08:01:31 Running ./model_zoo/TCIA_PROSTATEx_Prostate_MRI_Anatomy_Model.ipynb
08:01:31 Checking PEP8 compliance...
08:01:32 Running notebook...
08:01:45 MONAI version: 1.3.1rc2+2.ge9a5bfe4
08:01:45 Numpy version: 1.26.4
08:01:45 Pytorch version: 2.1.0a0+29c30b1
08:01:45 MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
08:01:45 MONAI rev id: e9a5bfe4693ce490c75616a97eb0812e1828539b
08:01:45 MONAI __file__: /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/__init__.py
08:01:45
08:01:45 Optional dependencies:
08:01:45 Pytorch Ignite version: 0.4.11
08:01:45 ITK version: 5.3.0
08:01:45 Nibabel version: 5.2.1
08:01:45 scikit-image version: 0.22.0
08:01:45 scipy version: 1.11.1
08:01:45 Pillow version: 9.2.0
08:01:45 Tensorboard version: 2.16.2
08:01:45 gdown version: 4.7.3
08:01:45 TorchVision version: 0.16.0a0
08:01:45 tqdm version: 4.65.0
08:01:45 lmdb version: 1.4.1
08:01:45 psutil version: 5.9.4
08:01:45 pandas version: 1.5.2
08:01:45 einops version: 0.6.1
08:01:45 transformers version: 4.39.3
08:01:45 mlflow version: 2.11.3
08:01:45 pynrrd version: 1.0.0
08:01:45 clearml version: 1.15.1
08:01:45
08:01:45 For details about installing the optional dependencies, please visit:
08:01:45 https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies
08:01:45
08:01:49 papermill --progress-bar --log-output -k python3
08:01:49 /usr/local/lib/python3.10/dist-packages/papermill/iorw.py:153: UserWarning: the file is not specified with any extension : -
08:01:49 warnings.warn(
08:03:12
Executing: 0%| | 0/32 [00:00<?, ?cell/s]
Executing: 3%|▎ | 1/32 [00:01<00:58, 1.89s/cell]
Executing: 22%|██▏ | 7/32 [01:17<04:47, 11.51s/cell]
Executing: 28%|██▊ | 9/32 [01:21<03:20, 8.71s/cell]
Executing: 28%|██▊ | 9/32 [01:23<03:32, 9.23s/cell]
08:03:12 /usr/local/lib/python3.10/dist-packages/papermill/iorw.py:153: UserWarning: the file is not specified with any extension : -
08:03:12 warnings.warn(
08:03:12 Traceback (most recent call last):
08:03:12 File "/usr/local/bin/papermill", line 8, in <module>
08:03:12 sys.exit(papermill())
08:03:12 File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1157, in __call__
08:03:12 return self.main(*args, **kwargs)
08:03:12 File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1078, in main
08:03:12 rv = self.invoke(ctx)
08:03:12 File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1434, in invoke
08:03:12 return ctx.invoke(self.callback, **ctx.params)
08:03:12 File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 783, in invoke
08:03:12 return __callback(*args, **kwargs)
08:03:12 File "/usr/local/lib/python3.10/dist-packages/click/decorators.py", line 33, in new_func
08:03:12 return f(get_current_context(), *args, **kwargs)
08:03:12 File "/usr/local/lib/python3.10/dist-packages/papermill/cli.py", line 254, in papermill
08:03:12 execute_notebook(
08:03:12 File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 134, in execute_notebook
08:03:12 raise_for_execution_errors(nb, output_path)
08:03:12 File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 241, in raise_for_execution_errors
08:03:12 raise error
08:03:12 papermill.exceptions.PapermillExecutionError:
08:03:12 ---------------------------------------------------------------------------
08:03:12 Exception encountered at "In [2]":
08:03:12 ---------------------------------------------------------------------------
08:03:12 AttributeError Traceback (most recent call last)
08:03:12 Cell In[2], line 15
08:03:12 12 import pydicom_seg
08:03:12 14 # for downloading data from TCIA
08:03:12 ---> 15 from tcia_utils import nbia
08:03:12 17 # This is the most common import command for itkWidgets.
08:03:12 18 # The view() function opens an interactive viewer for 2D and 3D
08:03:12 19 # data in a variety of formats.
08:03:12 20 from itkwidgets import view
08:03:12
08:03:12 File /usr/local/lib/python3.10/dist-packages/tcia_utils/__init__.py:1
08:03:12 ----> 1 from . import nbia
08:03:12 2 from . import datacite
08:03:12 3 from . import pathdb
08:03:12
08:03:12 File /usr/local/lib/python3.10/dist-packages/tcia_utils/nbia.py:17
08:03:12 15 import pydicom
08:03:12 16 import pydicom_seg
08:03:12 ---> 17 import rt_utils
08:03:12 18 import numpy as np
08:03:12 19 from ipywidgets import interact
08:03:12
08:03:12 File /usr/local/lib/python3.10/dist-packages/rt_utils/__init__.py:1
08:03:12 ----> 1 from .rtstruct import RTStruct
08:03:12 2 from .rtstruct_builder import RTStructBuilder
08:03:12
08:03:12 File /usr/local/lib/python3.10/dist-packages/rt_utils/rtstruct.py:7
08:03:12 4 from pydicom.dataset import FileDataset
08:03:12 6 from rt_utils.utils import ROIData
08:03:12 ----> 7 from . import ds_helper, image_helper
08:03:12 10 class RTStruct:
08:03:12 11 """
08:03:12 12 Wrapper class to facilitate appending and extracting ROI's within an RTStruct
08:03:12 13 """
08:03:12
08:03:12 File /usr/local/lib/python3.10/dist-packages/rt_utils/ds_helper.py:2
08:03:12 1 import datetime
08:03:12 ----> 2 from rt_utils.image_helper import get_contours_coords
08:03:12 3 from rt_utils.utils import ROIData, SOPClassUID
08:03:12 4 import numpy as np
08:03:12
08:03:12 File /usr/local/lib/python3.10/dist-packages/rt_utils/image_helper.py:5
08:03:12 2 from typing import List
08:03:12 3 from enum import IntEnum
08:03:12 ----> 5 import cv2 as cv
08:03:12 6 import numpy as np
08:03:12 7 from pydicom import dcmread
08:03:12
08:03:12 File /usr/local/lib/python3.10/dist-packages/cv2/__init__.py:181
08:03:12 176 if DEBUG: print("Extra Python code for", submodule, "is loaded")
08:03:12 178 if DEBUG: print('OpenCV loader: DONE')
08:03:12 --> 181 bootstrap()
08:03:12
08:03:12 File /usr/local/lib/python3.10/dist-packages/cv2/__init__.py:175, in bootstrap()
08:03:12 172 if DEBUG: print('OpenCV loader: binary extension... OK')
08:03:12 174 for submodule in __collect_extra_submodules(DEBUG):
08:03:12 --> 175 if __load_extra_py_code_for_module("cv2", submodule, DEBUG):
08:03:12 176 if DEBUG: print("Extra Python code for", submodule, "is loaded")
08:03:12 178 if DEBUG: print('OpenCV loader: DONE')
08:03:12
08:03:12 File /usr/local/lib/python3.10/dist-packages/cv2/__init__.py:28, in __load_extra_py_code_for_module(base, name, enable_debug_print)
08:03:12 26 native_module = sys.modules.pop(module_name, None)
08:03:12 27 try:
08:03:12 ---> 28 py_module = importlib.import_module(module_name)
08:03:12 29 except ImportError as err:
08:03:12 30 if enable_debug_print:
08:03:12
08:03:12 File /usr/lib/python3.10/importlib/__init__.py:126, in import_module(name, package)
08:03:12 124 break
08:03:12 125 level += 1
08:03:12 --> 126 return _bootstrap._gcd_import(name[level:], package, level)
08:03:12
08:03:12 File /usr/local/lib/python3.10/dist-packages/cv2/typing/__init__.py:168
08:03:12 166 ExtractArgsCallback = _typing.Callable[[_typing.Sequence[GTypeInfo]], _typing.Sequence[GRunArg]]
08:03:12 167 ExtractMetaCallback = _typing.Callable[[_typing.Sequence[GTypeInfo]], _typing.Sequence[GMetaArg]]
08:03:12 --> 168 LayerId = cv2.dnn.DictValue
08:03:12 169 IndexParams = _typing.Dict[str, _typing.Union[bool, int, float, str]]
08:03:12 170 SearchParams = _typing.Dict[str, _typing.Union[bool, int, float, str]]
08:03:12
08:03:12 AttributeError: module 'cv2.dnn' has no attribute 'DictValue'
