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Ran this notebook with dev version of holoscan v0.6
Signed-off-by: M Q <mingmelvinq@nvidia.com>
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‎notebooks/tutorials/02_mednist_app-prebuilt.ipynb

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"Requirement already satisfied: monai-deploy-app-sdk in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.8/site-packages (0.5.0)\n",
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"Requirement already satisfied: holoscan>=0.5.0 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.8/site-packages (from monai-deploy-app-sdk) (0.5.0)\n",
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"Requirement already satisfied: holoscan>=0.5.0 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.8/site-packages (from monai-deploy-app-sdk) (0.5.0+46.gc05e4dbd)\n",
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"Requirement already satisfied: nvidia-cudnn-cu11==8.5.0.96 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.8/site-packages (from torch>=1.8->monai) (8.5.0.96)\n",
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"Requirement already satisfied: setuptools in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.8/site-packages (from nvidia-cublas-cu11==11.10.3.66->torch>=1.8->monai) (67.7.2)\n",
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"Requirement already satisfied: setuptools in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.8/site-packages (from nvidia-cublas-cu11==11.10.3.66->torch>=1.8->monai) (67.8.0)\n",
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"From: https://drive.google.com/uc?id=1yJ4P-xMNEfN6lIOq_u6x1eMAq1_MJu-E\n",
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"To: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/mednist_classifier_data.zip\n",
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"execution_count": 10,
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"metadata": {},
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"\u001b[0m2023-06-02 16:37:55.428 INFO /workspace/holoscan-sdk/src/core/executors/gxf/gxf_executor.cpp@71: Creating context\u001b[0m\n",
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"\u001b[0m2023-06-02 16:37:55.491 INFO gxf/std/greedy_scheduler.cpp@184: Scheduling 3 entities\u001b[0m\n"
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"[2023-05-16 00:06:38.923] [holoscan] [info] [gxf_executor.cpp:100] Loading extensions from configs...\n",
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"[2023-05-16 00:06:38.930] [holoscan] [info] [gxf_executor.cpp:291] Activating Graph...\n",
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"[2023-05-16 00:06:38.931] [holoscan] [info] [gxf_executor.cpp:293] Running Graph...\n",
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"[2023-05-16 00:06:38.931] [holoscan] [info] [gxf_executor.cpp:295] Waiting for completion...\n",
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"[2023-06-02 16:37:55.483] [holoscan] [info] [gxf_executor.cpp:100] Loading extensions from configs...\n",
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"[2023-06-02 16:37:55.491] [holoscan] [info] [gxf_executor.cpp:291] Activating Graph...\n",
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"[2023-06-02 16:37:55.491] [holoscan] [info] [gxf_executor.cpp:293] Running Graph...\n",
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"[2023-06-02 16:37:55.491] [holoscan] [info] [gxf_executor.cpp:295] Waiting for completion...\n",
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"/home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.8/site-packages/monai/utils/deprecate_utils.py:107: FutureWarning: <class 'monai.transforms.utility.array.AddChannel'>: Class `AddChannel` has been deprecated since version 0.8. please use MetaTensor data type and monai.transforms.EnsureChannelFirst instead.\n",
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" warn_deprecated(obj, msg, warning_category)\n",
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"/home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.8/site-packages/monai/utils/type_conversion.py:138: UserWarning: The given NumPy array is not writable, and PyTorch does not support non-writable tensors. This means writing to this tensor will result in undefined behavior. You may want to copy the array to protect its data or make it writable before converting it to a tensor. This type of warning will be suppressed for the rest of this program. (Triggered internally at ../torch/csrc/utils/tensor_numpy.cpp:199.)\n",
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"\u001b[0m2023-05-16 00:06:38.880 INFO /workspace/holoscan-sdk/src/core/executors/gxf/gxf_executor.cpp@71: Creating context\u001b[0m\n",
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"\u001b[0m2023-05-16 00:06:38.931 INFO gxf/std/greedy_scheduler.cpp@184: Scheduling 3 entities\u001b[0m\n",
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"AbdomenCT\n",
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"2023-05-16 00:06:41,947 - Finished writing DICOM instance to file output/1.2.826.0.1.3680043.8.498.10337316154341231457694740853140828112.dcm\n",
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"2023-05-16 00:06:41,949 - DICOM SOP instance saved in output/1.2.826.0.1.3680043.8.498.10337316154341231457694740853140828112.dcm\n",
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"\u001b[0m2023-05-16 00:06:41.950 INFO gxf/std/greedy_scheduler.cpp@343: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n",
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"\u001b[0m2023-05-16 00:06:41.950 INFO gxf/std/greedy_scheduler.cpp@367: Scheduler finished.\u001b[0m\n"
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"2023-06-02 16:37:58,455 - Finished writing DICOM instance to file output/1.2.826.0.1.3680043.8.498.14935734453092731870796445490620890214.dcm\n",
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"2023-06-02 16:37:58,457 - DICOM SOP instance saved in output/1.2.826.0.1.3680043.8.498.14935734453092731870796445490620890214.dcm\n",
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"\u001b[0m2023-06-02 16:37:58.458 INFO gxf/std/greedy_scheduler.cpp@343: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n",
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"text": [
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"/home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.8/site-packages/pydicom/valuerep.py:290: UserWarning: Invalid value for VR UI: 'xyz'. Please see <https://dicom.nema.org/medical/dicom/current/output/html/part05.html#table_6.2-1> for allowed values for each VR.\n",
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" warnings.warn(msg)\n",
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"[2023-05-16 00:06:41.950] [holoscan] [info] [gxf_executor.cpp:297] Deactivating Graph...\n"
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"[2023-06-02 16:37:58.459] [holoscan] [info] [gxf_executor.cpp:297] Deactivating Graph...\n"
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"\u001b[0m2023-05-16 00:06:46.757 INFO /workspace/holoscan-sdk/src/core/executors/gxf/gxf_executor.cpp@71: Creating context\u001b[0m\n",
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"[2023-05-16 00:06:46.779] [holoscan] [\u001b[32minfo\u001b[m] [gxf_executor.cpp:100] Loading extensions from configs...\n",
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"[2023-05-16 00:06:46.785] [holoscan] [\u001b[32minfo\u001b[m] [gxf_executor.cpp:291] Activating Graph...\n",
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"[2023-05-16 00:06:46.786] [holoscan] [\u001b[32minfo\u001b[m] [gxf_executor.cpp:293] Running Graph...\n",
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"[2023-05-16 00:06:46.786] [holoscan] [\u001b[32minfo\u001b[m] [gxf_executor.cpp:295] Waiting for completion...\n",
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"\u001b[0m2023-05-16 00:06:46.786 INFO gxf/std/greedy_scheduler.cpp@184: Scheduling 3 entities\u001b[0m\n",
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"\u001b[0m2023-06-02 16:38:03.023 INFO /workspace/holoscan-sdk/src/core/executors/gxf/gxf_executor.cpp@71: Creating context\u001b[0m\n",
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"[2023-06-02 16:38:03.046] [holoscan] [\u001b[32minfo\u001b[m] [gxf_executor.cpp:100] Loading extensions from configs...\n",
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"[2023-06-02 16:38:03.052] [holoscan] [\u001b[32minfo\u001b[m] [gxf_executor.cpp:291] Activating Graph...\n",
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"[2023-06-02 16:38:03.052] [holoscan] [\u001b[32minfo\u001b[m] [gxf_executor.cpp:293] Running Graph...\n",
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"[2023-06-02 16:38:03.052] [holoscan] [\u001b[32minfo\u001b[m] [gxf_executor.cpp:295] Waiting for completion...\n",
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"\u001b[0m2023-06-02 16:38:03.052 INFO gxf/std/greedy_scheduler.cpp@184: Scheduling 3 entities\u001b[0m\n",
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"/home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.8/site-packages/monai/utils/deprecate_utils.py:107: FutureWarning: <class 'monai.transforms.utility.array.AddChannel'>: Class `AddChannel` has been deprecated since version 0.8. please use MetaTensor data type and monai.transforms.EnsureChannelFirst instead.\n",
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" warn_deprecated(obj, msg, warning_category)\n",
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"/home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.8/site-packages/monai/utils/type_conversion.py:138: UserWarning: The given NumPy array is not writable, and PyTorch does not support non-writable tensors. This means writing to this tensor will result in undefined behavior. You may want to copy the array to protect its data or make it writable before converting it to a tensor. This type of warning will be suppressed for the rest of this program. (Triggered internally at ../torch/csrc/utils/tensor_numpy.cpp:199.)\n",
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"AbdomenCT\n",
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"/home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.8/site-packages/pydicom/valuerep.py:290: UserWarning: Invalid value for VR UI: 'xyz'. Please see <https://dicom.nema.org/medical/dicom/current/output/html/part05.html#table_6.2-1> for allowed values for each VR.\n",
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" warnings.warn(msg)\n",
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"2023-05-16 00:06:48,646 - Finished writing DICOM instance to file output/1.2.826.0.1.3680043.8.498.92740346106070946128804068751213493495.dcm\n",
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"2023-05-16 00:06:48,647 - DICOM SOP instance saved in output/1.2.826.0.1.3680043.8.498.92740346106070946128804068751213493495.dcm\n",
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"\u001b[0m2023-05-16 00:06:48.647 INFO gxf/std/greedy_scheduler.cpp@343: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n",
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"[2023-05-16 00:06:48.648] [holoscan] [\u001b[32minfo\u001b[m] [gxf_executor.cpp:297] Deactivating Graph...\n",
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"\u001b[0m2023-05-16 00:06:48.648 INFO /workspace/holoscan-sdk/src/core/executors/gxf/gxf_executor.cpp@88: Destroying context\u001b[0m\n"
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"2023-06-02 16:38:04,951 - Finished writing DICOM instance to file output/1.2.826.0.1.3680043.8.498.62224327477319136031855752709641027145.dcm\n",
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"2023-06-02 16:38:04,952 - DICOM SOP instance saved in output/1.2.826.0.1.3680043.8.498.62224327477319136031855752709641027145.dcm\n",
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"\u001b[0m2023-06-02 16:38:04.953 INFO gxf/std/greedy_scheduler.cpp@343: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n",
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"\u001b[0m2023-06-02 16:38:04.953 INFO gxf/std/greedy_scheduler.cpp@367: Scheduler finished.\u001b[0m\n",
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"[2023-06-02 16:38:04.953] [holoscan] [\u001b[32minfo\u001b[m] [gxf_executor.cpp:297] Deactivating Graph...\n",
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"\u001b[0m2023-06-02 16:38:04.953 INFO /workspace/holoscan-sdk/src/core/executors/gxf/gxf_executor.cpp@88: Destroying context\u001b[0m\n"
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