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deepedit/ignite/infoANDinference.ipynb #1529

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wyli opened this issue Sep 25, 2023 · 0 comments · Fixed by #1533
Closed

deepedit/ignite/infoANDinference.ipynb #1529

wyli opened this issue Sep 25, 2023 · 0 comments · Fixed by #1533
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@wyli
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wyli commented Sep 25, 2023 

[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!
@wyli wyli added the bug Something isn't working label Sep 25, 2023
KumoLiu added a commit to KumoLiu/tutorials that referenced this issue Sep 26, 2023
@KumoLiu
fix Project-MONAI#1529
b3fade1 
Signed-off-by: KumoLiu <[email protected]>
@KumoLiu KumoLiu mentioned this issue Sep 26, 2023
Merged
5 tasks
wyli pushed a commit that referenced this issue Sep 26, 2023
@KumoLiu
Fix deepedit/ignite/infoANDinference.ipynb (#1533)
97e4b0d 
Fixes #1529 

### Description
Update `image_only=False` in `LoadImaged` since the default value of
`image_only` has been changed by
Project-MONAI/MONAI#7019

### Checks
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Avoid including large-size files in the PR.
- [x] Clean up long text outputs from code cells in the notebook.
- [ ] For security purposes, please check the contents and remove any
sensitive info such as user names and private key.
- [ ] Ensure (1) hyperlinks and markdown anchors are working (2) use
relative paths for tutorial repo files (3) put figure and graphs in the
`./figure` folder
- [ ] Notebook runs automatically `./runner.sh -t <path to .ipynb file>`

Signed-off-by: KumoLiu <[email protected]>
boneseva pushed a commit to boneseva/MONAI-tutorials that referenced this issue Apr 21, 2024
@KumoLiu
Fix deepedit/ignite/infoANDinference.ipynb (Project-MONAI#1533)
6696dda 
Fixes Project-MONAI#1529 

### Description
Update `image_only=False` in `LoadImaged` since the default value of
`image_only` has been changed by
Project-MONAI/MONAI#7019

### Checks
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Avoid including large-size files in the PR.
- [x] Clean up long text outputs from code cells in the notebook.
- [ ] For security purposes, please check the contents and remove any
sensitive info such as user names and private key.
- [ ] Ensure (1) hyperlinks and markdown anchors are working (2) use
relative paths for tutorial repo files (3) put figure and graphs in the
`./figure` folder
- [ ] Notebook runs automatically `./runner.sh -t <path to .ipynb file>`

Signed-off-by: KumoLiu <[email protected]>
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Fix deepedit/ignite/infoANDinference.ipynb KumoLiu/tutorials
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