Open
Description
[2025-06-16T22:42:14.473Z] Running ./model_zoo/TCIA_PROSTATEx_Prostate_MRI_Anatomy_Model.ipynb
[2025-06-16T22:42:14.728Z] Running notebook...
[2025-06-16T22:42:22.802Z] In the future `np.bool` will be defined as the corresponding NumPy scalar.
[2025-06-16T22:42:22.802Z] In the future `np.bool` will be defined as the corresponding NumPy scalar.
[2025-06-16T22:42:22.802Z] In the future `np.bool` will be defined as the corresponding NumPy scalar.
[2025-06-16T22:42:24.685Z] MONAI version: 1.5.0
[2025-06-16T22:42:24.685Z] Numpy version: 1.26.4
[2025-06-16T22:42:24.685Z] Pytorch version: 2.6.0+cu124
[2025-06-16T22:42:24.685Z] MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
[2025-06-16T22:42:24.685Z] MONAI rev id: d388d1c6fec8cb3a0eebee5b5a0b9776ca59ca83
[2025-06-16T22:42:24.685Z] MONAI __file__: /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/__init__.py
[2025-06-16T22:42:24.685Z]
[2025-06-16T22:42:24.685Z] Optional dependencies:
[2025-06-16T22:42:24.685Z] In the future `np.bool` will be defined as the corresponding NumPy scalar.
[2025-06-16T22:42:24.941Z] Pytorch Ignite version: 0.4.11
[2025-06-16T22:42:24.941Z] ITK version: NOT INSTALLED or UNKNOWN VERSION.
[2025-06-16T22:42:24.941Z] Nibabel version: 5.3.2
[2025-06-16T22:42:24.941Z] scikit-image version: 0.25.2
[2025-06-16T22:42:24.941Z] scipy version: 1.14.0
[2025-06-16T22:42:24.941Z] Pillow version: 10.4.0
[2025-06-16T22:42:24.941Z] Tensorboard version: 2.16.2
[2025-06-16T22:42:24.941Z] gdown version: 5.2.0
[2025-06-16T22:42:24.941Z] TorchVision version: 0.21.0+cu124
[2025-06-16T22:42:24.941Z] tqdm version: 4.66.5
[2025-06-16T22:42:24.941Z] lmdb version: 1.6.2
[2025-06-16T22:42:24.941Z] psutil version: 6.0.0
[2025-06-16T22:42:24.941Z] pandas version: 2.2.2
[2025-06-16T22:42:24.941Z] einops version: 0.8.0
[2025-06-16T22:42:24.941Z] transformers version: 4.40.2
[2025-06-16T22:42:24.941Z] mlflow version: 3.1.0
[2025-06-16T22:42:24.941Z] pynrrd version: 1.1.3
[2025-06-16T22:42:24.941Z] clearml version: 2.0.0
[2025-06-16T22:42:24.941Z]
[2025-06-16T22:42:24.941Z] For details about installing the optional dependencies, please visit:
[2025-06-16T22:42:24.941Z] https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies
[2025-06-16T22:42:24.941Z]
[2025-06-16T22:42:27.448Z] papermill --progress-bar --log-output -k python3
[2025-06-16T22:42:27.448Z] /usr/local/lib/python3.10/dist-packages/papermill/iorw.py:149: UserWarning: the file is not specified with any extension : -
[2025-06-16T22:42:27.448Z] warnings.warn(f"the file is not specified with any extension : {os.path.basename(path)}")
[2025-06-16T22:43:36.231Z]
Executing: 0%| | 0/32 [00:00<?, ?cell/s]
Executing: 3%|▎ | 1/32 [00:00<00:29, 1.06cell/s]
Executing: 22%|██▏ | 7/32 [01:01<03:46, 9.08s/cell]
Executing: 28%|██▊ | 9/32 [01:01<02:28, 6.47s/cell]
Executing: 28%|██▊ | 9/32 [01:02<02:38, 6.90s/cell]
[2025-06-16T22:43:36.231Z] /usr/local/lib/python3.10/dist-packages/papermill/iorw.py:149: UserWarning: the file is not specified with any extension : -
[2025-06-16T22:43:36.231Z] warnings.warn(f"the file is not specified with any extension : {os.path.basename(path)}")
[2025-06-16T22:43:36.231Z] Traceback (most recent call last):
[2025-06-16T22:43:36.231Z] File "/usr/local/bin/papermill", line 8, in <module>
[2025-06-16T22:43:36.231Z] sys.exit(papermill())
[2025-06-16T22:43:36.231Z] File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1157, in __call__
[2025-06-16T22:43:36.231Z] return self.main(*args, **kwargs)
[2025-06-16T22:43:36.231Z] File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1078, in main
[2025-06-16T22:43:36.231Z] rv = self.invoke(ctx)
[2025-06-16T22:43:36.231Z] File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1434, in invoke
[2025-06-16T22:43:36.231Z] return ctx.invoke(self.callback, **ctx.params)
[2025-06-16T22:43:36.231Z] File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 783, in invoke
[2025-06-16T22:43:36.231Z] return __callback(*args, **kwargs)
[2025-06-16T22:43:36.231Z] File "/usr/local/lib/python3.10/dist-packages/click/decorators.py", line 33, in new_func
[2025-06-16T22:43:36.231Z] return f(get_current_context(), *args, **kwargs)
[2025-06-16T22:43:36.231Z] File "/usr/local/lib/python3.10/dist-packages/papermill/cli.py", line 235, in papermill
[2025-06-16T22:43:36.231Z] execute_notebook(
[2025-06-16T22:43:36.231Z] File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 131, in execute_notebook
[2025-06-16T22:43:36.231Z] raise_for_execution_errors(nb, output_path)
[2025-06-16T22:43:36.231Z] File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 251, in raise_for_execution_errors
[2025-06-16T22:43:36.231Z] raise error
[2025-06-16T22:43:36.231Z] papermill.exceptions.PapermillExecutionError:
[2025-06-16T22:43:36.231Z] ---------------------------------------------------------------------------
[2025-06-16T22:43:36.231Z] Exception encountered at "In [2]":
[2025-06-16T22:43:36.231Z] ---------------------------------------------------------------------------
[2025-06-16T22:43:36.231Z] AttributeError Traceback (most recent call last)
[2025-06-16T22:43:36.231Z] Cell In[2], line 8
[2025-06-16T22:43:36.231Z] 5 import numpy as np
[2025-06-16T22:43:36.231Z] 7 # Include ITK for DICOM reading.
[2025-06-16T22:43:36.231Z] ----> 8 import itk
[2025-06-16T22:43:36.231Z] 10 # Include pydicom_seg for DICOM SEG objects
[2025-06-16T22:43:36.231Z] 11 import pydicom
[2025-06-16T22:43:36.231Z]
[2025-06-16T22:43:36.231Z] File /usr/local/lib/python3.10/dist-packages/itk/__init__.py:28
[2025-06-16T22:43:36.231Z] 21 # Must import module from python path, not local reference
[2025-06-16T22:43:36.231Z] 22 # in order to maintain the singular value of the module values.
[2025-06-16T22:43:36.231Z] 23 # `import .conf.itkConfig` is a different context than
[2025-06-16T22:43:36.231Z] 24 # `import itkConfig`, even if they are the same file. The
[2025-06-16T22:43:36.231Z] 25 # LazyLoading and other values may be different in the two contexts.
[2025-06-16T22:43:36.231Z] 26 from itkConfig import ITK_GLOBAL_VERSION_STRING as __version__
[2025-06-16T22:43:36.231Z] ---> 28 from itk.support.extras import *
[2025-06-16T22:43:36.231Z] 29 from itk.support.init_helpers import *
[2025-06-16T22:43:36.231Z] 30 from itk.support.types import (
[2025-06-16T22:43:36.231Z] 31 itkCType,
[2025-06-16T22:43:36.231Z] 32 F,
[2025-06-16T22:43:36.231Z] (...)
[2025-06-16T22:43:36.231Z] 48 OT,
[2025-06-16T22:43:36.231Z] 49 )
[2025-06-16T22:43:36.231Z]
[2025-06-16T22:43:36.231Z] File /usr/local/lib/python3.10/dist-packages/itk/support/extras.py:37
[2025-06-16T22:43:36.231Z] 33 import builtins
[2025-06-16T22:43:36.231Z] 35 fileiotype = Union[str, bytes, os.PathLike]
[2025-06-16T22:43:36.231Z] ---> 37 import itk.support.types as itkt
[2025-06-16T22:43:36.231Z] 39 from .helpers import wasm_type_from_image_type, image_type_from_wasm_type
[2025-06-16T22:43:36.231Z] 40 from .helpers import wasm_type_from_mesh_type, mesh_type_from_wasm_type, python_to_js
[2025-06-16T22:43:36.231Z]
[2025-06-16T22:43:36.231Z] File /usr/local/lib/python3.10/dist-packages/itk/support/types.py:178
[2025-06-16T22:43:36.231Z] 160 SLL: itkCType
[2025-06-16T22:43:36.231Z] 161 B: itkCType
[2025-06-16T22:43:36.231Z] 163 (
[2025-06-16T22:43:36.231Z] 164 F,
[2025-06-16T22:43:36.231Z] 165 D,
[2025-06-16T22:43:36.231Z] 166 UC,
[2025-06-16T22:43:36.231Z] 167 US,
[2025-06-16T22:43:36.231Z] 168 UI,
[2025-06-16T22:43:36.231Z] 169 UL,
[2025-06-16T22:43:36.231Z] 170 SL,
[2025-06-16T22:43:36.231Z] 171 LD,
[2025-06-16T22:43:36.231Z] 172 ULL,
[2025-06-16T22:43:36.231Z] 173 SC,
[2025-06-16T22:43:36.231Z] 174 SS,
[2025-06-16T22:43:36.231Z] 175 SI,
[2025-06-16T22:43:36.231Z] 176 SLL,
[2025-06-16T22:43:36.231Z] 177 B,
[2025-06-16T22:43:36.231Z] --> 178 ) = itkCType.initialize_c_types_once()
[2025-06-16T22:43:36.231Z] 180 # Aliases for SizeValueType, IdentifierType, OffsetType
[2025-06-16T22:43:36.231Z] 181 ST = UL
[2025-06-16T22:43:36.231Z]
[2025-06-16T22:43:36.231Z] File /usr/local/lib/python3.10/dist-packages/itk/support/types.py:143, in itkCType.initialize_c_types_once()
[2025-06-16T22:43:36.231Z] 141 _SI: "itkCType" = itkCType("signed int", "SI", np.dtype(np.int32))
[2025-06-16T22:43:36.231Z] 142 _SLL: "itkCType" = itkCType("signed long long", "SLL", np.dtype(np.int64))
[2025-06-16T22:43:36.231Z] --> 143 _B: "itkCType" = itkCType("bool", "B", np.dtype(np.bool))
[2025-06-16T22:43:36.231Z] 144 return _F, _D, _UC, _US, _UI, _UL, _SL, _LD, _ULL, _SC, _SS, _SI, _SLL, _B
[2025-06-16T22:43:36.231Z]
[2025-06-16T22:43:36.231Z] File /usr/local/lib/python3.10/dist-packages/numpy/__init__.py:324, in __getattr__(attr)
[2025-06-16T22:43:36.231Z] 319 warnings.warn(
[2025-06-16T22:43:36.231Z] 320 f"In the future `np.{attr}` will be defined as the "
[2025-06-16T22:43:36.231Z] 321 "corresponding NumPy scalar.", FutureWarning, stacklevel=2)
[2025-06-16T22:43:36.231Z] 323 if attr in __former_attrs__:
[2025-06-16T22:43:36.231Z] --> 324 raise AttributeError(__former_attrs__[attr])
[2025-06-16T22:43:36.231Z] 326 if attr == 'testing':
[2025-06-16T22:43:36.231Z] 327 import numpy.testing as testing
[2025-06-16T22:43:36.231Z]
[2025-06-16T22:43:36.231Z] AttributeError: module 'numpy' has no attribute 'bool'.
[2025-06-16T22:43:36.231Z] `np.bool` was a deprecated alias for the builtin `bool`. To avoid this error in existing code, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
[2025-06-16T22:43:36.231Z] The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
[2025-06-16T22:43:36.231Z] https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
[2025-06-16T22:43:36.231Z]
[2025-06-16T22:43:36.231Z]
[2025-06-16T22:43:36.231Z] real 1m2.905s
[2025-06-16T22:43:36.231Z] user 0m39.893s
[2025-06-16T22:43:36.231Z] sys 0m6.458s
[2025-06-16T22:43:36.231Z] Check failed!