testing error modules/transform_visualization.ipynb

Describe the bug

[2023-01-10T15:57:42.182Z] Running ./modules/transform_visualization.ipynb
[2023-01-10T15:57:42.182Z] Checking PEP8 compliance...
[2023-01-10T15:57:42.182Z] .*federated_learning*
[2023-01-10T15:57:42.182Z] .*transchex_openi*
[2023-01-10T15:57:42.182Z] .*unetr_*
[2023-01-10T15:57:42.182Z] .*profiling_train_base_nvtx*
[2023-01-10T15:57:42.182Z] .*benchmark_global_mutual_information*
[2023-01-10T15:57:42.182Z] .*spleen_segmentation_3d_visualization_basic*
[2023-01-10T15:57:42.182Z] .*full_gpu_inference_pipeline*
[2023-01-10T15:57:42.182Z] .*generate_random_permutations*
[2023-01-10T15:57:42.182Z] .*transforms_update_meta_data*
[2023-01-10T15:57:42.182Z] .*video_seg*
[2023-01-10T15:57:42.182Z] .*tcia_dataset*
[2023-01-10T15:57:42.182Z] .*hovernet_torch*
[2023-01-10T15:57:42.182Z] .*preprocess_detect_scene_and_split_fold*
[2023-01-10T15:57:42.182Z] .*preprocess_to_build_detection_dataset*
[2023-01-10T15:57:42.182Z] .*preprocess_extract_images_from_video*
[2023-01-10T15:57:42.182Z] .*transfer_mmar*
[2023-01-10T15:57:42.182Z] .*MRI_reconstruction*
[2023-01-10T15:57:42.182Z] .*monailabel_HelloWorld_radiology_3dslicer*
[2023-01-10T15:57:42.182Z] .*monailabel_monaibundle_3dslicer_multiorgan_seg*
[2023-01-10T15:57:42.182Z] .*monailabel_pancreas_tumor_segmentation_3DSlicer*
[2023-01-10T15:57:42.182Z] .*monailabel_endoscopy_cvat_tooltracking*
[2023-01-10T15:57:42.182Z] .*monailabel_pathology_nuclei_segmentation_QuPath*
[2023-01-10T15:57:42.182Z] .*monailabel_radiology_spleen_segmentation_OHIF*
[2023-01-10T15:57:42.182Z] Running notebook...
[2023-01-10T15:57:47.426Z] MONAI version: 0.8.1+823.gea06e1ae
[2023-01-10T15:57:47.426Z] Numpy version: 1.22.2
[2023-01-10T15:57:47.426Z] Pytorch version: 1.10.2+cu102
[2023-01-10T15:57:47.426Z] MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
[2023-01-10T15:57:47.426Z] MONAI rev id: ea06e1ae1551c0c6e22a804f1094385371c5f6ff
[2023-01-10T15:57:47.426Z] MONAI __file__: /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/__init__.py
[2023-01-10T15:57:47.426Z] 
[2023-01-10T15:57:47.426Z] Optional dependencies:
[2023-01-10T15:57:47.426Z] Pytorch Ignite version: 0.4.10
[2023-01-10T15:57:47.426Z] Nibabel version: 5.0.0
[2023-01-10T15:57:47.426Z] scikit-image version: 0.19.3
[2023-01-10T15:57:47.426Z] Pillow version: 7.0.0
[2023-01-10T15:57:47.426Z] Tensorboard version: 2.9.0
[2023-01-10T15:57:47.426Z] gdown version: 4.6.0
[2023-01-10T15:57:47.426Z] TorchVision version: 0.11.3+cu102
[2023-01-10T15:57:47.426Z] tqdm version: 4.64.1
[2023-01-10T15:57:47.426Z] lmdb version: 1.4.0
[2023-01-10T15:57:47.426Z] psutil version: 5.9.4
[2023-01-10T15:57:47.426Z] pandas version: 1.1.5
[2023-01-10T15:57:47.426Z] einops version: 0.6.0
[2023-01-10T15:57:47.426Z] transformers version: 4.21.3
[2023-01-10T15:57:47.426Z] mlflow version: 2.1.1
[2023-01-10T15:57:47.426Z] pynrrd version: 1.0.0
[2023-01-10T15:57:47.426Z] 
[2023-01-10T15:57:47.426Z] For details about installing the optional dependencies, please visit:
[2023-01-10T15:57:47.426Z]     https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies
[2023-01-10T15:57:47.426Z] 
[2023-01-10T15:57:48.788Z] /usr/local/lib/python3.8/dist-packages/papermill/iorw.py:153: UserWarning: the file is not specified with any extension : -
[2023-01-10T15:57:48.788Z]   warnings.warn(
[2023-01-10T15:59:30.984Z] 
Executing:   0%|          | 0/38 [00:00<?, ?cell/s]
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Executing:  18%|█▊        | 7/38 [00:43<03:39,  7.09s/cell]
Executing:  32%|███▏      | 12/38 [01:26<03:30,  8.08s/cell]
Executing:  53%|█████▎    | 20/38 [01:29<01:02,  3.48s/cell]
Executing:  58%|█████▊    | 22/38 [01:41<01:02,  3.93s/cell]2023-01-10 15:59:30.041346: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  AVX2 AVX512F AVX512_VNNI FMA
[2023-01-10T15:59:30.984Z] To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
[2023-01-10T15:59:30.984Z] 2023-01-10 15:59:30.203670: I tensorflow/core/util/port.cc:104] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`.
[2023-01-10T15:59:30.984Z] 2023-01-10 15:59:30.942909: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer.so.7'; dlerror: libnvinfer.so.7: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /usr/local/lib/python3.8/dist-packages/torch/lib:/usr/local/lib/python3.8/dist-packages/torch_tensorrt/lib:/usr/local/cuda/compat/lib:/usr/local/nvidia/lib:/usr/local/nvidia/lib64
[2023-01-10T15:59:30.984Z] 2023-01-10 15:59:30.943033: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer_plugin.so.7'; dlerror: libnvinfer_plugin.so.7: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /usr/local/lib/python3.8/dist-packages/torch/lib:/usr/local/lib/python3.8/dist-packages/torch_tensorrt/lib:/usr/local/cuda/compat/lib:/usr/local/nvidia/lib:/usr/local/nvidia/lib64
[2023-01-10T15:59:30.984Z] 2023-01-10 15:59:30.943041: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Cannot dlopen some TensorRT libraries. If you would like to use Nvidia GPU with TensorRT, please make sure the missing libraries mentioned above are installed properly.
[2023-01-10T15:59:41.147Z] 
Executing:  63%|██████▎   | 24/38 [01:43<00:47,  3.36s/cell]
Executing:  66%|██████▌   | 25/38 [01:47<00:43,  3.38s/cell]
Executing:  74%|███████▎  | 28/38 [01:49<00:24,  2.45s/cell]
Executing:  74%|███████▎  | 28/38 [01:52<00:40,  4.00s/cell]
[2023-01-10T15:59:41.147Z] /usr/local/lib/python3.8/dist-packages/papermill/iorw.py:153: UserWarning: the file is not specified with any extension : -
[2023-01-10T15:59:41.147Z]   warnings.warn(
[2023-01-10T15:59:41.147Z] Traceback (most recent call last):
[2023-01-10T15:59:41.147Z]   File "/usr/local/bin/papermill", line 8, in <module>
[2023-01-10T15:59:41.147Z]     sys.exit(papermill())
[2023-01-10T15:59:41.147Z]   File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 1130, in __call__
[2023-01-10T15:59:41.147Z]     return self.main(*args, **kwargs)
[2023-01-10T15:59:41.147Z]   File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 1055, in main
[2023-01-10T15:59:41.147Z]     rv = self.invoke(ctx)
[2023-01-10T15:59:41.147Z]   File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 1404, in invoke
[2023-01-10T15:59:41.147Z]     return ctx.invoke(self.callback, **ctx.params)
[2023-01-10T15:59:41.147Z]   File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 760, in invoke
[2023-01-10T15:59:41.147Z]     return __callback(*args, **kwargs)
[2023-01-10T15:59:41.147Z]   File "/usr/local/lib/python3.8/dist-packages/click/decorators.py", line 26, in new_func
[2023-01-10T15:59:41.147Z]     return f(get_current_context(), *args, **kwargs)
[2023-01-10T15:59:41.147Z]   File "/usr/local/lib/python3.8/dist-packages/papermill/cli.py", line 250, in papermill
[2023-01-10T15:59:41.147Z]     execute_notebook(
[2023-01-10T15:59:41.147Z]   File "/usr/local/lib/python3.8/dist-packages/papermill/execute.py", line 128, in execute_notebook
[2023-01-10T15:59:41.147Z]     raise_for_execution_errors(nb, output_path)
[2023-01-10T15:59:41.147Z]   File "/usr/local/lib/python3.8/dist-packages/papermill/execute.py", line 232, in raise_for_execution_errors
[2023-01-10T15:59:41.147Z]     raise error
[2023-01-10T15:59:41.147Z] papermill.exceptions.PapermillExecutionError: 
[2023-01-10T15:59:41.147Z] ---------------------------------------------------------------------------
[2023-01-10T15:59:41.147Z] Exception encountered at "In [15]":
[2023-01-10T15:59:41.147Z] ---------------------------------------------------------------------------
[2023-01-10T15:59:41.147Z] TraitError                                Traceback (most recent call last)
[2023-01-10T15:59:41.147Z] Cell In[15], line 1
[2023-01-10T15:59:41.147Z] ----> 1 view(image=data["image"][0, 0, :, :, :] * 255, label_image=data["label"][0, 0, :, :, :] * 255, gradient_opacity=0.4)
[2023-01-10T15:59:41.147Z] 
[2023-01-10T15:59:41.147Z] File /usr/local/lib/python3.8/dist-packages/itkwidgets/widget_viewer.py:1090, in view(image, label_image, label_image_names, label_image_weights, label_image_blend, cmap, lut, select_roi, interpolation, gradient_opacity, opacity_gaussians, channels, slicing_planes, shadow, blend_mode, point_sets, point_set_colors, point_set_opacities, point_set_representations, point_set_sizes, geometries, geometry_colors, geometry_opacities, ui_collapsed, rotate, annotations, axes, mode, **kwargs)
[2023-01-10T15:59:41.147Z]    1087     if image is None and len(images):  # only one image is rendered
[2023-01-10T15:59:41.147Z]    1088         image = images[0]
[2023-01-10T15:59:41.147Z] -> 1090 viewer = Viewer(image=image,
[2023-01-10T15:59:41.147Z]    1091                 label_image=label_image,
[2023-01-10T15:59:41.147Z]    1092                 label_image_names=label_image_names,
[2023-01-10T15:59:41.147Z]    1093                 label_image_blend=label_image_blend,
[2023-01-10T15:59:41.147Z]    1094                 label_image_weights=label_image_weights,
[2023-01-10T15:59:41.147Z]    1095                 cmap=cmap,
[2023-01-10T15:59:41.147Z]    1096                 lut=lut,
[2023-01-10T15:59:41.147Z]    1097                 select_roi=select_roi,
[2023-01-10T15:59:41.147Z]    1098                 interpolation=interpolation,
[2023-01-10T15:59:41.147Z]    1099                 gradient_opacity=gradient_opacity,
[2023-01-10T15:59:41.147Z]    1100                 opacity_gaussians=opacity_gaussians,
[2023-01-10T15:59:41.147Z]    1101                 slicing_planes=slicing_planes,
[2023-01-10T15:59:41.147Z]    1102                 shadow=shadow, blend_mode=blend_mode,
[2023-01-10T15:59:41.147Z]    1103                 point_sets=point_sets,
[2023-01-10T15:59:41.147Z]    1104                 point_set_colors=point_set_colors,
[2023-01-10T15:59:41.147Z]    1105                 point_set_opacities=point_set_opacities,
[2023-01-10T15:59:41.147Z]    1106                 point_set_representations=point_set_representations,
[2023-01-10T15:59:41.147Z]    1107                 point_set_sizes=point_set_sizes,
[2023-01-10T15:59:41.147Z]    1108                 geometries=geometries, geometry_colors=geometry_colors,
[2023-01-10T15:59:41.147Z]    1109                 geometry_opacities=geometry_opacities,
[2023-01-10T15:59:41.147Z]    1110                 rotate=rotate, ui_collapsed=ui_collapsed,
[2023-01-10T15:59:41.147Z]    1111                 annotations=annotations, axes=axes, mode=mode,
[2023-01-10T15:59:41.147Z]    1112                 **kwargs)
[2023-01-10T15:59:41.147Z]    1113 return viewer
[2023-01-10T15:59:41.147Z] 
[2023-01-10T15:59:41.147Z] File /usr/local/lib/python3.8/dist-packages/itkwidgets/widget_viewer.py:369, in Viewer.__init__(self, **kwargs)
[2023-01-10T15:59:41.147Z]     365 if have_label_image:
[2023-01-10T15:59:41.147Z]     366     # Interpolation is not currently supported with label maps
[2023-01-10T15:59:41.147Z]     367     kwargs['interpolation'] = False
[2023-01-10T15:59:41.147Z] --> 369 super(Viewer, self).__init__(**kwargs)
[2023-01-10T15:59:41.147Z]     371 if not self.image and not self.label_image:
[2023-01-10T15:59:41.147Z]     372     return
[2023-01-10T15:59:41.147Z] 
[2023-01-10T15:59:41.147Z] File /usr/local/lib/python3.8/dist-packages/ipywidgets/widgets/widget.py:477, in Widget.__init__(self, **kwargs)
[2023-01-10T15:59:41.147Z]     475 """Public constructor"""
[2023-01-10T15:59:41.147Z]     476 self._model_id = kwargs.pop('model_id', None)
[2023-01-10T15:59:41.147Z] --> 477 super(Widget, self).__init__(**kwargs)
[2023-01-10T15:59:41.147Z]     479 Widget._call_widget_constructed(self)
[2023-01-10T15:59:41.147Z]     480 self.open()
[2023-01-10T15:59:41.147Z] 
[2023-01-10T15:59:41.147Z] File /usr/local/lib/python3.8/dist-packages/traitlets/traitlets.py:1358, in __init__(self, *args, **kwargs)
[2023-01-10T15:59:41.147Z]    1356 if change.type == "change":
[2023-01-10T15:59:41.147Z]    1357     if change.old is not Undefined:
[2023-01-10T15:59:41.147Z] -> 1358         self.set_trait(name, change.old)
[2023-01-10T15:59:41.147Z]    1359     else:
[2023-01-10T15:59:41.147Z]    1360         self._trait_values.pop(name)
[2023-01-10T15:59:41.147Z] 
[2023-01-10T15:59:41.147Z] File /usr/local/lib/python3.8/dist-packages/traitlets/traitlets.py:1738, in set_trait(self, name, value)
[2023-01-10T15:59:41.147Z]    1736     if name in c.__dict__.get("_trait_default_generators", {}):
[2023-01-10T15:59:41.147Z]    1737         return c._trait_default_generators[name]  # type:ignore[attr-defined]
[2023-01-10T15:59:41.147Z] -> 1738 return trait.default
[2023-01-10T15:59:41.147Z] 
[2023-01-10T15:59:41.147Z] File /usr/local/lib/python3.8/dist-packages/traittypes/traittypes.py:108, in Array.set(self, obj, value)
[2023-01-10T15:59:41.147Z]     107 def set(self, obj, value):
[2023-01-10T15:59:41.147Z] --> 108     new_value = self._validate(obj, value)
[2023-01-10T15:59:41.147Z]     109     old_value = obj._trait_values.get(self.name, self.default_value)
[2023-01-10T15:59:41.147Z]     110     obj._trait_values[self.name] = new_value
[2023-01-10T15:59:41.147Z] 
[2023-01-10T15:59:41.147Z] File /usr/local/lib/python3.8/dist-packages/traitlets/traitlets.py:735, in _validate(self, obj, value)
[2023-01-10T15:59:41.147Z]     731     meth_name = "_%s_validate" % self.name
[2023-01-10T15:59:41.147Z]     732     cross_validate = getattr(obj, meth_name)
[2023-01-10T15:59:41.147Z]     733     _deprecated_method(
[2023-01-10T15:59:41.147Z]     734         cross_validate,
[2023-01-10T15:59:41.147Z] --> 735         obj.__class__,
[2023-01-10T15:59:41.147Z]     736         meth_name,
[2023-01-10T15:59:41.147Z]     737         "use @validate decorator instead.",
[2023-01-10T15:59:41.147Z]     738     )
[2023-01-10T15:59:41.147Z]     739     value = cross_validate(value, self)
[2023-01-10T15:59:41.147Z]     740 return value
[2023-01-10T15:59:41.147Z] 
[2023-01-10T15:59:41.147Z] File /usr/local/lib/python3.8/dist-packages/ipydatawidgets/ndarray/traits.py:25, in NDArray.validate(self, obj, value)
[2023-01-10T15:59:41.147Z]      24 def validate(self, obj, value):
[2023-01-10T15:59:41.147Z] ---> 25     value = super(NDArray, self).validate(obj, value)
[2023-01-10T15:59:41.147Z]      26     if value is None or value is Undefined:
[2023-01-10T15:59:41.147Z]      27         return value
[2023-01-10T15:59:41.147Z] 
[2023-01-10T15:59:41.147Z] File /usr/local/lib/python3.8/dist-packages/traittypes/traittypes.py:105, in Array.validate(self, obj, value)
[2023-01-10T15:59:41.147Z]     103 except (ValueError, TypeError) as e:
[2023-01-10T15:59:41.147Z]     104     raise TraitError(e)
[2023-01-10T15:59:41.147Z] --> 105 return super(Array, self).validate(obj, value)
[2023-01-10T15:59:41.147Z] 
[2023-01-10T15:59:41.147Z] File /usr/local/lib/python3.8/dist-packages/traittypes/traittypes.py:76, in SciType.validate(self, obj, value)
[2023-01-10T15:59:41.147Z]      74 try:
[2023-01-10T15:59:41.147Z]      75     for validator in self.validators:
[2023-01-10T15:59:41.147Z] ---> 76         value = validator(self, value)
[2023-01-10T15:59:41.147Z]      77     return value
[2023-01-10T15:59:41.147Z]      78 except (ValueError, TypeError) as e:
[2023-01-10T15:59:41.147Z] 
[2023-01-10T15:59:41.147Z] File /usr/local/lib/python3.8/dist-packages/ipydatawidgets/ndarray/traits.py:40, in shape_constraints.<locals>.validator(trait, value)
[2023-01-10T15:59:41.147Z]      38     return value
[2023-01-10T15:59:41.147Z]      39 if len(value.shape) != len(args):
[2023-01-10T15:59:41.147Z] ---> 40     raise TraitError('%s shape expected to have %s components, but got %s components' % (
[2023-01-10T15:59:41.147Z]      41         trait.name, len(args), value.shape))
[2023-01-10T15:59:41.147Z]      42 for i, constraint in enumerate(args):
[2023-01-10T15:59:41.147Z]      43     if constraint is not None:
[2023-01-10T15:59:41.147Z] 
[2023-01-10T15:59:41.147Z] TraitError: label_image_weights shape expected to have 1 components, but got () components

cc @Nic-Ma @KumoLiu

Der fehlschlagende Einstiegspunkt ist modules/transform_visualization.ipynb, insbesondere die Zelle In [15], in der itkwidgets.view einen TraitError auslöst. Beginne damit, das Notebook mit papermill auszuführen, und untersuche diese Zelle in der gemeldeten Umgebung. Erledigt ist es, wenn das Notebook ohne einen PapermillExecutionError abgeschlossen wird.