Closed KumoLiu closed 3 months ago
Running ./modules/resample_benchmark.ipynb Checking PEP8 compliance... Running notebook... MONAI version: 1.3.1+2.g66a2fae4 Numpy version: 1.24.4 Pytorch version: 2.3.0+cu121 MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False MONAI rev id: 66a2fae406f8d83a4421edd86a04fa787dbbd091 MONAI __file__: /usr/local/lib/python3.10/dist-packages/monai/__init__.py Optional dependencies: Pytorch Ignite version: 0.4.11 ITK version: 5.4.0 Nibabel version: 5.2.1 scikit-image version: 0.19.3 scipy version: 1.12.0 Pillow version: 7.0.0 Tensorboard version: 2.16.2 gdown version: 5.2.0 TorchVision version: 0.18.0+cu121 tqdm version: 4.66.1 lmdb version: 1.4.1 psutil version: 5.9.4 pandas version: 1.5.3 einops version: 0.7.0 transformers version: 4.40.2 mlflow version: 2.13.0 pynrrd version: 1.0.0 clearml version: 1.16.2rc0 For details about installing the optional dependencies, please visit: https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies papermill --progress-bar --log-output -k python3 /usr/local/lib/python3.10/dist-packages/papermill/iorw.py:149: UserWarning: the file is not specified with any extension : - warnings.warn(f"the file is not specified with any extension : {os.path.basename(path)}") Executing: 0%| | 0/34 [00:00<?, ?cell/s] Executing: 3%|▎ | 1/34 [00:01<00:37, 1.14s/cell] Executing: 12%|█▏ | 4/34 [00:29<03:55, 7.87s/cell] Executing: 18%|█▊ | 6/34 [00:36<02:48, 6.03s/cell] Executing: 29%|██▉ | 10/34 [00:38<01:09, 2.89s/cell] Executing: 41%|████ | 14/34 [00:38<00:32, 1.62s/cell] Executing: 53%|█████▎ | 18/34 [00:38<00:16, 1.01s/cell] Executing: 71%|███████ | 24/34 [00:38<00:05, 1.75cell/s] Executing: 76%|███████▋ | 26/34 [00:39<00:04, 1.98cell/s] Executing: 82%|████████▏ | 28/34 [00:43<00:05, 1.12cell/s] Executing: 88%|████████▊ | 30/34 [00:45<00:03, 1.23cell/s] Executing: 88%|████████▊ | 30/34 [00:47<00:06, 1.57s/cell] /usr/local/lib/python3.10/dist-packages/papermill/iorw.py:149: UserWarning: the file is not specified with any extension : - warnings.warn(f"the file is not specified with any extension : {os.path.basename(path)}") Traceback (most recent call last): File "/usr/local/bin/papermill", line 8, in <module> sys.exit(papermill()) File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1157, in __call__ return self.main(*args, **kwargs) File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, **ctx.params) File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 783, in invoke return __callback(*args, **kwargs) File "/usr/local/lib/python3.10/dist-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), *args, **kwargs) File "/usr/local/lib/python3.10/dist-packages/papermill/cli.py", line 235, in papermill execute_notebook( File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 131, in execute_notebook raise_for_execution_errors(nb, output_path) File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 251, in raise_for_execution_errors raise error papermill.exceptions.PapermillExecutionError: --------------------------------------------------------------------------- Exception encountered at "In [14]": --------------------------------------------------------------------------- IndexError Traceback (most recent call last) Cell In[14], line 7 5 row[1].imshow(monai_warped_img[d]) 6 row[1].axis("off") ----> 7 row[2].imshow(itk_warped_img[d]) 8 row[2].axis("off") 10 if i == 0: IndexError: too many indices for array: array is 0-dimensional, but 1 were indexed real 0m47.902s user 0m56.003s sys 0m20.942s Check failed!
Like an issue from https://pypi.org/project/itk/#history. Will take a look later.