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KumoLiuericspod
KumoLiu
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ericspod
authored
Make notebooks under bundle folder runable (#1831)
### Checks <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [ ] Avoid including large-size files in the PR. - [ ] Clean up long text outputs from code cells in the notebook. - [ ] For security purposes, please check the contents and remove any sensitive info such as user names and private key. - [ ] Ensure (1) hyperlinks and markdown anchors are working (2) use relative paths for tutorial repo files (3) put figure and graphs in the `./figure` folder - [ ] Notebook runs automatically `./runner.sh -t <path to .ipynb file>` --------- Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
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‎bundle/01_bundle_intro.ipynb‎

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},
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"cell_type": "code",
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@@ -153,10 +153,10 @@
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" \"changelog\": {\n",
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" \"0.0.1\": \"Initial version\"\n",
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" },\n",
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" \"monai_version\": \"1.2.0\",\n",
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" \"pytorch_version\": \"2.0.0\",\n",
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" \"numpy_version\": \"1.23.5\",\n",
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" \"optional_packages_version\": {},\n",
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" \"monai_version\": \"1.4.0\",\n",
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" \"pytorch_version\": \"2.5.0\",\n",
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" \"numpy_version\": \"1.24.4\",\n",
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" \"required_packages_version\": {},\n",
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" \"task\": \"Describe what the network predicts\",\n",
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" \"description\": \"A longer description of what the network does, use context, inputs, outputs, etc.\",\n",
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" \"authors\": \"Your Name Here\",\n",
@@ -183,7 +183,7 @@
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"cell_type": "code",
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" \"monai_version\": \"1.2.0\",\n",
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" \"pytorch_version\": \"2.0.0\",\n",
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" \"numpy_version\": \"1.23.5\",\n",
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" \"optional_packages_version\": {},\n",
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" \"required_packages_version\": {},\n",
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" \"name\": \"TestBundle\",\n",
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" \"task\": \"Demonstration Bundle Network\",\n",
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" \"description\": \"This is a demonstration bundle meant to showcase features of the MONAI bundle system only and does nothing useful\",\n",
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},
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"cell_type": "code",
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"execution_count": 7,
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{
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"name": "stdout",
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"text": [
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"2023-07-14 15:34:52,646 - INFO - --- input summary of monai.bundle.scripts.run ---\n",
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"2023-07-14 15:34:52,647 - INFO - > run_id: 'test_config'\n",
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"2023-07-14 15:34:52,647 - INFO - > meta_file: './TestBundle/configs/metadata.json'\n",
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"2023-07-14 15:34:52,647 - INFO - > config_file: './TestBundle/configs/test_config.yaml'\n",
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"2023-07-14 15:34:52,647 - INFO - ---\n",
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"2024-09-18 08:15:12,299 - INFO - --- input summary of monai.bundle.scripts.run ---\n",
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"2024-09-18 08:15:12,299 - INFO - > config_file: './TestBundle/configs/test_config.yaml'\n",
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"2024-09-18 08:15:12,299 - INFO - > meta_file: './TestBundle/configs/metadata.json'\n",
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"2024-09-18 08:15:12,299 - INFO - > run_id: 'test_config'\n",
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"2024-09-18 08:15:12,299 - INFO - ---\n",
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},
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{
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"name": "stderr",
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"text": [
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"/home/localek10/workspace/monai/MONAI_mine/monai/bundle/workflows.py:213: UserWarning: Default logging file in 'configs/logging.conf' does not exist, skipping logging.\n",
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" warnings.warn(\"Default logging file in 'configs/logging.conf' does not exist, skipping logging.\")\n"
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]
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},
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{
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"name": "stdout",
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"text": [
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"MONAI version: 1.2.0\n",
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"Numpy version: 1.23.5\n",
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"Pytorch version: 2.0.0\n",
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"MONAI version: 1.4.0\n",
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"Numpy version: 1.24.4\n",
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"Pytorch version: 2.5.0a0+872d972e41.nv24.08\n",
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"MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False\n",
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"MONAI rev id: c33f1ba588ee00229a309000e888f9817b4f1934\n",
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"MONAI __file__: /home/localek10/workspace/monai/MONAI_mine/monai/__init__.py\n",
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"MONAI rev id: ab3ee18ba32bb9bd67cd3a55717684bbd343c94c\n",
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"MONAI __file__: /workspace/Code/MONAI/monai/__init__.py\n",
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"\n",
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"Optional dependencies:\n",
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"Pytorch Ignite version: 0.4.12\n",
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"ITK version: NOT INSTALLED or UNKNOWN VERSION.\n",
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"Nibabel version: 5.0.1\n",
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"scikit-image version: NOT INSTALLED or UNKNOWN VERSION.\n",
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"Pillow version: 9.4.0\n",
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"Tensorboard version: NOT INSTALLED or UNKNOWN VERSION.\n",
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"gdown version: NOT INSTALLED or UNKNOWN VERSION.\n",
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"TorchVision version: 0.15.0\n",
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"tqdm version: 4.65.0\n",
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"lmdb version: NOT INSTALLED or UNKNOWN VERSION.\n",
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"psutil version: 5.9.0\n",
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"pandas version: 1.5.3\n",
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"einops version: 0.6.1\n",
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"transformers version: NOT INSTALLED or UNKNOWN VERSION.\n",
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"mlflow version: NOT INSTALLED or UNKNOWN VERSION.\n",
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"pynrrd version: NOT INSTALLED or UNKNOWN VERSION.\n",
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"Pytorch Ignite version: 0.4.11\n",
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"ITK version: 5.4.0\n",
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"Nibabel version: 5.2.1\n",
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"scikit-image version: 0.23.2\n",
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"scipy version: 1.14.0\n",
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"Pillow version: 10.4.0\n",
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"Tensorboard version: 2.16.2\n",
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"gdown version: 5.2.0\n",
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"TorchVision version: 0.20.0a0\n",
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"tqdm version: 4.66.5\n",
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"lmdb version: 1.5.1\n",
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"psutil version: 6.0.0\n",
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"pandas version: 2.2.2\n",
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"einops version: 0.8.0\n",
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"transformers version: 4.40.2\n",
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"mlflow version: 2.16.0\n",
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"pynrrd version: 1.0.0\n",
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"clearml version: 1.16.4\n",
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"For details about installing the optional dependencies, please visit:\n",
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"\n",
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"Test tensor: tensor([[0.5281, 0.1114, 0.5124, 0.2523],\n",
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" [0.6561, 0.0298, 0.6393, 0.8636],\n",
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" [0.3730, 0.8315, 0.1390, 0.6233],\n",
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" [0.2646, 0.8929, 0.5250, 0.0472]], device='cuda:0')\n"
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"Test tensor: tensor([[0.7786, 0.5913, 0.6661, 0.2732],\n",
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" [0.6756, 0.3978, 0.7760, 0.7936],\n",
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" [0.0093, 0.6293, 0.1988, 0.0280],\n",
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" [0.8460, 0.5727, 0.6339, 0.7825]], device='cuda:0')\n"
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"Overwriting TestBundle/configs/test_object.yaml\n"
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"2023-07-14 15:28:36,063 - INFO - --- input summary of monai.bundle.scripts.run ---\n",
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"2023-07-14 15:28:36,063 - INFO - > run_id: 'test'\n",
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"2023-07-14 15:28:36,063 - INFO - > meta_file: './TestBundle/configs/metadata.json'\n",
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"2023-07-14 15:28:36,063 - INFO - > config_file: './TestBundle/configs/test_object.yaml'\n",
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"\n",
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"2024-09-18 08:15:22,338 - INFO - --- input summary of monai.bundle.scripts.run ---\n",
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"2024-09-18 08:15:22,338 - INFO - > config_file: './TestBundle/configs/test_object.yaml'\n",
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"2024-09-18 08:15:22,338 - INFO - > meta_file: './TestBundle/configs/metadata.json'\n",
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"2024-09-18 08:15:22,338 - INFO - > run_id: 'test'\n",
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"2024-09-18 08:15:22,338 - INFO - ---\n",
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"Dataset <monai.data.dataset.Dataset object at 0x7fa6d117f100>\n",
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"Dataset <monai.data.dataset.Dataset object at 0x7f1777fd7b20>\n",
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"Transform member None\n",
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"Transform member <monai.transforms.compose.Compose object at 0x7f1777fd5a20>\n",
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"Values [{0: 0}, {1: 1}, {2: 4}, {3: 9}, {4: 16}, {5: 25}, {6: 36}, {7: 49}, {8: 64}, {9: 81}]\n"
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"2024-09-18 08:15:32,092 - INFO - > config_file: './TestBundle/configs/test_cmdline.yaml'\n",
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"version": "3.10.12"
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"nbformat": 4,

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