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Description
Describe the bug
Running ./2d_registration/registration_mednist.ipynb
Checking PEP8 compliance...
Running notebook...
Before:
"max_epochs = 200\n",
After:
"max_epochs = 1\n",
Executing: 0%| | 0/20 [00:00<?, ?cell/s]
Executing: 5%|▌ | 1/20 [00:01<00:24, 1.27s/cell]
Executing: 20%|██ | 4/20 [00:04<00:18, 1.14s/cell]
Executing: 30%|███ | 6/20 [00:06<00:15, 1.14s/cell]
Executing: 40%|████ | 8/20 [00:16<00:30, 2.54s/cell]
Executing: 55%|█████▌ | 11/20 [00:16<00:12, 1.43s/cell]
Executing: 55%|█████▌ | 11/20 [00:17<00:14, 1.57s/cell]
Traceback (most recent call last):
File "/opt/conda/bin/papermill", line 8, in <module>
sys.exit(papermill())
File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1137, in __call__
return self.main(*args, **kwargs)
File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1062, in main
rv = self.invoke(ctx)
File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 763, in invoke
return __callback(*args, **kwargs)
File "/opt/conda/lib/python3.8/site-packages/click/decorators.py", line 26, in new_func
return f(get_current_context(), *args, **kwargs)
File "/opt/conda/lib/python3.8/site-packages/papermill/cli.py", line 250, in papermill
execute_notebook(
File "/opt/conda/lib/python3.8/site-packages/papermill/execute.py", line 122, in execute_notebook
raise_for_execution_errors(nb, output_path)
File "/opt/conda/lib/python3.8/site-packages/papermill/execute.py", line 234, in raise_for_execution_errors
raise error
papermill.exceptions.PapermillExecutionError:
---------------------------------------------------------------------------
Exception encountered at "In [6]":
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
/tmp/ipykernel_2509/823736021.py in <module>
1 check_ds = Dataset(data=training_datadict, transform=train_transforms)
----> 2 check_loader = DataLoader(check_ds, batch_size=1, shuffle=True)
3 check_data = first(check_loader)
4 fixed_image = check_data["fixed_hand"][0][0]
5 moving_image = check_data["moving_hand"][0][0]
/home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/data/dataloader.py in __init__(self, dataset, num_workers, **kwargs)
82 kwargs.update({"worker_init_fn": worker_init_fn})
83
---> 84 super().__init__(dataset=dataset, num_workers=num_workers, **kwargs) # type: ignore[call-overload]
/opt/conda/lib/python3.8/site-packages/torch/utils/data/dataloader.py in __init__(self, dataset, batch_size, shuffle, sampler, batch_sampler, num_workers, collate_fn, pin_memory, drop_last, timeout, worker_init_fn, multiprocessing_context, generator, prefetch_factor, persistent_workers)
266 else: # map-style
267 if shuffle:
--> 268 sampler = RandomSampler(dataset, generator=generator)
269 else:
270 sampler = SequentialSampler(dataset)
/opt/conda/lib/python3.8/site-packages/torch/utils/data/sampler.py in __init__(self, data_source, replacement, num_samples, generator)
100
101 if not isinstance(self.num_samples, int) or self.num_samples <= 0:
--> 102 raise ValueError("num_samples should be a positive integer "
103 "value, but got num_samples={}".format(self.num_samples))
104
ValueError: num_samples should be a positive integer value, but got num_samples=0
introduced since #3332
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