA error: device-side assert triggered
CUDA kernel errors might be asynchronously reported at some other API call,so the stacktrace below might be incorrect.
For debugging consider passing CUDA_LAUNCH_BLOCKING=1.

My gpu is enough for calculating,so I think it's caused by the package settings.Could you please tell me how to solve the error?

Elliot-QxZhang commented 10 months ago

@ljhOfGithub Hi, I solved this problem by correcting the version of some packages, hope this could help you.

addict==2.2.1 apex==0.9.10dev einops==0.3.0 h5py==2.10.0 numpy==1.20.0 nystrom_attention==0.0.9 opencv_python==4.2.0.34 pandas==1.2.3 pytorch_lightning==1.2.3 pytorch_toolbelt==0.4.0 PyYAML==6.0 scikit_learn==1.0.2 scipy==1.5.4 setuptools==58.0.4 tensorboard==2.7.0 timm==0.3.2 torch==1.7.1+cu110 torchmetrics==0.4.1 torchvision==0.8.2+cu110 tqdm==4.46.1

But remember not to install apex.

homadnmr commented 6 months ago

I also receieve error: ".... target = OmegaConf.create(target, flags=flags) File "/home/anaconda3/envs/there_new_transmil/lib/python3.7/site-packages/omegaconf/omegaconf.py", line 179, in create flags=flags, File "/home/anaconda3/envs/there_new_transmil/lib/python3.7/site-packages/omegaconf/omegaconf.py", line 851, in _create_impl flags=flags, File "/home/anaconda3/envs/there_new_transmil/lib/python3.7/site-packages/omegaconf/dictconfig.py", line 111, in init format_and_raise(node=None, key=key, value=None, cause=ex, msg=str(ex)) File "/home/anaconda3/envs/there_new_transmil/lib/python3.7/site-packages/omegaconf/dictconfig.py", line 109, in init self._set_value(content, flags=flags) File "/home/anaconda3/envs/there_new_transmil/lib/python3.7/site-packages/omegaconf/dictconfig.py", line 647, in _set_value raise e File "/home/anaconda3/envs/there_new_transmil/lib/python3.7/site-packages/omegaconf/dictconfig.py", line 644, in _set_value self._set_value_impl(value, flags) File "/home/anaconda3/envs/there_new_transmil/lib/python3.7/site-packages/omegaconf/dictconfig.py", line 690, in _set_value_impl self.setitem(k, v) File "/home/anaconda3/envs/there_new_transmil/lib/python3.7/site-packages/omegaconf/dictconfig.py", line 314, in setitem self._format_and_raise(key=key, value=value, cause=e) File "/home/anaconda3/envs/there_new_transmil/lib/python3.7/site-packages/omegaconf/base.py", line 237, in _format_and_raise type_override=type_override, File "/home/anaconda3/envs/there_new_transmil/lib/python3.7/site-packages/omegaconf/dictconfig.py", line 308, in setitem self.set_impl(key=key, value=value) File "/home/anaconda3/envs/there_new_transmil/lib/python3.7/site-packages/omegaconf/dictconfig.py", line 318, in __set_impl self._set_item_impl(key, value) File "/home/ anaconda3/envs/there_new_transmil/lib/python3.7/site-packages/omegaconf/basecontainer.py", line 618, in _set_item_impl self._wrap_value_and_set(key, value, target_type_hint) File "/home/ anaconda3/envs/there_new_transmil/lib/python3.7/site-packages/omegaconf/basecontainer.py", line 631, in _wrap_value_and_set parent=self, File "/home/ anaconda3/envs/there_new_transmil/lib/python3.7/site-packages/omegaconf/omegaconf.py", line 1095, in _maybe_wrap key=key, File "/home/ anaconda3/envs/there_new_transmil/lib/python3.7/site-packages/omegaconf/omegaconf.py", line 1019, in _node_wrap element_type=element_type, File "/home/ anaconda3/envs/there_new_transmil/lib/python3.7/site-packages/omegaconf/dictconfig.py", line 111, in init format_and_raise(node=None, key=key, value=None, cause=ex, msg=str(ex)) File "/home/ anaconda3/envs/there_new_transmil/lib/python3.7/site-packages/omegaconf/dictconfig.py", line 86, in init flags=flags, File "", line 12, in init File "/home/anaconda3/envs/there_new_transmil/lib/python3.7/site-packages/omegaconf/base.py", line 91, in post_init__ assert self.key_type is Any or isinstance(self.key_type, type) AssertionError "" HOW CAN I SOLVE THIS? is it related to pylightening and omegaconf?

homadnmr commented 6 months ago 
/home/jupyter-ljh/.local/lib/python3.9/site-packages/pytorch_lightning/utilities/distributed.py:50: UserWarning: Experiment logs directory logs/Camelyon/TransMIL/fold0 exists and is not empty. Previous log files in this directory will be deleted when the new ones are saved!
  warnings.warn(*args, **kwargs)
/home/jupyter-ljh/.local/lib/python3.9/site-packages/pytorch_lightning/utilities/distributed.py:50: UserWarning: Could not log computational graph since the `model.example_input_array` attribute is not set or `input_array` was not given
  warnings.warn(*args, **kwargs)
Traceback (most recent call last):
  File "/mnt/data0/LI_jihao/mydata/TransMIL-main/train.py", line 96, in <module>
    main(cfg)
  File "/mnt/data0/LI_jihao/mydata/TransMIL-main/train.py", line 74, in main
    if cfg.General.server == 'train':
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/pytorch_lightning/trainer/trainer.py", line 475, in fit
    self.setup_trainer(model)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/pytorch_lightning/trainer/trainer.py", line 423, in setup_trainer
    self.logger.save()
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/pytorch_lightning/loggers/base.py", line 388, in save
    logger.save()
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/pytorch_lightning/utilities/distributed.py", line 40, in wrapped_fn
    return fn(*args, **kwargs)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/pytorch_lightning/loggers/csv_logs.py", line 197, in save
    self.experiment.save()
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/pytorch_lightning/loggers/csv_logs.py", line 85, in save
    save_hparams_to_yaml(hparams_file, self.hparams)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/pytorch_lightning/core/saving.py", line 387, in save_hparams_to_yaml
    OmegaConf.save(hparams, fp)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/omegaconf.py", line 218, in save
    data = OmegaConf.to_yaml(config, resolve=resolve)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/omegaconf.py", line 746, in to_yaml
    cfg = _ensure_container(cfg)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/_utils.py", line 953, in _ensure_container
    target = OmegaConf.create(target, flags=flags)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/omegaconf.py", line 176, in create
    return OmegaConf._create_impl(
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/omegaconf.py", line 846, in _create_impl
    return DictConfig(
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/dictconfig.py", line 111, in __init__
    format_and_raise(node=None, key=key, value=None, cause=ex, msg=str(ex))
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/dictconfig.py", line 109, in __init__
    self._set_value(content, flags=flags)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/dictconfig.py", line 647, in _set_value
    raise e
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/dictconfig.py", line 644, in _set_value
    self._set_value_impl(value, flags)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/dictconfig.py", line 690, in _set_value_impl
    self.__setitem__(k, v)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/dictconfig.py", line 314, in __setitem__
    self._format_and_raise(key=key, value=value, cause=e)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/base.py", line 231, in _format_and_raise
    format_and_raise(
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/dictconfig.py", line 308, in __setitem__
    self.__set_impl(key=key, value=value)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/dictconfig.py", line 318, in __set_impl
    self._set_item_impl(key, value)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/basecontainer.py", line 618, in _set_item_impl
    self._wrap_value_and_set(key, value, target_type_hint)
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/basecontainer.py", line 626, in _wrap_value_and_set
    wrapped = _maybe_wrap(
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/omegaconf.py", line 1090, in _maybe_wrap
    return _node_wrap(
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/omegaconf.py", line 1012, in _node_wrap
    node = DictConfig(
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/dictconfig.py", line 111, in __init__
    format_and_raise(node=None, key=key, value=None, cause=ex, msg=str(ex))
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/dictconfig.py", line 79, in __init__
    metadata=ContainerMetadata(
  File "<string>", line 12, in __init__
  File "/home/jupyter-ljh/.local/lib/python3.9/site-packages/omegaconf/base.py", line 91, in __post_init__
    assert self.key_type is Any or isinstance(self.key_type, type)
AssertionError

您好，非常棒的工作！我分割patch之后提取了特征，将数据放在了~/data/mntdata/data0/LI_jihao/camelyon_clam/camelyon16/training_fea/pt_files_copy文件夹下面，使用了您的fold0.csv，并且修改了TransMIL.yaml文件，如下：

General:
    comment: 
    seed: 2021
    fp16: True
    amp_level: O2
    precision: 16 
    multi_gpu_mode: dp
    gpus: [0]
    # gpus: [1]
    epochs: &epoch 200 
    grad_acc: 2
    frozen_bn: False
    patience: 10
    server: train
    log_path: logs/

Data:
    dataset_name: camel_data
    data_shuffle: False
    # data_dir: Camelyon16/pt_files/
    data_dir: ~/data/mntdata/data0/LI_jihao/camelyon_clam/camelyon16/training_fea/pt_files_copy
    label_dir: dataset_csv/camelyon16/
    # label_dir: ~/data/mntdata/data0/LI_jihao/camelyon_clam/camelyon16/
    label_dir: ~/data/mydata/TransMIL-main/dataset_csv/camelyon16/
    fold: 0
    nfold: 4

    train_dataloader:
        batch_size: 1 
        num_workers: 8

    test_dataloader:
        batch_size: 1
        num_workers: 8

Model:
    name: TransMIL
    n_classes: 2

Optimizer:
    opt: lookahead_radam
    lr: 0.0002
    opt_eps: null 
    opt_betas: null
    momentum: null 
    weight_decay: 0.00001

Loss:
    base_loss: CrossEntropyLoss

但是我得到了一开始的错误，请问我的问题出在哪里，我该怎么样修改

Hi, may I ask how did you solve this error???

1803170327 commented 3 months ago

A conclusion of these solutions: 1、Delete omegaconf and modify "q = self.scale" to "q = q self.scale" in nystrom_attention.py(make sure nystrom_attention==0.0.9 ) Then comes a new bug. 1712651844862 2、Intasll timm==0.4.0 I installed timm of version 0.11 before so I met the "CUDA ERROR".After installing timm of version 0.4 ,I can successfully run train.py.

I don't know whether modifying "q = self.scale" to "q = q self.scale" will be useful for fixing this bug.The two sentences seem to be the same.But installing timm of version 0.4 is very important.Using ‘pip install timm’ will install a latest version of timm by defult and this will create some errors like" missing an argument 'task' " and " CUDA error ".

tymsoncyferki commented 3 months ago

hello @1803170327 , i have the same problem. however, uninstalling omegaconf did not help as now i get error:

File "(...)\site-packages\hydra\_internal\instantiate\_instantiate2.py", line 9, in <module>
    from omegaconf import OmegaConf, SCMode
ModuleNotFoundError: No module named 'omegaconf'
tymsoncyferki commented 3 months ago

I managed to fix it. I created env once again from scratch running 

conda create -n transmil python=3.7 -y
conda activate transmil
conda install pytorch==1.7.1 torchvision==0.8.2 torchaudio==0.7.2 cudatoolkit=11.0 -c pytorch

In requirements.txt I deleted omegaconf and added pytorch-toolbelt, torchmetrics in these versions:

addict==2.2.1
albumentations==0.4.3
einops==0.3.0
matplotlib==3.5.1
numpy==1.20.3
nystrom-attention==0.0.9
opencv-python==4.2.0.34
opencv-python-headless==4.2.0.34
pandas==1.2.3
Pillow==8.4.0
pytorch-lightning==1.2.3
pytorch-toolbelt==0.4.0
torchmetrics==0.4.1

and ran pip install -r requirements.txt

Then as stated before I modified q *= self.scale to q = q * self.scale in nystrom_attention.py. Now its up and running.