[2023-09-25T14:54:56.498Z] Running ./deepedit/ignite/infoANDinference.ipynb
[2023-09-25T14:54:56.498Z] Checking PEP8 compliance...
[2023-09-25T14:54:56.757Z] Running notebook...
[2023-09-25T14:55:03.287Z] MONAI version: 1.3.0rc1+4.g18a671a7
[2023-09-25T14:55:03.287Z] Numpy version: 1.26.0
[2023-09-25T14:55:03.287Z] Pytorch version: 2.1.0a0+29c30b1
[2023-09-25T14:55:03.287Z] MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
[2023-09-25T14:55:03.287Z] MONAI rev id: 18a671a7f12389dd8263a4c2232196dcca814bb9
[2023-09-25T14:55:03.287Z] MONAI __file__: /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/__init__.py
[2023-09-25T14:55:03.287Z]
[2023-09-25T14:55:03.287Z] Optional dependencies:
[2023-09-25T14:55:03.543Z] Pytorch Ignite version: 0.4.11
[2023-09-25T14:55:03.543Z] ITK version: 5.3.0
[2023-09-25T14:55:03.543Z] Nibabel version: 5.1.0
[2023-09-25T14:55:03.543Z] scikit-image version: 0.21.0
[2023-09-25T14:55:03.543Z] scipy version: 1.11.1
[2023-09-25T14:55:03.543Z] Pillow version: 9.2.0
[2023-09-25T14:55:03.543Z] Tensorboard version: 2.9.0
[2023-09-25T14:55:03.543Z] gdown version: 4.7.1
[2023-09-25T14:55:03.543Z] TorchVision version: 0.16.0a0
[2023-09-25T14:55:03.543Z] tqdm version: 4.65.0
[2023-09-25T14:55:03.543Z] lmdb version: 1.4.1
[2023-09-25T14:55:03.543Z] psutil version: 5.9.4
[2023-09-25T14:55:03.543Z] pandas version: 2.1.1
[2023-09-25T14:55:03.543Z] einops version: 0.6.1
[2023-09-25T14:55:03.543Z] transformers version: 4.21.3
[2023-09-25T14:55:03.543Z] mlflow version: 2.7.1
[2023-09-25T14:55:03.543Z] pynrrd version: 1.0.0
[2023-09-25T14:55:03.543Z] clearml version: 1.13.0
[2023-09-25T14:55:03.543Z]
[2023-09-25T14:55:03.543Z] For details about installing the optional dependencies, please visit:
[2023-09-25T14:55:03.543Z] https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies
[2023-09-25T14:55:03.543Z]
[2023-09-25T14:55:06.058Z] papermill --progress-bar -k python3
[2023-09-25T14:55:06.314Z] /usr/local/lib/python3.10/dist-packages/papermill/iorw.py:153: UserWarning: the file is not specified with any extension : -
[2023-09-25T14:55:06.314Z] warnings.warn(
[2023-09-25T14:55:33.080Z]
Executing: 0%| | 0/13 [00:00<?, ?cell/s]
Executing: 8%|▊ | 1/13 [00:01<00:17, 1.50s/cell]
Executing: 23%|██▎ | 3/13 [00:09<00:34, 3.43s/cell]
Executing: 38%|███▊ | 5/13 [00:14<00:24, 3.02s/cell]
Executing: 69%|██████▉ | 9/13 [00:15<00:05, 1.29s/cell]
Executing: 77%|███████▋ | 10/13 [00:19<00:05, 1.69s/cell]
Executing: 85%|████████▍ | 11/13 [00:24<00:04, 2.36s/cell]
Executing: 85%|████████▍ | 11/13 [00:26<00:04, 2.41s/cell]
[2023-09-25T14:55:33.080Z] /usr/local/lib/python3.10/dist-packages/papermill/iorw.py:153: UserWarning: the file is not specified with any extension : -
[2023-09-25T14:55:33.080Z] warnings.warn(
[2023-09-25T14:55:33.080Z] Traceback (most recent call last):
[2023-09-25T14:55:33.080Z] File "/usr/local/bin/papermill", line 8, in <module>
[2023-09-25T14:55:33.080Z] sys.exit(papermill())
[2023-09-25T14:55:33.080Z] File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1157, in __call__
[2023-09-25T14:55:33.080Z] return self.main(*args, **kwargs)
[2023-09-25T14:55:33.080Z] File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1078, in main
[2023-09-25T14:55:33.080Z] rv = self.invoke(ctx)
[2023-09-25T14:55:33.080Z] File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1434, in invoke
[2023-09-25T14:55:33.080Z] return ctx.invoke(self.callback, **ctx.params)
[2023-09-25T14:55:33.080Z] File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 783, in invoke
[2023-09-25T14:55:33.080Z] return __callback(*args, **kwargs)
[2023-09-25T14:55:33.080Z] File "/usr/local/lib/python3.10/dist-packages/click/decorators.py", line 33, in new_func
[2023-09-25T14:55:33.080Z] return f(get_current_context(), *args, **kwargs)
[2023-09-25T14:55:33.080Z] File "/usr/local/lib/python3.10/dist-packages/papermill/cli.py", line 250, in papermill
[2023-09-25T14:55:33.080Z] execute_notebook(
[2023-09-25T14:55:33.080Z] File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 128, in execute_notebook
[2023-09-25T14:55:33.080Z] raise_for_execution_errors(nb, output_path)
[2023-09-25T14:55:33.080Z] File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 232, in raise_for_execution_errors
[2023-09-25T14:55:33.080Z] raise error
[2023-09-25T14:55:33.080Z] papermill.exceptions.PapermillExecutionError:
[2023-09-25T14:55:33.080Z] ---------------------------------------------------------------------------
[2023-09-25T14:55:33.080Z] Exception encountered at "In [6]":
[2023-09-25T14:55:33.080Z] ---------------------------------------------------------------------------
[2023-09-25T14:55:33.080Z] RuntimeError Traceback (most recent call last)
[2023-09-25T14:55:33.080Z] Cell In[6], line 40
[2023-09-25T14:55:33.080Z] 38 for t in pre_transforms:
[2023-09-25T14:55:33.080Z] 39 tname = type(t).__name__
[2023-09-25T14:55:33.080Z] ---> 40 data = t(data)
[2023-09-25T14:55:33.080Z] 41 image = data["image"]
[2023-09-25T14:55:33.080Z] 42 label = data.get("label")
[2023-09-25T14:55:33.080Z]
[2023-09-25T14:55:33.080Z] File /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/apps/deepedit/transforms.py:666, in AddGuidanceFromPointsDeepEditd.__call__(self, data)
[2023-09-25T14:55:33.080Z] 664 meta_dict_key = self.meta_keys or f"{self.ref_image}_{self.meta_key_postfix}"
[2023-09-25T14:55:33.080Z] 665 if meta_dict_key not in d:
[2023-09-25T14:55:33.080Z] --> 666 raise RuntimeError(f"Missing meta_dict {meta_dict_key} in data!")
[2023-09-25T14:55:33.080Z] 667 if "spatial_shape" not in d[meta_dict_key]:
[2023-09-25T14:55:33.081Z] 668 raise RuntimeError('Missing "spatial_shape" in meta_dict!')
[2023-09-25T14:55:33.081Z]
[2023-09-25T14:55:33.081Z] RuntimeError: Missing meta_dict image_meta_dict in data!
