Project-MONAI / Project-MONAI/tutorials
cron test error 3d_segmentation/unetr_btcv_segmentation_3d.ipynb
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bug
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Description
Describe the bug
log: https://github.com/Project-MONAI/MONAI/runs/3073470810?check_suite_focus=true
Running ./3d_segmentation/unetr_btcv_segmentation_3d.ipynb
Checking PEP8 compliance...
stdin:384:2: N816 variable 'split_JSON' in global scope should not be mixedCase
split_JSON = "dataset_0.json"
^
stdin:464:17: C408 Unnecessary list call - rewrite as a literal.
dice_vals = list()
^
stdin:466:13: B007 Loop control variable 'step' not used within the loop body. If this is intended, start the name with an underscore.
for step, batch in enumerate(epoch_iterator_val):
^
Error: Try running with autofixes: --autofix.
Check failed!
Running notebook...
Executing: 0%| | 0/23 [00:00<?, ?cell/s]
Executing: 4%|▍ | 1/23 [00:00<00:18, 1.19cell/s]
Executing: 13%|█▎ | 3/23 [00:06<00:27, 1.37s/cell]
Executing: 17%|█▋ | 4/23 [00:08<00:32, 1.73s/cell]
Executing: 43%|████▎ | 10/23 [00:08<00:15, 1.23s/cell]
Executing: 43%|████▎ | 10/23 [00:10<00:13, 1.02s/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 829, in __call__
return self.main(*args, **kwargs)
File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/opt/conda/lib/python3.8/site-packages/click/decorators.py", line 21, 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 [5]":
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-5-73b1e433c495> in <module>
2 split_JSON = "dataset_0.json"
3 datasets = data_dir + split_JSON
----> 4 datalist = load_decathlon_datalist(datasets, True, "training")
5 val_files = load_decathlon_datalist(datasets, True, "validation")
6 train_ds = CacheDataset(
/opt/conda/lib/python3.8/site-packages/monai/data/decathlon_datalist.py in load_decathlon_datalist(data_list_file_path, is_segmentation, data_list_key, base_dir)
114 """
115 if not os.path.isfile(data_list_file_path):
--> 116 raise ValueError(f"Data list file {data_list_file_path} does not exist.")
117 with open(data_list_file_path) as json_file:
118 json_data = json.load(json_file)
ValueError: Data list file /dataset/dataset_0.json does not exist.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with 3d_segmentation/unetr_btcv_segmentation_3d.ipynb, reviewing the lint findings around split_JSON, dice_vals, and the step loop, then inspect cell In [5] and its /dataset/dataset_0.json input. Run the cron notebook checks and execution to confirm the lint errors and missing data-list failure are resolved.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python
- Domain
- ci-cd, testing-qa
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100