Wenqi Li

MONAI bundle developers guide for the pytorch users

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**Is your feature request related to a problem? Please describe.** bundle templates, minimal examples for bundle workflow for pytorch users to get started migrating existing workflows - 90% use cases...

pathology/nuclick/nuclick_infer.ipynb

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https://warwick.ac.uk/fac/cross_fac/tia/data/hovernet/consep_dataset.zip not available ``` [2023-10-05T01:48:32.818Z] Running ./pathology/nuclick/nuclick_infer.ipynb [2023-10-05T01:48:32.818Z] Checking PEP8 compliance... [2023-10-05T01:48:33.381Z] Running notebook... [2023-10-05T01:48:33.942Z] Before: [2023-10-05T01:48:33.942Z] "max_epochs = 1" [2023-10-05T01:48:34.197Z] After: [2023-10-05T01:48:34.197Z] "max_epochs = 1" [2023-10-05T01:48:44.136Z] MONAI version: 1.3.0rc2+14.g141bcf0a...

**Is your feature request related to a problem? Please describe.** follow-up of - https://github.com/Project-MONAI/MONAI/discussions/6584 - https://github.com/Project-MONAI/MONAI/discussions/6582 it's unclear what the recommended way is for modifying the default algorithms and templates...

**Is your feature request related to a problem? Please describe.** would be great to make a tutorial about how to create customized monai transforms, with recommended approaches of different base...

**Describe the bug** set the value to avoid the warning messages ``` monai.transforms.io.dictionary LoadImaged.__init__: image_only: Current default value of argument `image_only=False` has been deprecated since version 1.1. ```

testing error modules/transform_visualization.ipynb

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**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]...

https://github.com/Project-MONAI/tutorials/blob/main/modules/TorchIO_MONAI_PyTorch_Lightning.ipynb ``` FIXME: Temporarily install PyTorch 1.10.2 during to PyTorchLightning issue: https://github.com/PyTorchLightning/pytorch-lightning/issues/10597 ``` this currently changes the test environment when launching notebooks with `runner.sh `