Closed KumoLiu closed 2 months ago
[2024-09-02T23:25:00.613Z] Running ./pathology/tumor_detection/ignite/profiling_camelyon_pipeline.ipynb [2024-09-02T23:25:04.387Z] from torch.distributed.optim import ZeroRedundancyOptimizer [2024-09-02T23:25:08.550Z] MONAI version: 1.4.0rc6+2.gdbfe418c [2024-09-02T23:25:08.550Z] Numpy version: 1.24.4 [2024-09-02T23:25:08.550Z] Pytorch version: 2.4.0+cu121 [2024-09-02T23:25:08.550Z] MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False [2024-09-02T23:25:08.550Z] MONAI rev id: dbfe418c03073baf07a0e14cd7606571f3d0de18 [2024-09-02T23:25:08.550Z] MONAI __file__: /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/__init__.py [2024-09-02T23:25:08.550Z] [2024-09-02T23:25:08.550Z] Optional dependencies: [2024-09-02T23:25:08.550Z] Pytorch Ignite version: 0.4.11 [2024-09-02T23:25:08.550Z] ITK version: 5.4.0 [2024-09-02T23:25:08.550Z] Nibabel version: 5.2.1 [2024-09-02T23:25:08.550Z] scikit-image version: 0.23.2 [2024-09-02T23:25:08.550Z] scipy version: 1.14.0 [2024-09-02T23:25:08.550Z] Pillow version: 10.4.0 [2024-09-02T23:25:08.550Z] Tensorboard version: 2.16.2 [2024-09-02T23:25:08.550Z] gdown version: 5.2.0 [2024-09-02T23:25:08.550Z] TorchVision version: 0.19.0+cu121 [2024-09-02T23:25:08.550Z] tqdm version: 4.66.5 [2024-09-02T23:25:08.550Z] lmdb version: 1.5.1 [2024-09-02T23:25:08.550Z] psutil version: 6.0.0 [2024-09-02T23:25:08.550Z] pandas version: 2.2.2 [2024-09-02T23:25:08.550Z] einops version: 0.7.0 [2024-09-02T23:25:08.550Z] transformers version: 4.40.2 [2024-09-02T23:25:08.550Z] mlflow version: 2.16.0 [2024-09-02T23:25:08.550Z] pynrrd version: 1.0.0 [2024-09-02T23:25:08.550Z] clearml version: 1.16.4 [2024-09-02T23:25:08.550Z] [2024-09-02T23:25:08.550Z] For details about installing the optional dependencies, please visit: [2024-09-02T23:25:08.550Z] https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies [2024-09-02T23:25:08.550Z] [2024-09-02T23:25:10.436Z] papermill --progress-bar --log-output -k python3 [2024-09-02T23:25:10.690Z] /usr/local/lib/python3.10/dist-packages/papermill/iorw.py:149: UserWarning: the file is not specified with any extension : - [2024-09-02T23:25:10.690Z] warnings.warn(f"the file is not specified with any extension : {os.path.basename(path)}") [2024-09-02T23:26:21.391Z] Executing: 0%| | 0/19 [00:00<?, ?cell/s] Executing: 5%|▌ | 1/19 [00:00<00:15, 1.15cell/s] Executing: 32%|███▏ | 6/19 [00:19<00:43, 3.33s/cell] Executing: 42%|████▏ | 8/19 [00:26<00:37, 3.41s/cell] Executing: 53%|█████▎ | 10/19 [00:43<00:45, 5.07s/cell] Executing: 63%|██████▎ | 12/19 [01:05<00:48, 6.90s/cell] Executing: 68%|██████▊ | 13/19 [01:06<00:35, 5.88s/cell] Executing: 89%|████████▉ | 17/19 [01:07<00:05, 2.97s/cell] Executing: 89%|████████▉ | 17/19 [01:10<00:08, 4.13s/cell] [2024-09-02T23:26:21.391Z] /usr/local/lib/python3.10/dist-packages/papermill/iorw.py:149: UserWarning: the file is not specified with any extension : - [2024-09-02T23:26:21.391Z] warnings.warn(f"the file is not specified with any extension : {os.path.basename(path)}") [2024-09-02T23:26:21.391Z] Traceback (most recent call last): [2024-09-02T23:26:21.391Z] File "/usr/local/bin/papermill", line 8, in <module> [2024-09-02T23:26:21.391Z] sys.exit(papermill()) [2024-09-02T23:26:21.391Z] File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1157, in __call__ [2024-09-02T23:26:21.391Z] return self.main(*args, **kwargs) [2024-09-02T23:26:21.391Z] File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1078, in main [2024-09-02T23:26:21.391Z] rv = self.invoke(ctx) [2024-09-02T23:26:21.391Z] File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1434, in invoke [2024-09-02T23:26:21.391Z] return ctx.invoke(self.callback, **ctx.params) [2024-09-02T23:26:21.391Z] File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 783, in invoke [2024-09-02T23:26:21.391Z] return __callback(*args, **kwargs) [2024-09-02T23:26:21.391Z] File "/usr/local/lib/python3.10/dist-packages/click/decorators.py", line 33, in new_func [2024-09-02T23:26:21.391Z] return f(get_current_context(), *args, **kwargs) [2024-09-02T23:26:21.391Z] File "/usr/local/lib/python3.10/dist-packages/papermill/cli.py", line 235, in papermill [2024-09-02T23:26:21.391Z] execute_notebook( [2024-09-02T23:26:21.391Z] File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 131, in execute_notebook [2024-09-02T23:26:21.391Z] raise_for_execution_errors(nb, output_path) [2024-09-02T23:26:21.391Z] File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 251, in raise_for_execution_errors [2024-09-02T23:26:21.391Z] raise error [2024-09-02T23:26:21.391Z] papermill.exceptions.PapermillExecutionError: [2024-09-02T23:26:21.392Z] --------------------------------------------------------------------------- [2024-09-02T23:26:21.392Z] Exception encountered at "In [7]": [2024-09-02T23:26:21.392Z] --------------------------------------------------------------------------- [2024-09-02T23:26:21.392Z] KeyError Traceback (most recent call last) [2024-09-02T23:26:21.392Z] Cell In[7], line 9 [2024-09-02T23:26:21.392Z] 6 summary.set_index("Range", inplace=True) [2024-09-02T23:26:21.392Z] 8 # Get the entries for training transforms only (to avoid nested ranges) [2024-09-02T23:26:21.392Z] ----> 9 summary = summary.loc[transforms] [2024-09-02T23:26:21.392Z] 11 # Nsys output column names are different in different versions, [2024-09-02T23:26:21.392Z] 12 # so we need to find the corresponding columns [2024-09-02T23:26:21.392Z] 13 avg_col = [c for c in summary.columns if c.startswith("Av")] [2024-09-02T23:26:21.392Z] [2024-09-02T23:26:21.392Z] File /usr/local/lib/python3.10/dist-packages/pandas/core/indexing.py:1191, in _LocationIndexer.__getitem__(self, key) [2024-09-02T23:26:21.392Z] 1189 maybe_callable = com.apply_if_callable(key, self.obj) [2024-09-02T23:26:21.392Z] 1190 maybe_callable = self._check_deprecated_callable_usage(key, maybe_callable) [2024-09-02T23:26:21.392Z] -> 1191 return self._getitem_axis(maybe_callable, axis=axis) [2024-09-02T23:26:21.392Z] [2024-09-02T23:26:21.392Z] File /usr/local/lib/python3.10/dist-packages/pandas/core/indexing.py:1420, in _LocIndexer._getitem_axis(self, key, axis) [2024-09-02T23:26:21.392Z] 1417 if hasattr(key, "ndim") and key.ndim > 1: [2024-09-02T23:26:21.392Z] 1418 raise ValueError("Cannot index with multidimensional key") [2024-09-02T23:26:21.392Z] -> 1420 return self._getitem_iterable(key, axis=axis) [2024-09-02T23:26:21.392Z] 1422 # nested tuple slicing [2024-09-02T23:26:21.392Z] 1423 if is_nested_tuple(key, labels): [2024-09-02T23:26:21.392Z] [2024-09-02T23:26:21.392Z] File /usr/local/lib/python3.10/dist-packages/pandas/core/indexing.py:1360, in _LocIndexer._getitem_iterable(self, key, axis) [2024-09-02T23:26:21.392Z] 1357 self._validate_key(key, axis) [2024-09-02T23:26:21.392Z] 1359 # A collection of keys [2024-09-02T23:26:21.392Z] -> 1360 keyarr, indexer = self._get_listlike_indexer(key, axis) [2024-09-02T23:26:21.392Z] 1361 return self.obj._reindex_with_indexers( [2024-09-02T23:26:21.392Z] 1362 {axis: [keyarr, indexer]}, copy=True, allow_dups=True [2024-09-02T23:26:21.392Z] 1363 ) [2024-09-02T23:26:21.392Z] [2024-09-02T23:26:21.392Z] File /usr/local/lib/python3.10/dist-packages/pandas/core/indexing.py:1558, in _LocIndexer._get_listlike_indexer(self, key, axis) [2024-09-02T23:26:21.392Z] 1555 ax = self.obj._get_axis(axis) [2024-09-02T23:26:21.392Z] 1556 axis_name = self.obj._get_axis_name(axis) [2024-09-02T23:26:21.392Z] -> 1558 keyarr, indexer = ax._get_indexer_strict(key, axis_name) [2024-09-02T23:26:21.392Z] 1560 return keyarr, indexer [2024-09-02T23:26:21.392Z] [2024-09-02T23:26:21.392Z] File /usr/local/lib/python3.10/dist-packages/pandas/core/indexes/base.py:6200, in Index._get_indexer_strict(self, key, axis_name) [2024-09-02T23:26:21.392Z] 6197 else: [2024-09-02T23:26:21.392Z] 6198 keyarr, indexer, new_indexer = self._reindex_non_unique(keyarr) [2024-09-02T23:26:21.392Z] -> 6200 self._raise_if_missing(keyarr, indexer, axis_name) [2024-09-02T23:26:21.392Z] 6202 keyarr = self.take(indexer) [2024-09-02T23:26:21.392Z] 6203 if isinstance(key, Index): [2024-09-02T23:26:21.392Z] 6204 # GH 42790 - Preserve name from an Index [2024-09-02T23:26:21.392Z] [2024-09-02T23:26:21.392Z] File /usr/local/lib/python3.10/dist-packages/pandas/core/indexes/base.py:6249, in Index._raise_if_missing(self, key, indexer, axis_name) [2024-09-02T23:26:21.392Z] 6247 if nmissing: [2024-09-02T23:26:21.392Z] 6248 if nmissing == len(indexer): [2024-09-02T23:26:21.392Z] -> 6249 raise KeyError(f"None of [{key}] are in the [{axis_name}]") [2024-09-02T23:26:21.392Z] 6251 not_found = list(ensure_index(key)[missing_mask.nonzero()[0]].unique()) [2024-09-02T23:26:21.392Z] 6252 raise KeyError(f"{not_found} not in index") [2024-09-02T23:26:21.392Z] [2024-09-02T23:26:21.392Z] KeyError: "None of [Index(['ToTensord', 'Lambdad', 'GridSplitd', 'TorchVisiond_ColorJitter',\n 'ToNumpyd', 'RandFlipd', 'RandRotate90d', 'CastToTyped', 'RandZoomd',\n 'ScaleIntensityRanged', 'ToTensord_2', 'Activationsd', 'AsDiscreted'],\n dtype='object', name='Range')] are in the [index]"
KumoLiu
commented
2 months ago KumoLiu
commented
2 months ago