Project-MONAI / Project-MONAI/tutorials
cron test error 3d_segmentation/unetr_btcv_segmentation_3d.ipynb
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bug
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Descripción
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.
Guía de contribución
Primeros pasos
- Lee el issue completo y luego la guía de contribución del proyecto.
- Comenta en el issue que vas a ocuparte — evita que dos personas hagan lo mismo.
- Haz un fork del repositorio y trabaja en una rama.
- Abre un pull request que haga referencia al número del issue.
Línea de trabajo
Comienza con 3d_segmentation/unetr_btcv_segmentation_3d.ipynb, revisa los hallazgos de lint relacionados con split_JSON, dice_vals y el bucle de pasos, y luego inspecciona la celda In [5] y su entrada /dataset/dataset_0.json. Ejecuta las comprobaciones del notebook de cron y la ejecución para confirmar que los errores de lint y el fallo por la falta de la lista de datos se han resuelto.
Escrito por el modelo de indexación a partir del texto del issue.
Evaluación
- Stack tecnológico
- jupyter-notebook, python
- Área
- ci-cd, testing-qa
- Tipo de issue
- Error
- Dificultad
- 3/5
- Tiempo estimado
- 1-2 días
- Estado de actividad
- Estancado
- Claridad
- Bastante claro
- Aptitud para principiantes
- 35/100