Project-MONAI / Project-MONAI/tutorials

cron test error 3d_segmentation/unetr_btcv_segmentation_3d.ipynb

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#276 6 comentarios 0 reacciones 0 asignados Ver en GitHub

Nadie ha tomado este issue todavía.

bug
Lenguaje dominante
Jupyter Notebook
Estrellas
2.5k
Forks
803
Merge medio
6 d 22 h
PR fusionados (30 d)
3

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

Abrir la guía de contribución

Primeros pasos

  1. Lee el issue completo y luego la guía de contribución del proyecto.
  2. Comenta en el issue que vas a ocuparte — evita que dos personas hagan lo mismo.
  3. Haz un fork del repositorio y trabaja en una rama.
  4. 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

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