If image reader chokes on a file, put the file name into exception message #2226
Description
Is your feature request related to a problem? Please describe.
I am running training on a big set (5000) of images, and somewhere in the middle I get TypeError: stat: path should be string, bytes, os.PathLike or integer, not float. I have no idea which image is the problem.
Describe the solution you'd like
I would like the path of the offending image to be mentioned somewhere in the stack trace. Possibly by special handling of exceptions by read method in monai/data/image_reader.py.
Describe alternatives you've considered
Create and run my own script which checks consistency of the data I work with.
Additional context
Code: https://github.com/dzenanz/miqa/blob/b8409864bd53de9de000aaf5085ad54729d4bc1e/nn_classifier.py
Here is a full stack trace:
epoch 2 average loss: 0.4841
confusion matrix:
[[1516 565]
[ 407 1701]]
Evaluating on validation set
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.......input data information of the runtime error transform:
Traceback (most recent call last):
File "/home/dzenan/miqa/nn_classifier.py", line 402, in <module>
process_folds(args.folds, args.vfold, args.evaluate, args.nfolds)
File "/home/dzenan/miqa/nn_classifier.py", line 366, in process_folds
sizes = train_and_save_model(df, count_train, save_path=model_path, num_epochs=50, val_interval=2,
File "/home/dzenan/miqa/nn_classifier.py", line 321, in train_and_save_model
auc_metric = evaluate_model(model, val_loader, device, writer, epoch, "val")
File "/home/dzenan/miqa/nn_classifier.py", line 146, in evaluate_model
for val_data in data_loader:
File "/home/dzenan/.local/lib/python3.8/site-packages/torch/utils/data/dataloader.py", line 517, in __next__
data = self._next_data()
File "/home/dzenan/.local/lib/python3.8/site-packages/torch/utils/data/dataloader.py", line 1199, in _next_data
return self._process_data(data)
File "/home/dzenan/.local/lib/python3.8/site-packages/torch/utils/data/dataloader.py", line 1225, in _process_data
data.reraise()
File "/home/dzenan/.local/lib/python3.8/site-packages/torch/_utils.py", line 429, in reraise
raise self.exc_type(msg)
RuntimeError: Caught RuntimeError in DataLoader worker process 0.
Original Traceback (most recent call last):
File "/home/dzenan/.local/lib/python3.8/site-packages/monai/transforms/transform.py", line 48, in apply_transform
return transform(data)
File "/home/dzenan/.local/lib/python3.8/site-packages/monai/transforms/io/dictionary.py", line 105, in __call__
data = self._loader(d[key], reader)
File "/home/dzenan/.local/lib/python3.8/site-packages/monai/transforms/io/array.py", line 154, in __call__
img = reader.read(filename)
File "/home/dzenan/.local/lib/python3.8/site-packages/monai/data/image_reader.py", line 180, in read
if os.path.isdir(name):
File "/usr/lib/python3.8/genericpath.py", line 42, in isdir
st = os.stat(s)
TypeError: stat: path should be string, bytes, os.PathLike or integer, not float
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/dzenan/.local/lib/python3.8/site-packages/monai/transforms/transform.py", line 48, in apply_transform
return transform(data)
File "/home/dzenan/.local/lib/python3.8/site-packages/monai/transforms/compose.py", line 144, in __call__
input_ = apply_transform(_transform, input_)
File "/home/dzenan/.local/lib/python3.8/site-packages/monai/transforms/transform.py", line 71, in apply_transform
raise RuntimeError(f"applying transform {transform}") from e
RuntimeError: applying transform <monai.transforms.io.dictionary.LoadImaged object at 0x7fea0f4f1910>
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/dzenan/.local/lib/python3.8/site-packages/torch/utils/data/_utils/worker.py", line 202, in _worker_loop
data = fetcher.fetch(index)
File "/home/dzenan/.local/lib/python3.8/site-packages/torch/utils/data/_utils/fetch.py", line 44, in fetch
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/home/dzenan/.local/lib/python3.8/site-packages/torch/utils/data/_utils/fetch.py", line 44, in <listcomp>
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/home/dzenan/.local/lib/python3.8/site-packages/monai/data/dataset.py", line 92, in __getitem__
return self._transform(index)
File "/home/dzenan/.local/lib/python3.8/site-packages/monai/data/dataset.py", line 78, in _transform
return apply_transform(self.transform, data_i) if self.transform is not None else data_i
File "/home/dzenan/.local/lib/python3.8/site-packages/monai/transforms/transform.py", line 71, in apply_transform
raise RuntimeError(f"applying transform {transform}") from e
RuntimeError: applying transform <monai.transforms.compose.Compose object at 0x7fea0f4c7b50>
INFO:DataStats:input data information of the runtime error transform:
img statistics:
Type: <class 'float'>
Value: nan
INFO:DataStats:img statistics:
Type: <class 'float'>
Value: nan
label statistics:
Type: <class 'numpy.int64'>
Value: 1
INFO:DataStats:label statistics:
Type: <class 'numpy.int64'>
Value: 1
input data information of the runtime error transform:
input data information of the runtime error transform:
INFO:DataStats:input data information of the runtime error transform:
img statistics:
Type: <class 'float'>
Value: nan
img statistics:
Type: <class 'float'>
Value: nan
INFO:DataStats:img statistics:
Type: <class 'float'>
Value: nan
label statistics:
Type: <class 'numpy.int64'>
Value: 1
label statistics:
Type: <class 'numpy.int64'>
Value: 1
INFO:DataStats:label statistics:
Type: <class 'numpy.int64'>
Value: 1
.input data information of the runtime error transform:
input data information of the runtime error transform:
input data information of the runtime error transform:
INFO:DataStats:input data information of the runtime error transform:
img statistics:
Type: <class 'float'>
Value: nan
img statistics:
Type: <class 'float'>
Value: nan
img statistics:
Type: <class 'float'>
Value: nan
INFO:DataStats:img statistics:
Type: <class 'float'>
Value: nan
label statistics:
Type: <class 'numpy.int64'>
Value: 1
label statistics:
Type: <class 'numpy.int64'>
Value: 1
label statistics:
Type: <class 'numpy.int64'>
Value: 1
INFO:DataStats:label statistics:
Type: <class 'numpy.int64'>
Value: 1